--- /dev/null
+format-version: 1.2
+date: 22:06:2015 10:18
+saved-by: kareneilbeck
+auto-generated-by: OBO-Edit 2.3.1
+subsetdef: biosapiens "biosapiens protein feature ontology"
+subsetdef: DBVAR "database of genomic structural variation"
+subsetdef: SOFA "SO feature annotation"
+synonymtypedef: aa1 "amino acid 1 letter code"
+synonymtypedef: aa3 "amino acid 3 letter code"
+synonymtypedef: AAMOD "amino acid modification"
+synonymtypedef: BS "biosapiens"
+synonymtypedef: dbsnp "dbsnp variant terms"
+synonymtypedef: dbvar "DBVAR"
+synonymtypedef: ebi_variants "ensembl variant terms"
+synonymtypedef: RNAMOD "RNA modification" EXACT
+synonymtypedef: VAR "variant annotation term"
+default-namespace: sequence
+remark: autogenerated-by: DAG-Edit version 1.417\nsaved-by: eilbeck\ndate: Tue May 11 15:18:44 PDT 2004\nversion: $Revision: 1.45 $
+ontology: so-xp.obo
+
+[Term]
+id: SO:0000000
+name: Sequence_Ontology
+subset: SOFA
+is_obsolete: true
+
+[Term]
+id: SO:0000001
+name: region
+def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]
+subset: SOFA
+synonym: "sequence" EXACT []
+is_a: SO:0000110 ! sequence_feature
+disjoint_from: SO:0000699 ! junction
+
+[Term]
+id: SO:0000002
+name: sequence_secondary_structure
+def: "A folded sequence." [SO:ke]
+synonym: "sequence secondary structure" EXACT []
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000003
+name: G_quartet
+def: "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]
+synonym: "G quartet" EXACT []
+synonym: "G tetrad" EXACT []
+synonym: "G-quadruplex" EXACT []
+synonym: "G-quartet" EXACT []
+synonym: "G-tetrad" EXACT []
+synonym: "G_quadruplex" EXACT []
+synonym: "guanine tetrad" EXACT []
+xref: http://en.wikipedia.org/wiki/G-quadruplex "wiki"
+is_a: SO:0000002 ! sequence_secondary_structure
+
+[Term]
+id: SO:0000004
+name: interior_coding_exon
+subset: SOFA
+synonym: "interior coding exon" EXACT []
+is_a: SO:0000195 ! coding_exon
+
+[Term]
+id: SO:0000005
+name: satellite_DNA
+def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+subset: SOFA
+synonym: "satellite DNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki"
+is_a: SO:0000705 ! tandem_repeat
+
+[Term]
+id: SO:0000006
+name: PCR_product
+def: "A region amplified by a PCR reaction." [SO:ke]
+comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
+subset: SOFA
+synonym: "amplicon" RELATED []
+synonym: "PCR product" EXACT []
+xref: http://en.wikipedia.org/wiki/RAPD "wiki"
+is_a: SO:0000695 ! reagent
+
+[Term]
+id: SO:0000007
+name: read_pair
+def: "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]
+subset: SOFA
+synonym: "mate pair" EXACT []
+synonym: "read-pair" EXACT []
+is_a: SO:0000150 ! read
+relationship: part_of SO:0000149 ! contig
+relationship: part_of SO:0001790 ! paired_end_fragment
+
+[Term]
+id: SO:0000008
+name: gene_sensu_your_favorite_organism
+is_obsolete: true
+
+[Term]
+id: SO:0000009
+name: gene_class
+is_obsolete: true
+
+[Term]
+id: SO:0000010
+name: protein_coding
+synonym: "protein-coding" EXACT []
+is_a: SO:0000401 ! gene_attribute
+
+[Term]
+id: SO:0000011
+name: non_protein_coding
+synonym: "non protein-coding" EXACT []
+is_a: SO:0000401 ! gene_attribute
+
+[Term]
+id: SO:0000012
+name: scRNA_primary_transcript
+def: "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
+synonym: "scRNA primary transcript" EXACT []
+synonym: "scRNA transcript" EXACT []
+synonym: "small cytoplasmic RNA" RELATED []
+synonym: "small cytoplasmic RNA transcript" EXACT []
+synonym: "small_cytoplasmic_RNA" RELATED []
+is_a: SO:0000483 ! nc_primary_transcript
+
+[Term]
+id: SO:0000013
+name: scRNA
+def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke]
+subset: SOFA
+synonym: "small cytoplasmic RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0000012 ! scRNA_primary_transcript
+
+[Term]
+id: SO:0000014
+name: INR_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]
+comment: Binds TAF1, TAF2.
+synonym: "DMp2" RELATED []
+synonym: "initiator" EXACT []
+synonym: "initiator motif" EXACT []
+synonym: "INR motif" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0001669 ! RNApol_II_core_promoter
+
+[Term]
+id: SO:0000015
+name: DPE_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]
+comment: Binds TAF6, TAF9.
+synonym: "CRWMGCGWKCGCTTS" NARROW []
+synonym: "downstream core promoter element" EXACT []
+synonym: "DPE motif" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0001669 ! RNApol_II_core_promoter
+
+[Term]
+id: SO:0000016
+name: BREu_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]
+comment: Binds TFIIB.
+synonym: "B-recognition element" EXACT []
+synonym: "BRE motif" EXACT []
+synonym: "BREu" RELATED []
+synonym: "BREu motif" EXACT []
+synonym: "TFIIB recognition element" RELATED []
+synonym: "transcription factor B-recognition element" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0001669 ! RNApol_II_core_promoter
+
+[Term]
+id: SO:0000017
+name: PSE_motif
+def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]
+synonym: "proximal sequence element" EXACT []
+synonym: "PSE motif" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000167 ! promoter
+
+[Term]
+id: SO:0000018
+name: linkage_group
+def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]
+synonym: "linkage group" EXACT []
+xref: http://en.wikipedia.org/wiki/Linkage_group "wiki"
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000020
+name: RNA_internal_loop
+def: "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]
+synonym: "RNA internal loop" EXACT []
+is_a: SO:0000715 ! RNA_motif
+
+[Term]
+id: SO:0000021
+name: asymmetric_RNA_internal_loop
+def: "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]
+synonym: "asymmetric RNA internal loop" EXACT []
+is_a: SO:0000020 ! RNA_internal_loop
+
+[Term]
+id: SO:0000022
+name: A_minor_RNA_motif
+def: "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]
+synonym: "A minor RNA motif" EXACT []
+is_a: SO:0000715 ! RNA_motif
+
+[Term]
+id: SO:0000023
+name: K_turn_RNA_motif
+def: "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]
+synonym: "K turn RNA motif" EXACT []
+synonym: "K-turn" EXACT []
+synonym: "kink turn" EXACT []
+synonym: "kink-turn motif" EXACT []
+xref: http://en.wikipedia.org/wiki/K-turn "wiki"
+is_a: SO:0000021 ! asymmetric_RNA_internal_loop
+
+[Term]
+id: SO:0000024
+name: sarcin_like_RNA_motif
+def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]
+synonym: "sarcin like RNA motif" EXACT []
+synonym: "sarcin/ricin domain" EXACT []
+synonym: "sarcin/ricin loop" EXACT []
+synonym: "sarcin/ricin RNA domain" EXACT []
+is_a: SO:0000021 ! asymmetric_RNA_internal_loop
+
+[Term]
+id: SO:0000025
+name: symmetric_RNA_internal_loop
+def: "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]
+synonym: "A-minor RNA motif" EXACT []
+is_a: SO:0000020 ! RNA_internal_loop
+
+[Term]
+id: SO:0000026
+name: RNA_junction_loop
+synonym: "RNA junction loop" EXACT []
+is_a: SO:0000715 ! RNA_motif
+
+[Term]
+id: SO:0000027
+name: RNA_hook_turn
+synonym: "hook turn" RELATED []
+synonym: "hook-turn motif" EXACT []
+synonym: "RNA hook turn" EXACT []
+is_a: SO:0000026 ! RNA_junction_loop
+
+[Term]
+id: SO:0000028
+name: base_pair
+synonym: "base pair" EXACT []
+xref: http://en.wikipedia.org/wiki/Base_pair "wiki"
+is_a: SO:0000002 ! sequence_secondary_structure
+
+[Term]
+id: SO:0000029
+name: WC_base_pair
+def: "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]
+synonym: "canonical base pair" EXACT []
+synonym: "Watson Crick base pair" EXACT []
+synonym: "Watson-Crick base pair" RELATED []
+synonym: "Watson-Crick pair" EXACT []
+synonym: "WC base pair" EXACT []
+is_a: SO:0000028 ! base_pair
+
+[Term]
+id: SO:0000030
+name: sugar_edge_base_pair
+def: "A type of non-canonical base-pairing." [PMID:12177293]
+synonym: "sugar edge base pair" EXACT []
+is_a: SO:0000028 ! base_pair
+
+[Term]
+id: SO:0000031
+name: aptamer
+def: "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]
+xref: http://en.wikipedia.org/wiki/Aptamer "wiki"
+is_a: SO:0000696 ! oligo
+
+[Term]
+id: SO:0000032
+name: DNA_aptamer
+def: "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]
+synonym: "DNA aptamer" EXACT []
+is_a: SO:0000031 ! aptamer
+
+[Term]
+id: SO:0000033
+name: RNA_aptamer
+def: "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]
+synonym: "RNA aptamer" EXACT []
+is_a: SO:0000031 ! aptamer
+
+[Term]
+id: SO:0000034
+name: morpholino_oligo
+def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]
+synonym: "morphant" BROAD []
+synonym: "morpholino" EXACT []
+synonym: "morpholino oligo" EXACT []
+is_a: SO:0001247 ! synthetic_oligo
+relationship: has_quality SO:0001183 ! morpholino_backbone
+
+[Term]
+id: SO:0000035
+name: riboswitch
+def: "A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]
+synonym: "riboswitch RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Riboswitch "wiki"
+is_a: SO:0000836 ! mRNA_region
+relationship: part_of SO:0000234 ! mRNA
+
+[Term]
+id: SO:0000036
+name: matrix_attachment_site
+def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]
+synonym: "MAR" EXACT []
+synonym: "matrix association region" EXACT []
+synonym: "matrix attachment region" EXACT []
+synonym: "matrix attachment site" EXACT []
+synonym: "nuclear matrix association region" EXACT []
+synonym: "nuclear matrix attachment site" EXACT []
+synonym: "S/MAR" EXACT []
+synonym: "S/MAR element" RELATED []
+synonym: "scaffold attachment site" EXACT []
+synonym: "scaffold matrix attachment region" EXACT []
+synonym: "SMAR" EXACT []
+xref: http://en.wikipedia.org/wiki/Matrix_attachment_site "wiki"
+is_a: SO:0000626 ! chromosomal_regulatory_element
+
+[Term]
+id: SO:0000037
+name: locus_control_region
+def: "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]
+synonym: "LCR" EXACT []
+synonym: "locus control element" RELATED []
+synonym: "locus control region" EXACT []
+xref: http://en.wikipedia.org/wiki/Locus_control_region "wiki"
+is_a: SO:0000727 ! CRM
+
+[Term]
+id: SO:0000038
+name: match_set
+def: "A collection of match parts." [SO:ke]
+subset: SOFA
+is_obsolete: true
+
+[Term]
+id: SO:0000039
+name: match_part
+def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke]
+subset: SOFA
+synonym: "match part" EXACT []
+is_a: SO:0001410 ! experimental_feature
+relationship: part_of SO:0000343 ! match
+
+[Term]
+id: SO:0000040
+name: genomic_clone
+def: "A clone of a DNA region of a genome." [SO:ma]
+synonym: "genomic clone" EXACT []
+is_a: SO:0000151 ! clone
+relationship: has_quality SO:0000991 ! genomic_DNA
+
+[Term]
+id: SO:0000041
+name: sequence_operation
+def: "An operation that can be applied to a sequence, that results in a change." [SO:ke]
+synonym: "sequence operation" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000042
+name: pseudogene_attribute
+def: "An attribute of a pseudogene (SO:0000336)." [SO:ma]
+synonym: "pseudogene attribute" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000043
+name: processed_pseudogene
+def: "A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]
+comment: Please not the synonym R psi M uses the spelled out form of the greek letter.
+synonym: "processed pseudogene" EXACT []
+synonym: "pseudogene by reverse transcription" RELATED []
+synonym: "R psi G" RELATED []
+synonym: "retropseudogene" EXACT []
+is_a: SO:0000336 ! pseudogene
+
+[Term]
+id: SO:0000044
+name: pseudogene_by_unequal_crossing_over
+def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke]
+synonym: "pseudogene by unequal crossing over" EXACT []
+is_a: SO:0001760 ! non_processed_pseudogene
+
+[Term]
+id: SO:0000045
+name: delete
+def: "To remove a subsection of sequence." [SO:ke]
+is_obsolete: true
+
+[Term]
+id: SO:0000046
+name: insert
+def: "To insert a subsection of sequence." [SO:ke]
+is_obsolete: true
+
+[Term]
+id: SO:0000047
+name: invert
+def: "To invert a subsection of sequence." [SO:ke]
+is_obsolete: true
+
+[Term]
+id: SO:0000048
+name: substitute
+def: "To substitute a subsection of sequence for another." [SO:ke]
+is_obsolete: true
+
+[Term]
+id: SO:0000049
+name: translocate
+def: "To translocate a subsection of sequence." [SO:ke]
+is_obsolete: true
+
+[Term]
+id: SO:0000050
+name: gene_part
+def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke]
+subset: SOFA
+is_obsolete: true
+
+[Term]
+id: SO:0000051
+name: probe
+def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]
+xref: http://en.wikipedia.org/wiki/Hybridization_probe "wiki"
+is_a: SO:0000696 ! oligo
+
+[Term]
+id: SO:0000052
+name: assortment_derived_deficiency
+synonym: "assortment-derived_deficiency" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0000053
+name: sequence_variant_affecting_regulatory_region
+def: "A sequence_variant_effect which changes the regulatory region of a gene." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting regulatory region" RELATED []
+synonym: "sequence variant affecting regulatory region" EXACT []
+is_obsolete: true
+replaced_by: SO:0001556
+
+[Term]
+id: SO:0000054
+name: aneuploid
+def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Aneuploid "wiki"
+is_a: SO:1000182 ! chromosome_number_variation
+
+[Term]
+id: SO:0000055
+name: hyperploid
+def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Hyperploid "wiki"
+is_a: SO:0000054 ! aneuploid
+
+[Term]
+id: SO:0000056
+name: hypoploid
+def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Hypoploid "wiki"
+is_a: SO:0000054 ! aneuploid
+
+[Term]
+id: SO:0000057
+name: operator
+def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]
+subset: SOFA
+synonym: "operator segment" EXACT []
+xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki"
+is_a: SO:0000752 ! gene_group_regulatory_region
+
+[Term]
+id: SO:0000058
+name: assortment_derived_aneuploid
+synonym: "assortment-derived_aneuploid" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0000059
+name: nuclease_binding_site
+def: "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]
+subset: SOFA
+synonym: "nuclease binding site" EXACT []
+is_a: SO:0001654 ! nucleotide_to_protein_binding_site
+
+[Term]
+id: SO:0000060
+name: compound_chromosome_arm
+comment: FLAG - this term is should probably be a part of rather than an is_a.
+synonym: "compound chromosome arm" EXACT []
+is_a: SO:1000042 ! compound_chromosome
+
+[Term]
+id: SO:0000061
+name: restriction_enzyme_binding_site
+def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]
+comment: A region of a molecule that binds to a restriction enzyme.
+synonym: "restriction endonuclease binding site" EXACT []
+synonym: "restriction enzyme binding site" EXACT []
+is_a: SO:0000059 ! nuclease_binding_site
+
+[Term]
+id: SO:0000062
+name: deficient_intrachromosomal_transposition
+def: "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]
+synonym: "deficient intrachromosomal transposition" EXACT []
+is_a: SO:1000029 ! chromosomal_deletion
+is_a: SO:1000041 ! intrachromosomal_transposition
+relationship: has_part SO:0000159 ! deletion
+
+[Term]
+id: SO:0000063
+name: deficient_interchromosomal_transposition
+def: "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]
+synonym: "deficient interchromosomal transposition" EXACT []
+is_a: SO:1000155 ! interchromosomal_transposition
+
+[Term]
+id: SO:0000064
+name: gene_by_transcript_attribute
+comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
+is_obsolete: true
+
+[Term]
+id: SO:0000065
+name: free_chromosome_arm
+def: "A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]
+synonym: "free chromosome arm" EXACT []
+is_a: SO:1000183 ! chromosome_structure_variation
+
+[Term]
+id: SO:0000066
+name: gene_by_polyadenylation_attribute
+is_obsolete: true
+
+[Term]
+id: SO:0000067
+name: gene_to_gene_feature
+synonym: "gene to gene feature" EXACT []
+is_a: SO:0000401 ! gene_attribute
+
+[Term]
+id: SO:0000068
+name: overlapping
+def: "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]
+is_a: SO:0000067 ! gene_to_gene_feature
+
+[Term]
+id: SO:0000069
+name: inside_intron
+def: "An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]
+synonym: "inside intron" EXACT []
+is_a: SO:0000068 ! overlapping
+
+[Term]
+id: SO:0000070
+name: inside_intron_antiparallel
+def: "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]
+synonym: "inside intron antiparallel" EXACT []
+is_a: SO:0000069 ! inside_intron
+
+[Term]
+id: SO:0000071
+name: inside_intron_parallel
+def: "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]
+synonym: "inside intron parallel" EXACT []
+is_a: SO:0000069 ! inside_intron
+
+[Term]
+id: SO:0000072
+name: end_overlapping_gene
+is_obsolete: true
+
+[Term]
+id: SO:0000073
+name: five_prime_three_prime_overlap
+def: "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]
+synonym: "five prime-three prime overlap" EXACT []
+is_a: SO:0000068 ! overlapping
+
+[Term]
+id: SO:0000074
+name: five_prime_five_prime_overlap
+def: "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]
+synonym: "five prime-five prime overlap" EXACT []
+is_a: SO:0000068 ! overlapping
+
+[Term]
+id: SO:0000075
+name: three_prime_three_prime_overlap
+def: "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]
+synonym: "three prime-three prime overlap" EXACT []
+is_a: SO:0000068 ! overlapping
+
+[Term]
+id: SO:0000076
+name: three_prime_five_prime_overlap
+def: "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]
+synonym: "5' 3' overlap" EXACT []
+synonym: "three prime five prime overlap" EXACT []
+is_a: SO:0000068 ! overlapping
+
+[Term]
+id: SO:0000077
+name: antisense
+def: "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Antisense "wiki"
+is_a: SO:0000068 ! overlapping
+
+[Term]
+id: SO:0000078
+name: polycistronic_transcript
+def: "A transcript that is polycistronic." [SO:xp]
+synonym: "polycistronic transcript" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: has_quality SO:0000880 ! polycistronic
+
+[Term]
+id: SO:0000079
+name: dicistronic_transcript
+def: "A transcript that is dicistronic." [SO:ke]
+synonym: "dicistronic transcript" EXACT []
+is_a: SO:0000078 ! polycistronic_transcript
+relationship: has_quality SO:0000879 ! dicistronic
+
+[Term]
+id: SO:0000080
+name: operon_member
+synonym: "operon member" EXACT []
+is_a: SO:0000081 ! gene_array_member
+
+[Term]
+id: SO:0000081
+name: gene_array_member
+synonym: "gene array member" EXACT []
+is_a: SO:0000401 ! gene_attribute
+
+[Term]
+id: SO:0000082
+name: processed_transcript_attribute
+is_obsolete: true
+
+[Term]
+id: SO:0000083
+name: macronuclear_sequence
+synonym: "macronuclear sequence" EXACT []
+is_a: SO:0000736 ! organelle_sequence
+
+[Term]
+id: SO:0000084
+name: micronuclear_sequence
+synonym: "micronuclear sequence" EXACT []
+is_a: SO:0000736 ! organelle_sequence
+
+[Term]
+id: SO:0000085
+name: gene_by_genome_location
+is_obsolete: true
+
+[Term]
+id: SO:0000086
+name: gene_by_organelle_of_genome
+is_obsolete: true
+
+[Term]
+id: SO:0000087
+name: nuclear_gene
+def: "A gene from nuclear sequence." [SO:xp]
+synonym: "nuclear gene" EXACT []
+xref: http://en.wikipedia.org/wiki/Nuclear_gene "wiki"
+is_a: SO:0000704 ! gene
+relationship: has_origin SO:0000738 ! nuclear_sequence
+
+[Term]
+id: SO:0000088
+name: mt_gene
+def: "A gene located in mitochondrial sequence." [SO:xp]
+synonym: "mitochondrial gene" EXACT []
+synonym: "mt gene" EXACT []
+xref: http://en.wikipedia.org/wiki/Mitochondrial_gene "wiki"
+is_a: SO:0000704 ! gene
+relationship: has_origin SO:0000737 ! mitochondrial_sequence
+
+[Term]
+id: SO:0000089
+name: kinetoplast_gene
+def: "A gene located in kinetoplast sequence." [SO:xp]
+synonym: "kinetoplast gene" EXACT []
+is_a: SO:0000088 ! mt_gene
+relationship: has_origin SO:0000741 ! kinetoplast
+
+[Term]
+id: SO:0000090
+name: plastid_gene
+def: "A gene from plastid sequence." [SO:xp]
+synonym: "plastid gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_origin SO:0000740 ! plastid_sequence
+
+[Term]
+id: SO:0000091
+name: apicoplast_gene
+def: "A gene from apicoplast sequence." [SO:xp]
+synonym: "apicoplast gene" EXACT []
+is_a: SO:0000090 ! plastid_gene
+relationship: has_origin SO:0000743 ! apicoplast_sequence
+
+[Term]
+id: SO:0000092
+name: ct_gene
+def: "A gene from chloroplast sequence." [SO:xp]
+synonym: "chloroplast gene" EXACT []
+synonym: "ct gene" EXACT []
+is_a: SO:0000090 ! plastid_gene
+relationship: has_origin SO:0000745 ! chloroplast_sequence
+
+[Term]
+id: SO:0000093
+name: chromoplast_gene
+def: "A gene from chromoplast_sequence." [SO:xp]
+synonym: "chromoplast gene" EXACT []
+is_a: SO:0000090 ! plastid_gene
+relationship: has_origin SO:0000744 ! chromoplast_sequence
+
+[Term]
+id: SO:0000094
+name: cyanelle_gene
+def: "A gene from cyanelle sequence." [SO:xp]
+synonym: "cyanelle gene" EXACT []
+is_a: SO:0000090 ! plastid_gene
+relationship: has_origin SO:0000746 ! cyanelle_sequence
+
+[Term]
+id: SO:0000095
+name: leucoplast_gene
+def: "A plastid gene from leucoplast sequence." [SO:xp]
+synonym: "leucoplast gene" EXACT []
+is_a: SO:0000090 ! plastid_gene
+relationship: has_origin SO:0000747 ! leucoplast_sequence
+
+[Term]
+id: SO:0000096
+name: proplastid_gene
+def: "A gene from proplastid sequence." [SO:ke]
+synonym: "proplastid gene" EXACT []
+is_a: SO:0000090 ! plastid_gene
+relationship: has_origin SO:0000748 ! proplastid_sequence
+
+[Term]
+id: SO:0000097
+name: nucleomorph_gene
+def: "A gene from nucleomorph sequence." [SO:xp]
+synonym: "nucleomorph gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_origin SO:0000739 ! nucleomorphic_sequence
+
+[Term]
+id: SO:0000098
+name: plasmid_gene
+def: "A gene from plasmid sequence." [SO:xp]
+synonym: "plasmid gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_origin SO:0000749 ! plasmid_location
+
+[Term]
+id: SO:0000099
+name: proviral_gene
+def: "A gene from proviral sequence." [SO:xp]
+synonym: "proviral gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_origin SO:0000751 ! proviral_location
+
+[Term]
+id: SO:0000100
+name: endogenous_retroviral_gene
+def: "A proviral gene with origin endogenous retrovirus." [SO:xp]
+synonym: "endogenous retroviral gene" EXACT []
+is_a: SO:0000099 ! proviral_gene
+relationship: has_origin SO:0000903 ! endogenous_retroviral_sequence
+
+[Term]
+id: SO:0000101
+name: transposable_element
+def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]
+subset: SOFA
+synonym: "transposable element" EXACT []
+synonym: "transposon" EXACT []
+xref: http://en.wikipedia.org/wiki/Transposable_element "wiki"
+is_a: SO:0001039 ! integrated_mobile_genetic_element
+
+[Term]
+id: SO:0000102
+name: expressed_sequence_match
+def: "A match to an EST or cDNA sequence." [SO:ke]
+subset: SOFA
+synonym: "expressed sequence match" EXACT []
+is_a: SO:0000347 ! nucleotide_match
+
+[Term]
+id: SO:0000103
+name: clone_insert_end
+def: "The end of the clone insert." [SO:ke]
+subset: SOFA
+synonym: "clone insert end" EXACT []
+is_a: SO:0000699 ! junction
+relationship: part_of SO:0000753 ! clone_insert
+
+[Term]
+id: SO:0000104
+name: polypeptide
+alt_id: SO:0000358
+def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
+subset: SOFA
+synonym: "protein" EXACT []
+xref: http://en.wikipedia.org/wiki/Polypeptide "wiki"
+is_a: SO:0001411 ! biological_region
+relationship: derives_from SO:0000316 ! CDS
+
+[Term]
+id: SO:0000105
+name: chromosome_arm
+def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]
+synonym: "chromosome arm" EXACT []
+is_a: SO:0000830 ! chromosome_part
+
+[Term]
+id: SO:0000106
+name: non_capped_primary_transcript
+is_obsolete: true
+
+[Term]
+id: SO:0000107
+name: sequencing_primer
+synonym: "sequencing primer" EXACT []
+is_a: SO:0000112 ! primer
+
+[Term]
+id: SO:0000108
+name: mRNA_with_frameshift
+def: "An mRNA with a frameshift." [SO:xp]
+synonym: "frameshifted mRNA" EXACT []
+synonym: "mRNA with frameshift" EXACT []
+is_a: SO:0000234 ! mRNA
+relationship: has_quality SO:0000865 ! frameshift
+
+[Term]
+id: SO:0000109
+name: sequence_variant_obs
+def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
+subset: SOFA
+synonym: "mutation" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0000110
+name: sequence_feature
+def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]
+subset: SOFA
+synonym: "located sequence feature" RELATED []
+synonym: "located_sequence_feature" EXACT []
+synonym: "sequence feature" EXACT []
+disjoint_from: SO:0000400 ! sequence_attribute
+
+[Term]
+id: SO:0000111
+name: transposable_element_gene
+def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]
+synonym: "transposable element gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: part_of SO:0000101 ! transposable_element
+
+[Term]
+id: SO:0000112
+name: primer
+def: "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]
+subset: SOFA
+synonym: "DNA primer" EXACT []
+synonym: "primer oligonucleotide" EXACT []
+synonym: "primer polynucleotide" EXACT []
+synonym: "primer sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki"
+is_a: SO:0000441 ! ss_oligo
+
+[Term]
+id: SO:0000113
+name: proviral_region
+def: "A viral sequence which has integrated into a host genome." [SO:ke]
+subset: SOFA
+synonym: "proviral region" EXACT []
+synonym: "proviral sequence" RELATED []
+is_a: SO:0001039 ! integrated_mobile_genetic_element
+
+[Term]
+id: SO:0000114
+name: methylated_cytosine
+def: "A methylated deoxy-cytosine." [SO:ke]
+subset: SOFA
+synonym: "methylated C" EXACT []
+synonym: "methylated cytosine" EXACT []
+synonym: "methylated cytosine base" EXACT []
+synonym: "methylated cytosine residue" EXACT []
+synonym: "methylated_C" EXACT []
+is_a: SO:0000306 ! methylated_DNA_base_feature
+is_a: SO:0001963 ! modified_cytosine
+
+[Term]
+id: SO:0000115
+name: transcript_feature
+is_obsolete: true
+
+[Term]
+id: SO:0000116
+name: edited
+def: "An attribute describing a sequence that is modified by editing." [SO:ke]
+is_a: SO:0000237 ! transcript_attribute
+
+[Term]
+id: SO:0000117
+name: transcript_with_readthrough_stop_codon
+is_obsolete: true
+
+[Term]
+id: SO:0000118
+name: transcript_with_translational_frameshift
+def: "A transcript with a translational frameshift." [SO:xp]
+synonym: "transcript with translational frameshift" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: has_quality SO:0000887 ! translationally_frameshifted
+
+[Term]
+id: SO:0000119
+name: regulated
+def: "An attribute to describe a sequence that is regulated." [SO:ke]
+is_a: SO:0000401 ! gene_attribute
+
+[Term]
+id: SO:0000120
+name: protein_coding_primary_transcript
+def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]
+comment: May contain introns.
+subset: SOFA
+synonym: "pre mRNA" RELATED []
+synonym: "protein coding primary transcript" EXACT []
+is_a: SO:0000185 ! primary_transcript
+
+[Term]
+id: SO:0000121
+name: forward_primer
+def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "DNA forward primer" EXACT []
+synonym: "forward DNA primer" EXACT []
+synonym: "forward primer" EXACT []
+synonym: "forward primer oligo" EXACT []
+synonym: "forward primer oligonucleotide" EXACT []
+synonym: "forward primer polynucleotide" EXACT []
+synonym: "forward primer sequence" EXACT []
+is_a: SO:0000112 ! primer
+relationship: has_quality SO:0001030 ! forward
+
+[Term]
+id: SO:0000122
+name: RNA_sequence_secondary_structure
+def: "A folded RNA sequence." [SO:ke]
+synonym: "RNA sequence secondary structure" EXACT []
+is_a: SO:0000002 ! sequence_secondary_structure
+
+[Term]
+id: SO:0000123
+name: transcriptionally_regulated
+def: "An attribute describing a gene that is regulated at transcription." [SO:ma]
+comment: By:<protein_id>.
+synonym: "transcriptionally regulated" EXACT []
+is_a: SO:0000119 ! regulated
+
+[Term]
+id: SO:0000124
+name: transcriptionally_constitutive
+def: "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]
+synonym: "transcriptionally constitutive" EXACT []
+is_a: SO:0000123 ! transcriptionally_regulated
+
+[Term]
+id: SO:0000125
+name: transcriptionally_induced
+def: "An inducer molecule is required for transcription to occur." [SO:ke]
+synonym: "transcriptionally induced" EXACT []
+is_a: SO:0000123 ! transcriptionally_regulated
+
+[Term]
+id: SO:0000126
+name: transcriptionally_repressed
+def: "A repressor molecule is required for transcription to stop." [SO:ke]
+synonym: "transcriptionally repressed" EXACT []
+is_a: SO:0000123 ! transcriptionally_regulated
+
+[Term]
+id: SO:0000127
+name: silenced_gene
+def: "A gene that is silenced." [SO:xp]
+synonym: "silenced gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000893 ! silenced
+
+[Term]
+id: SO:0000128
+name: gene_silenced_by_DNA_modification
+def: "A gene that is silenced by DNA modification." [SO:xp]
+synonym: "gene silenced by DNA modification" EXACT []
+is_a: SO:0000127 ! silenced_gene
+relationship: has_quality SO:0000894 ! silenced_by_DNA_modification
+
+[Term]
+id: SO:0000129
+name: gene_silenced_by_DNA_methylation
+def: "A gene that is silenced by DNA methylation." [SO:xp]
+synonym: "gene silenced by DNA methylation" EXACT []
+synonym: "methylation-silenced gene" EXACT []
+is_a: SO:0000128 ! gene_silenced_by_DNA_modification
+relationship: has_quality SO:0000895 ! silenced_by_DNA_methylation
+
+[Term]
+id: SO:0000130
+name: post_translationally_regulated
+def: "An attribute describing a gene that is regulated after it has been translated." [SO:ke]
+synonym: "post translationally regulated" EXACT []
+synonym: "post-translationally regulated" EXACT []
+is_a: SO:0000119 ! regulated
+
+[Term]
+id: SO:0000131
+name: translationally_regulated
+def: "An attribute describing a gene that is regulated as it is translated." [SO:ke]
+synonym: "translationally regulated" EXACT []
+is_a: SO:0000119 ! regulated
+
+[Term]
+id: SO:0000132
+name: reverse_primer
+def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "DNA reverse primer" EXACT []
+synonym: "reverse DNA primer" EXACT []
+synonym: "reverse primer" EXACT []
+synonym: "reverse primer oligo" EXACT []
+synonym: "reverse primer oligonucleotide" EXACT []
+synonym: "reverse primer sequence" EXACT []
+is_a: SO:0000112 ! primer
+relationship: has_quality SO:0001031 ! reverse
+
+[Term]
+id: SO:0000133
+name: epigenetically_modified
+def: "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]
+synonym: "epigenetically modified" EXACT []
+is_a: SO:0000401 ! gene_attribute
+
+[Term]
+id: SO:0000134
+name: genomically_imprinted
+def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]
+synonym: "genomically imprinted" EXACT []
+synonym: "imprinted" BROAD []
+xref: http:http://en.wikipedia.org/wiki/Genomic_imprinting "wiki"
+is_a: SO:0000119 ! regulated
+is_a: SO:0000133 ! epigenetically_modified
+
+[Term]
+id: SO:0000135
+name: maternally_imprinted
+def: "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]
+synonym: "maternally imprinted" EXACT []
+is_a: SO:0000134 ! genomically_imprinted
+
+[Term]
+id: SO:0000136
+name: paternally_imprinted
+def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]
+synonym: "paternally imprinted" EXACT []
+is_a: SO:0000134 ! genomically_imprinted
+
+[Term]
+id: SO:0000137
+name: allelically_excluded
+def: "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]
+comment: Examples are x-inactivation and immunoglobulin formation.
+synonym: "allelically excluded" EXACT []
+is_a: SO:0000133 ! epigenetically_modified
+
+[Term]
+id: SO:0000138
+name: gene_rearranged_at_DNA_level
+def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp]
+synonym: "gene rearranged at DNA level" EXACT []
+is_a: SO:0000898 ! epigenetically_modified_gene
+relationship: has_quality SO:0000904 ! rearranged_at_DNA_level
+
+[Term]
+id: SO:0000139
+name: ribosome_entry_site
+def: "Region in mRNA where ribosome assembles." [SO:ke]
+subset: SOFA
+synonym: "ribosome entry site" EXACT []
+is_a: SO:0000836 ! mRNA_region
+relationship: part_of SO:0000204 ! five_prime_UTR
+
+[Term]
+id: SO:0000140
+name: attenuator
+def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]
+subset: SOFA
+synonym: "attenuator sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Attenuator "wiki"
+is_a: SO:0001680 ! translation_regulatory_region
+relationship: part_of SO:0000234 ! mRNA
+
+[Term]
+id: SO:0000141
+name: terminator
+def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+subset: SOFA
+synonym: "terminator sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki"
+is_a: SO:0001679 ! transcription_regulatory_region
+relationship: part_of SO:0000673 ! transcript
+
+[Term]
+id: SO:0000142
+name: DNA_sequence_secondary_structure
+def: "A folded DNA sequence." [SO:ke]
+synonym: "DNA sequence secondary structure" EXACT []
+is_a: SO:0000002 ! sequence_secondary_structure
+
+[Term]
+id: SO:0000143
+name: assembly_component
+def: "A region of known length which may be used to manufacture a longer region." [SO:ke]
+subset: SOFA
+synonym: "assembly component" EXACT []
+is_a: SO:0001410 ! experimental_feature
+
+[Term]
+id: SO:0000144
+name: primary_transcript_attribute
+is_obsolete: true
+
+[Term]
+id: SO:0000145
+name: recoded_codon
+def: "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]
+synonym: "recoded codon" EXACT []
+is_a: SO:0000360 ! codon
+
+[Term]
+id: SO:0000146
+name: capped
+def: "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke]
+is_a: SO:0000237 ! transcript_attribute
+
+[Term]
+id: SO:0000147
+name: exon
+def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Exon "wiki"
+is_a: SO:0000833 ! transcript_region
+
+[Term]
+id: SO:0000148
+name: supercontig
+def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]
+subset: SOFA
+synonym: "scaffold" RELATED []
+is_a: SO:0001876 ! partial_genomic_sequence_assembly
+relationship: part_of SO:0000719 ! ultracontig
+
+[Term]
+id: SO:0000149
+name: contig
+def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Contig "wiki"
+is_a: SO:0000143 ! assembly_component
+is_a: SO:0000353 ! sequence_assembly
+relationship: part_of SO:0000148 ! supercontig
+
+[Term]
+id: SO:0000150
+name: read
+def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]
+subset: SOFA
+is_a: SO:0000143 ! assembly_component
+relationship: part_of SO:0000149 ! contig
+
+[Term]
+id: SO:0000151
+name: clone
+def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]
+subset: SOFA
+xref: http:http://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
+is_a: SO:0000695 ! reagent
+
+[Term]
+id: SO:0000152
+name: YAC
+def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "yeast artificial chromosome" EXACT []
+is_a: SO:0000440 ! vector_replicon
+
+[Term]
+id: SO:0000153
+name: BAC
+def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "bacterial artificial chromosome" EXACT []
+is_a: SO:0000440 ! vector_replicon
+
+[Term]
+id: SO:0000154
+name: PAC
+def: "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.
+synonym: "P1" EXACT []
+synonym: "P1 artificial chromosome" EXACT []
+xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome "wiki"
+is_a: SO:0000440 ! vector_replicon
+
+[Term]
+id: SO:0000155
+name: plasmid
+def: "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "plasmid sequence" EXACT []
+is_a: SO:0001235 ! replicon
+
+[Term]
+id: SO:0000156
+name: cosmid
+def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]
+comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "cosmid vector" EXACT []
+xref: http://en.wikipedia.org/wiki/Cosmid "wiki"
+is_a: SO:0000440 ! vector_replicon
+
+[Term]
+id: SO:0000157
+name: phagemid
+def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]
+synonym: "phagemid vector" RELATED []
+xref: http://en.wikipedia.org/wiki/Phagemid "wiki"
+is_a: SO:0000440 ! vector_replicon
+
+[Term]
+id: SO:0000158
+name: fosmid
+def: "A cloning vector that utilizes the E. coli F factor." [SO:ma]
+comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
+synonym: "fosmid vector" RELATED []
+xref: http://en.wikipedia.org/wiki/Fosmid "wiki"
+is_a: SO:0000440 ! vector_replicon
+
+[Term]
+id: SO:0000159
+name: deletion
+alt_id: SO:1000033
+def: "The point at which one or more contiguous nucleotides were excised." [SO:ke]
+subset: SOFA
+synonym: "deleted_sequence" EXACT []
+synonym: "nucleotide deletion" EXACT []
+synonym: "nucleotide_deletion" EXACT []
+xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki"
+xref: loinc:LA6692-3 "Deletion"
+is_a: SO:0001059 ! sequence_alteration
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000160
+name: lambda_clone
+def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]
+is_obsolete: true
+
+[Term]
+id: SO:0000161
+name: methylated_adenine
+def: "A modified base in which adenine has been methylated." [SO:ke]
+subset: SOFA
+synonym: "methylated A" EXACT []
+synonym: "methylated adenine" EXACT []
+synonym: "methylated adenine base" EXACT []
+synonym: "methylated adenine residue" EXACT []
+synonym: "methylated_A" EXACT []
+is_a: SO:0000306 ! methylated_DNA_base_feature
+is_a: SO:0001962 ! modified_adenine
+
+[Term]
+id: SO:0000162
+name: splice_site
+def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]
+comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery.
+subset: SOFA
+synonym: "splice site" EXACT []
+xref: http://en.wikipedia.org/wiki/Splice_site "wiki"
+is_a: SO:0000835 ! primary_transcript_region
+
+[Term]
+id: SO:0000163
+name: five_prime_cis_splice_site
+def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]
+subset: SOFA
+synonym: "5' splice site" EXACT []
+synonym: "donor" RELATED []
+synonym: "donor splice site" EXACT []
+synonym: "five prime splice site" EXACT []
+synonym: "splice donor site" EXACT []
+is_a: SO:0001419 ! cis_splice_site
+
+[Term]
+id: SO:0000164
+name: three_prime_cis_splice_site
+def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]
+subset: SOFA
+synonym: "3' splice site" RELATED []
+synonym: "acceptor" RELATED []
+synonym: "acceptor splice site" EXACT []
+synonym: "splice acceptor site" EXACT []
+synonym: "three prime splice site" EXACT []
+is_a: SO:0001419 ! cis_splice_site
+
+[Term]
+id: SO:0000165
+name: enhancer
+def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki"
+is_a: SO:0000727 ! CRM
+
+[Term]
+id: SO:0000166
+name: enhancer_bound_by_factor
+def: "An enhancer bound by a factor." [SO:xp]
+synonym: "enhancer bound by factor" EXACT []
+is_a: SO:0000165 ! enhancer
+relationship: has_quality SO:0000277 ! bound_by_factor
+
+[Term]
+id: SO:0000167
+name: promoter
+def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
+subset: SOFA
+synonym: "promoter sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Promoter "wiki"
+is_a: SO:0001055 ! transcriptional_cis_regulatory_region
+
+[Term]
+id: SO:0000168
+name: restriction_enzyme_cut_site
+def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma]
+is_obsolete: true
+
+[Term]
+id: SO:0000169
+name: RNApol_I_promoter
+def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]
+synonym: "pol I promoter" EXACT []
+synonym: "polymerase I promoter" EXACT []
+synonym: "RNA polymerase A promoter" EXACT []
+synonym: "RNApol I promoter" EXACT []
+is_a: SO:0001203 ! RNA_polymerase_promoter
+
+[Term]
+id: SO:0000170
+name: RNApol_II_promoter
+def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]
+synonym: "pol II promoter" RELATED []
+synonym: "polymerase II promoter" EXACT []
+synonym: "RNA polymerase B promoter" EXACT []
+synonym: "RNApol II promoter" EXACT []
+is_a: SO:0001203 ! RNA_polymerase_promoter
+
+[Term]
+id: SO:0000171
+name: RNApol_III_promoter
+def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]
+synonym: "pol III promoter" EXACT []
+synonym: "polymerase III promoter" EXACT []
+synonym: "RNA polymerase C promoter" EXACT []
+synonym: "RNApol III promoter" EXACT []
+is_a: SO:0001203 ! RNA_polymerase_promoter
+
+[Term]
+id: SO:0000172
+name: CAAT_signal
+def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "CAAT box" EXACT []
+synonym: "CAAT signal" EXACT []
+synonym: "CAAT-box" EXACT []
+xref: http://en.wikipedia.org/wiki/CAAT_box "wiki"
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0000173
+name: GC_rich_promoter_region
+def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "GC rich promoter region" EXACT []
+synonym: "GC-rich region" EXACT []
+is_a: SO:0001659 ! promoter_element
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0000174
+name: TATA_box
+def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]
+comment: Binds TBP.
+synonym: "Goldstein-Hogness box" EXACT []
+synonym: "TATA box" EXACT []
+xref: http://en.wikipedia.org/wiki/TATA_box "wiki"
+is_a: SO:0001660 ! core_promoter_element
+
+[Term]
+id: SO:0000175
+name: minus_10_signal
+def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "-10 signal" EXACT []
+synonym: "minus 10 signal" EXACT []
+synonym: "Pribnow box" EXACT []
+synonym: "Pribnow Schaller box" EXACT []
+synonym: "Pribnow-Schaller box" EXACT []
+xref: http://en.wikipedia.org/wiki/Pribnow_box "wiki"
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70
+relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf
+
+[Term]
+id: SO:0000176
+name: minus_35_signal
+def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "-35 signal" EXACT []
+synonym: "minus 35 signal" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70
+relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf
+
+[Term]
+id: SO:0000177
+name: cross_genome_match
+def: "A nucleotide match against a sequence from another organism." [SO:ma]
+subset: SOFA
+synonym: "cross genome match" EXACT []
+is_a: SO:0000347 ! nucleotide_match
+
+[Term]
+id: SO:0000178
+name: operon
+def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Operon "wiki"
+is_a: SO:0005855 ! gene_group
+
+[Term]
+id: SO:0000179
+name: clone_insert_start
+def: "The start of the clone insert." [SO:ke]
+subset: SOFA
+synonym: "clone insert start" EXACT []
+is_a: SO:0000699 ! junction
+relationship: part_of SO:0000753 ! clone_insert
+
+[Term]
+id: SO:0000180
+name: retrotransposon
+def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]
+synonym: "class I" RELATED []
+synonym: "class I transposon" EXACT []
+synonym: "retrotransposon element" EXACT []
+xref: http://en.wikipedia.org/wiki/Retrotransposon "wiki"
+is_a: SO:0000101 ! transposable_element
+
+[Term]
+id: SO:0000181
+name: translated_nucleotide_match
+def: "A match against a translated sequence." [SO:ke]
+subset: SOFA
+synonym: "translated nucleotide match" EXACT []
+is_a: SO:0000347 ! nucleotide_match
+
+[Term]
+id: SO:0000182
+name: DNA_transposon
+def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]
+synonym: "class II" RELATED []
+synonym: "class II transposon" EXACT []
+synonym: "DNA transposon" EXACT []
+is_a: SO:0000101 ! transposable_element
+
+[Term]
+id: SO:0000183
+name: non_transcribed_region
+def: "A region of the gene which is not transcribed." [SO:ke]
+subset: SOFA
+synonym: "non transcribed region" EXACT []
+synonym: "non-transcribed sequence" EXACT []
+synonym: "nontranscribed region" EXACT []
+synonym: "nontranscribed sequence" EXACT []
+is_a: SO:0000842 ! gene_component_region
+
+[Term]
+id: SO:0000184
+name: U2_intron
+def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]
+comment: May have either GT-AG or AT-AG 5' and 3' boundaries.
+synonym: "U2 intron" EXACT []
+is_a: SO:0000662 ! spliceosomal_intron
+
+[Term]
+id: SO:0000185
+name: primary_transcript
+def: "A transcript that in its initial state requires modification to be functional." [SO:ma]
+subset: SOFA
+synonym: "precursor RNA" EXACT []
+synonym: "primary transcript" EXACT []
+xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki"
+is_a: SO:0000673 ! transcript
+
+[Term]
+id: SO:0000186
+name: LTR_retrotransposon
+def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke]
+synonym: "long terminal repeat retrotransposon" EXACT []
+synonym: "LTR retrotransposon" EXACT []
+is_a: SO:0000180 ! retrotransposon
+
+[Term]
+id: SO:0000187
+name: repeat_family
+def: "A group of characterized repeat sequences." [SO:ke]
+subset: SOFA
+is_obsolete: true
+
+[Term]
+id: SO:0000188
+name: intron
+def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Intron "wiki"
+is_a: SO:0000835 ! primary_transcript_region
+
+[Term]
+id: SO:0000189
+name: non_LTR_retrotransposon
+def: "A retrotransposon without long terminal repeat sequences." [SO:ke]
+synonym: "non LTR retrotransposon" EXACT []
+is_a: SO:0000180 ! retrotransposon
+
+[Term]
+id: SO:0000190
+name: five_prime_intron
+synonym: "5' intron" EXACT []
+synonym: "5' intron sequence" EXACT []
+synonym: "five prime intron" EXACT []
+is_a: SO:0000188 ! intron
+
+[Term]
+id: SO:0000191
+name: interior_intron
+synonym: "interior intron" EXACT []
+is_a: SO:0000188 ! intron
+
+[Term]
+id: SO:0000192
+name: three_prime_intron
+synonym: "3' intron" EXACT []
+synonym: "3' intron sequence" RELATED []
+synonym: "three prime intron" EXACT []
+is_a: SO:0000188 ! intron
+
+[Term]
+id: SO:0000193
+name: RFLP_fragment
+def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]
+subset: SOFA
+synonym: "restriction fragment length polymorphism" EXACT []
+synonym: "RFLP" EXACT []
+synonym: "RFLP fragment" EXACT []
+xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki"
+is_a: SO:0000412 ! restriction_fragment
+
+[Term]
+id: SO:0000194
+name: LINE_element
+def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
+synonym: "LINE" EXACT []
+synonym: "LINE element" EXACT []
+synonym: "Long interspersed element" EXACT []
+synonym: "Long interspersed nuclear element" EXACT []
+is_a: SO:0000189 ! non_LTR_retrotransposon
+
+[Term]
+id: SO:0000195
+name: coding_exon
+def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]
+subset: SOFA
+synonym: "coding exon" EXACT []
+is_a: SO:0000147 ! exon
+
+[Term]
+id: SO:0000196
+name: five_prime_coding_exon_coding_region
+def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]
+subset: SOFA
+synonym: "five prime exon coding region" EXACT []
+is_a: SO:0001215 ! coding_region_of_exon
+relationship: part_of SO:0000200 ! five_prime_coding_exon
+
+[Term]
+id: SO:0000197
+name: three_prime_coding_exon_coding_region
+def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]
+subset: SOFA
+synonym: "three prime exon coding region" EXACT []
+is_a: SO:0001215 ! coding_region_of_exon
+relationship: part_of SO:0000202 ! three_prime_coding_exon
+
+[Term]
+id: SO:0000198
+name: noncoding_exon
+def: "An exon that does not contain any codons." [SO:ke]
+subset: SOFA
+synonym: "noncoding exon" EXACT []
+is_a: SO:0000147 ! exon
+
+[Term]
+id: SO:0000199
+name: translocation
+def: "A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." [NCBI:th, SO:ke]
+subset: DBVAR
+synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/]
+synonym: "translocated sequence" EXACT []
+is_a: SO:0001785 ! structural_alteration
+
+[Term]
+id: SO:0000200
+name: five_prime_coding_exon
+def: "The 5' most coding exon." [SO:ke]
+subset: SOFA
+synonym: "5' coding exon" EXACT []
+synonym: "five prime coding exon" EXACT []
+is_a: SO:0000195 ! coding_exon
+
+[Term]
+id: SO:0000201
+name: interior_exon
+def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]
+synonym: "interior exon" EXACT []
+is_a: SO:0000147 ! exon
+
+[Term]
+id: SO:0000202
+name: three_prime_coding_exon
+def: "The coding exon that is most 3-prime on a given transcript." [SO:ma]
+synonym: "3' coding exon" RELATED []
+synonym: "three prime coding exon" EXACT []
+is_a: SO:0000195 ! coding_exon
+
+[Term]
+id: SO:0000203
+name: UTR
+def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]
+subset: SOFA
+synonym: "untranslated region" EXACT []
+is_a: SO:0000836 ! mRNA_region
+
+[Term]
+id: SO:0000204
+name: five_prime_UTR
+def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+subset: SOFA
+synonym: "5' UTR" EXACT []
+synonym: "five prime UTR" EXACT []
+synonym: "five_prime_untranslated_region" EXACT []
+xref: http://en.wikipedia.org/wiki/5'_UTR "wiki"
+is_a: SO:0000203 ! UTR
+
+[Term]
+id: SO:0000205
+name: three_prime_UTR
+def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+subset: SOFA
+synonym: "three prime untranslated region" EXACT []
+synonym: "three prime UTR" EXACT []
+xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki"
+is_a: SO:0000203 ! UTR
+
+[Term]
+id: SO:0000206
+name: SINE_element
+def: "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]
+synonym: "Short interspersed element" EXACT []
+synonym: "Short interspersed nuclear element" EXACT []
+synonym: "SINE element" EXACT []
+xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element "wiki"
+is_a: SO:0000189 ! non_LTR_retrotransposon
+
+[Term]
+id: SO:0000207
+name: simple_sequence_length_variation
+synonym: "simple sequence length polymorphism" RELATED []
+synonym: "simple sequence length variation" EXACT []
+synonym: "SSLP" RELATED []
+is_a: SO:0000248 ! sequence_length_variation
+
+[Term]
+id: SO:0000208
+name: terminal_inverted_repeat_element
+def: "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]
+synonym: "terminal inverted repeat element" EXACT []
+synonym: "TIR element" EXACT []
+is_a: SO:0000182 ! DNA_transposon
+
+[Term]
+id: SO:0000209
+name: rRNA_primary_transcript
+def: "A primary transcript encoding a ribosomal RNA." [SO:ke]
+subset: SOFA
+synonym: "ribosomal RNA primary transcript" EXACT []
+synonym: "rRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+
+[Term]
+id: SO:0000210
+name: tRNA_primary_transcript
+def: "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]
+synonym: "tRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+
+[Term]
+id: SO:0000211
+name: alanine_tRNA_primary_transcript
+def: "A primary transcript encoding alanyl tRNA." [SO:ke]
+synonym: "alanine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000212
+name: arginine_tRNA_primary_transcript
+def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]
+synonym: "arginine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000213
+name: asparagine_tRNA_primary_transcript
+def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]
+synonym: "asparagine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000214
+name: aspartic_acid_tRNA_primary_transcript
+def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]
+synonym: "aspartic acid tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000215
+name: cysteine_tRNA_primary_transcript
+def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]
+synonym: "cysteine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000216
+name: glutamic_acid_tRNA_primary_transcript
+def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]
+synonym: "glutamic acid tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000217
+name: glutamine_tRNA_primary_transcript
+def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]
+synonym: "glutamine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000218
+name: glycine_tRNA_primary_transcript
+def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]
+synonym: "glycine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000219
+name: histidine_tRNA_primary_transcript
+def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]
+synonym: "histidine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000220
+name: isoleucine_tRNA_primary_transcript
+def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]
+synonym: "isoleucine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000221
+name: leucine_tRNA_primary_transcript
+def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]
+synonym: "leucine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000222
+name: lysine_tRNA_primary_transcript
+def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]
+synonym: "lysine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000223
+name: methionine_tRNA_primary_transcript
+def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]
+synonym: "methionine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000224
+name: phenylalanine_tRNA_primary_transcript
+def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]
+synonym: "phenylalanine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000225
+name: proline_tRNA_primary_transcript
+def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]
+synonym: "proline tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000226
+name: serine_tRNA_primary_transcript
+def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
+synonym: "serine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000227
+name: threonine_tRNA_primary_transcript
+def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]
+synonym: "threonine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000228
+name: tryptophan_tRNA_primary_transcript
+def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]
+synonym: "tryptophan tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000229
+name: tyrosine_tRNA_primary_transcript
+def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]
+synonym: "tyrosine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000230
+name: valine_tRNA_primary_transcript
+def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]
+synonym: "valine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000231
+name: snRNA_primary_transcript
+def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]
+synonym: "snRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+
+[Term]
+id: SO:0000232
+name: snoRNA_primary_transcript
+def: "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]
+synonym: "snoRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+
+[Term]
+id: SO:0000233
+name: mature_transcript
+def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]
+comment: A processed transcript cannot contain introns.
+subset: SOFA
+synonym: "mature transcript" EXACT []
+xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki"
+is_a: SO:0000673 ! transcript
+relationship: derives_from SO:0000185 ! primary_transcript
+
+[Term]
+id: SO:0000234
+name: mRNA
+def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]
+comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+synonym: "messenger RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/MRNA "wiki"
+is_a: SO:0000233 ! mature_transcript
+
+[Term]
+id: SO:0000235
+name: TF_binding_site
+def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]
+subset: SOFA
+synonym: "TF binding site" EXACT []
+synonym: "transcription factor binding site" EXACT []
+is_a: SO:0001654 ! nucleotide_to_protein_binding_site
+is_a: SO:0001679 ! transcription_regulatory_region
+
+[Term]
+id: SO:0000236
+name: ORF
+def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]
+comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+synonym: "open reading frame" EXACT []
+is_a: SO:0000717 ! reading_frame
+
+[Term]
+id: SO:0000237
+name: transcript_attribute
+synonym: "transcript attribute" EXACT []
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000238
+name: foldback_element
+def: "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]
+synonym: "foldback element" EXACT []
+synonym: "long inverted repeat element" RELATED []
+synonym: "LVR element" RELATED []
+is_a: SO:0000182 ! DNA_transposon
+
+[Term]
+id: SO:0000239
+name: flanking_region
+def: "The sequences extending on either side of a specific region." [SO:ke]
+subset: SOFA
+synonym: "flanking region" EXACT []
+is_a: SO:0001412 ! topologically_defined_region
+
+[Term]
+id: SO:0000240
+name: chromosome_variation
+synonym: "chromosome variation" EXACT []
+is_a: SO:0001507 ! variant_collection
+disjoint_from: SO:0000400 ! sequence_attribute
+relationship: part_of SO:0001524 ! chromosomally_aberrant_genome
+
+[Term]
+id: SO:0000241
+name: internal_UTR
+def: "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]
+synonym: "internal UTR" EXACT []
+is_a: SO:0000203 ! UTR
+
+[Term]
+id: SO:0000242
+name: untranslated_region_polycistronic_mRNA
+def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]
+synonym: "untranslated region polycistronic mRNA" EXACT []
+is_a: SO:0000203 ! UTR
+
+[Term]
+id: SO:0000243
+name: internal_ribosome_entry_site
+def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]
+synonym: "internal ribosomal entry sequence" EXACT []
+synonym: "internal ribosomal entry site" EXACT []
+synonym: "internal ribosome entry sequence" RELATED []
+synonym: "internal ribosome entry site" EXACT []
+synonym: "IRES" EXACT []
+xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site "wiki"
+is_a: SO:0000139 ! ribosome_entry_site
+
+[Term]
+id: SO:0000244
+name: four_cutter_restriction_site
+synonym: "4-cutter_restriction_site" RELATED []
+synonym: "four-cutter_restriction_sit" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0000245
+name: mRNA_by_polyadenylation_status
+is_obsolete: true
+
+[Term]
+id: SO:0000246
+name: polyadenylated
+def: "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]
+is_a: SO:0000863 ! mRNA_attribute
+
+[Term]
+id: SO:0000247
+name: mRNA_not_polyadenylated
+is_obsolete: true
+
+[Term]
+id: SO:0000248
+name: sequence_length_variation
+synonym: "sequence length variation" EXACT []
+is_a: SO:1000002 ! substitution
+
+[Term]
+id: SO:0000249
+name: six_cutter_restriction_site
+synonym: "6-cutter_restriction_site" RELATED []
+synonym: "six-cutter_restriction_site" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0000250
+name: modified_RNA_base_feature
+def: "A post_transcriptionally modified base." [SO:ke]
+synonym: "modified RNA base feature" EXACT []
+is_a: SO:0001236 ! base
+
+[Term]
+id: SO:0000251
+name: eight_cutter_restriction_site
+synonym: "8-cutter_restriction_site" RELATED []
+synonym: "eight-cutter_restriction_site" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0000252
+name: rRNA
+def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]
+subset: SOFA
+synonym: "ribosomal ribonucleic acid" EXACT []
+synonym: "ribosomal RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/RRNA "wiki"
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0000209 ! rRNA_primary_transcript
+
+[Term]
+id: SO:0000253
+name: tRNA
+def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+synonym: "transfer ribonucleic acid" RELATED []
+synonym: "transfer RNA" RELATED []
+xref: http://en.wikipedia.org/wiki/TRNA "wiki"
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0000254
+name: alanyl_tRNA
+def: "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]
+synonym: "alanyl tRNA" EXACT []
+synonym: "alanyl-transfer ribonucleic acid" EXACT []
+synonym: "alanyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000211 ! alanine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000255
+name: rRNA_small_subunit_primary_transcript
+def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]
+synonym: "rRNA small subunit primary transcript" EXACT []
+is_a: SO:0000209 ! rRNA_primary_transcript
+
+[Term]
+id: SO:0000256
+name: asparaginyl_tRNA
+def: "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]
+synonym: "asparaginyl tRNA" EXACT []
+synonym: "asparaginyl-transfer ribonucleic acid" EXACT []
+synonym: "asparaginyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000213 ! asparagine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000257
+name: aspartyl_tRNA
+def: "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]
+synonym: "aspartyl tRNA" EXACT []
+synonym: "aspartyl-transfer ribonucleic acid" EXACT []
+synonym: "aspartyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000214 ! aspartic_acid_tRNA_primary_transcript
+
+[Term]
+id: SO:0000258
+name: cysteinyl_tRNA
+def: "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]
+synonym: "cysteinyl tRNA" EXACT []
+synonym: "cysteinyl-transfer ribonucleic acid" EXACT []
+synonym: "cysteinyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000215 ! cysteine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000259
+name: glutaminyl_tRNA
+def: "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]
+synonym: "glutaminyl tRNA" EXACT []
+synonym: "glutaminyl-transfer ribonucleic acid" EXACT []
+synonym: "glutaminyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000216 ! glutamic_acid_tRNA_primary_transcript
+
+[Term]
+id: SO:0000260
+name: glutamyl_tRNA
+def: "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]
+synonym: "glutamyl tRNA" EXACT []
+synonym: "glutamyl-transfer ribonucleic acid" EXACT []
+synonym: "glutamyl-transfer RNA" RELATED []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000217 ! glutamine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000261
+name: glycyl_tRNA
+def: "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]
+synonym: "glycyl tRNA" EXACT []
+synonym: "glycyl-transfer ribonucleic acid" RELATED []
+synonym: "glycyl-transfer RNA" RELATED []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000218 ! glycine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000262
+name: histidyl_tRNA
+def: "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]
+synonym: "histidyl tRNA" EXACT []
+synonym: "histidyl-transfer ribonucleic acid" EXACT []
+synonym: "histidyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000219 ! histidine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000263
+name: isoleucyl_tRNA
+def: "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]
+synonym: "isoleucyl tRNA" EXACT []
+synonym: "isoleucyl-transfer ribonucleic acid" EXACT []
+synonym: "isoleucyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000220 ! isoleucine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000264
+name: leucyl_tRNA
+def: "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]
+synonym: "leucyl tRNA" EXACT []
+synonym: "leucyl-transfer ribonucleic acid" EXACT []
+synonym: "leucyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000221 ! leucine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000265
+name: lysyl_tRNA
+def: "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]
+synonym: "lysyl tRNA" EXACT []
+synonym: "lysyl-transfer ribonucleic acid" EXACT []
+synonym: "lysyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000222 ! lysine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000266
+name: methionyl_tRNA
+def: "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]
+synonym: "methionyl tRNA" EXACT []
+synonym: "methionyl-transfer ribonucleic acid" EXACT []
+synonym: "methionyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000223 ! methionine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000267
+name: phenylalanyl_tRNA
+def: "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]
+synonym: "phenylalanyl tRNA" EXACT []
+synonym: "phenylalanyl-transfer ribonucleic acid" EXACT []
+synonym: "phenylalanyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000224 ! phenylalanine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000268
+name: prolyl_tRNA
+def: "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]
+synonym: "prolyl tRNA" EXACT []
+synonym: "prolyl-transfer ribonucleic acid" EXACT []
+synonym: "prolyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000225 ! proline_tRNA_primary_transcript
+
+[Term]
+id: SO:0000269
+name: seryl_tRNA
+def: "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]
+synonym: "seryl tRNA" EXACT []
+synonym: "seryl-transfer ribonucleic acid" RELATED []
+synonym: "seryl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000226 ! serine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000270
+name: threonyl_tRNA
+def: "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]
+synonym: "threonyl tRNA" EXACT []
+synonym: "threonyl-transfer ribonucleic acid" EXACT []
+synonym: "threonyl-transfer RNA" RELATED []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000227 ! threonine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000271
+name: tryptophanyl_tRNA
+def: "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]
+synonym: "tryptophanyl tRNA" EXACT []
+synonym: "tryptophanyl-transfer ribonucleic acid" EXACT []
+synonym: "tryptophanyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000228 ! tryptophan_tRNA_primary_transcript
+
+[Term]
+id: SO:0000272
+name: tyrosyl_tRNA
+def: "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]
+synonym: "tyrosyl tRNA" EXACT []
+synonym: "tyrosyl-transfer ribonucleic acid" EXACT []
+synonym: "tyrosyl-transfer RNA" RELATED []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000229 ! tyrosine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000273
+name: valyl_tRNA
+def: "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]
+synonym: "valyl tRNA" EXACT []
+synonym: "valyl-transfer ribonucleic acid" EXACT []
+synonym: "valyl-transfer RNA" RELATED []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000230 ! valine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000274
+name: snRNA
+def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+synonym: "small nuclear RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/SnRNA "wiki"
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0000231 ! snRNA_primary_transcript
+
+[Term]
+id: SO:0000275
+name: snoRNA
+def: "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]
+subset: SOFA
+synonym: "small nucleolar RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/SnoRNA "wiki"
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0000232 ! snoRNA_primary_transcript
+
+[Term]
+id: SO:0000276
+name: miRNA
+alt_id: SO:0000649
+def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:11081512, PMID:12592000]
+subset: SOFA
+synonym: "micro RNA" EXACT []
+synonym: "microRNA" EXACT []
+synonym: "small temporal RNA" EXACT []
+synonym: "stRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/MiRNA "wiki"
+xref: http://en.wikipedia.org/wiki/StRNA "wiki"
+is_a: SO:0000370 ! small_regulatory_ncRNA
+relationship: part_of SO:0001244 ! pre_miRNA
+
+[Term]
+id: SO:0000277
+name: bound_by_factor
+def: "An attribute describing a sequence that is bound by another molecule." [SO:ke]
+comment: Formerly called transcript_by_bound_factor.
+synonym: "bound by factor" EXACT []
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000278
+name: transcript_bound_by_nucleic_acid
+def: "A transcript that is bound by a nucleic acid." [SO:xp]
+comment: Formerly called transcript_by_bound_nucleic_acid.
+synonym: "transcript bound by nucleic acid" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: has_quality SO:0000876 ! bound_by_nucleic_acid
+
+[Term]
+id: SO:0000279
+name: transcript_bound_by_protein
+def: "A transcript that is bound by a protein." [SO:xp]
+comment: Formerly called transcript_by_bound_protein.
+synonym: "transcript bound by protein" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: has_quality SO:0000875 ! bound_by_protein
+
+[Term]
+id: SO:0000280
+name: engineered_gene
+def: "A gene that is engineered." [SO:xp]
+synonym: "engineered gene" EXACT []
+is_a: SO:0000704 ! gene
+is_a: SO:0000804 ! engineered_region
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000281
+name: engineered_foreign_gene
+def: "A gene that is engineered and foreign." [SO:xp]
+synonym: "engineered foreign gene" EXACT []
+is_a: SO:0000280 ! engineered_gene
+is_a: SO:0000285 ! foreign_gene
+is_a: SO:0000805 ! engineered_foreign_region
+relationship: has_quality SO:0000783 ! engineered
+relationship: has_quality SO:0000784 ! foreign
+
+[Term]
+id: SO:0000282
+name: mRNA_with_minus_1_frameshift
+def: "An mRNA with a minus 1 frameshift." [SO:xp]
+synonym: "mRNA with minus 1 frameshift" EXACT []
+is_a: SO:0000108 ! mRNA_with_frameshift
+relationship: has_quality SO:0000866 ! minus_1_frameshift
+
+[Term]
+id: SO:0000283
+name: engineered_foreign_transposable_element_gene
+def: "A transposable_element that is engineered and foreign." [SO:xp]
+synonym: "engineered foreign transposable element gene" EXACT []
+is_a: SO:0000111 ! transposable_element_gene
+is_a: SO:0000281 ! engineered_foreign_gene
+relationship: has_quality SO:0000783 ! engineered
+relationship: has_quality SO:0000784 ! foreign
+
+[Term]
+id: SO:0000284
+name: type_I_enzyme_restriction_site
+def: "The recognition site is bipartite and interrupted." [http://www.promega.com]
+is_obsolete: true
+
+[Term]
+id: SO:0000285
+name: foreign_gene
+def: "A gene that is foreign." [SO:xp]
+synonym: "foreign gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000784 ! foreign
+
+[Term]
+id: SO:0000286
+name: long_terminal_repeat
+def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "direct terminal repeat" RELATED []
+synonym: "long terminal repeat" EXACT []
+synonym: "LTR" EXACT []
+xref: http://en.wikipedia.org/wiki/Long_terminal_repeat "wiki"
+is_a: SO:0000657 ! repeat_region
+relationship: part_of SO:0000186 ! LTR_retrotransposon
+
+[Term]
+id: SO:0000287
+name: fusion_gene
+def: "A gene that is a fusion." [SO:xp]
+synonym: "fusion gene" EXACT []
+xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki"
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000806 ! fusion
+
+[Term]
+id: SO:0000288
+name: engineered_fusion_gene
+def: "A fusion gene that is engineered." [SO:xp]
+synonym: "engineered fusion gene" EXACT []
+is_a: SO:0000280 ! engineered_gene
+is_a: SO:0000287 ! fusion_gene
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000289
+name: microsatellite
+def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]
+subset: SOFA
+synonym: "microsatellite locus" EXACT []
+synonym: "microsatellite marker" EXACT []
+synonym: "VNTR" EXACT []
+xref: http://en.wikipedia.org/wiki/Microsatellite "wiki"
+is_a: SO:0000005 ! satellite_DNA
+
+[Term]
+id: SO:0000290
+name: dinucleotide_repeat_microsatellite_feature
+synonym: "dinucleotide repeat microsatellite" EXACT []
+synonym: "dinucleotide repeat microsatellite feature" EXACT []
+synonym: "dinucleotide repeat microsatellite locus" EXACT []
+synonym: "dinucleotide repeat microsatellite marker" EXACT []
+is_a: SO:0000289 ! microsatellite
+
+[Term]
+id: SO:0000291
+name: trinucleotide_repeat_microsatellite_feature
+synonym: "dinucleotide repeat microsatellite marker" RELATED []
+synonym: "rinucleotide repeat microsatellite" EXACT []
+synonym: "trinucleotide repeat microsatellite feature" EXACT []
+synonym: "trinucleotide repeat microsatellite locus" EXACT []
+is_a: SO:0000289 ! microsatellite
+
+[Term]
+id: SO:0000292
+name: repetitive_element
+is_obsolete: true
+
+[Term]
+id: SO:0000293
+name: engineered_foreign_repetitive_element
+def: "A repetitive element that is engineered and foreign." [SO:xp]
+synonym: "engineered foreign repetitive element" EXACT []
+is_a: SO:0000657 ! repeat_region
+is_a: SO:0000805 ! engineered_foreign_region
+relationship: has_quality SO:0000783 ! engineered
+relationship: has_quality SO:0000784 ! foreign
+
+[Term]
+id: SO:0000294
+name: inverted_repeat
+def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]
+subset: SOFA
+synonym: "inverted repeat" EXACT []
+synonym: "inverted repeat sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki"
+is_a: SO:0000657 ! repeat_region
+
+[Term]
+id: SO:0000295
+name: U12_intron
+def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]
+comment: May have either GT-AC or AT-AC 5' and 3' boundaries.
+synonym: "U12 intron" EXACT []
+synonym: "U12-dependent intron" EXACT []
+is_a: SO:0000662 ! spliceosomal_intron
+
+[Term]
+id: SO:0000296
+name: origin_of_replication
+def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+subset: SOFA
+synonym: "ori" EXACT []
+synonym: "origin of replication" EXACT []
+xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki"
+is_a: SO:0001411 ! biological_region
+relationship: part_of SO:0001235 ! replicon
+
+[Term]
+id: SO:0000297
+name: D_loop
+def: "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "D-loop" EXACT []
+synonym: "displacement loop" RELATED []
+xref: http://en.wikipedia.org/wiki/D_loop "wiki"
+is_a: SO:0000296 ! origin_of_replication
+
+[Term]
+id: SO:0000298
+name: recombination_feature
+synonym: "recombination feature" EXACT []
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000299
+name: specific_recombination_site
+synonym: "specific recombination site" EXACT []
+is_a: SO:0000669 ! sequence_rearrangement_feature
+
+[Term]
+id: SO:0000300
+name: recombination_feature_of_rearranged_gene
+synonym: "recombination feature of rearranged gene" EXACT []
+is_a: SO:0000299 ! specific_recombination_site
+
+[Term]
+id: SO:0000301
+name: vertebrate_immune_system_gene_recombination_feature
+synonym: "vertebrate immune system gene recombination feature" EXACT []
+is_a: SO:0000300 ! recombination_feature_of_rearranged_gene
+
+[Term]
+id: SO:0000302
+name: J_gene_recombination_feature
+def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "J gene recombination feature" EXACT []
+synonym: "J-RS" EXACT []
+is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
+
+[Term]
+id: SO:0000303
+name: clip
+def: "Part of the primary transcript that is clipped off during processing." [SO:ke]
+subset: SOFA
+is_a: SO:0000835 ! primary_transcript_region
+
+[Term]
+id: SO:0000304
+name: type_II_enzyme_restriction_site
+def: "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com]
+is_obsolete: true
+
+[Term]
+id: SO:0000305
+name: modified_DNA_base
+def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+comment: Modified base:<modified_base>.
+subset: SOFA
+synonym: "modified base site" EXACT []
+is_a: SO:0001236 ! base
+is_a: SO:0001720 ! epigenetically_modified_region
+
+[Term]
+id: SO:0000306
+name: methylated_DNA_base_feature
+def: "A nucleotide modified by methylation." [SO:ke]
+subset: SOFA
+synonym: "methylated base feature" EXACT []
+is_a: SO:0000305 ! modified_DNA_base
+
+[Term]
+id: SO:0000307
+name: CpG_island
+def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]
+subset: SOFA
+synonym: "CG island" EXACT []
+synonym: "CpG island" EXACT []
+xref: http://en.wikipedia.org/wiki/CpG_island "wiki"
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000308
+name: sequence_feature_locating_method
+is_obsolete: true
+
+[Term]
+id: SO:0000309
+name: computed_feature
+is_obsolete: true
+
+[Term]
+id: SO:0000310
+name: predicted_ab_initio_computation
+is_obsolete: true
+
+[Term]
+id: SO:0000311
+name: computed_feature_by_similarity
+def: "." [SO:ma]
+comment: similar to:<sequence_id>
+is_obsolete: true
+
+[Term]
+id: SO:0000312
+name: experimentally_determined
+def: "Attribute to describe a feature that has been experimentally verified." [SO:ke]
+synonym: "experimentally determined" EXACT []
+is_a: SO:0000789 ! validated
+
+[Term]
+id: SO:0000313
+name: stem_loop
+alt_id: SO:0000019
+def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "RNA_hairpin_loop" EXACT []
+synonym: "stem loop" EXACT []
+synonym: "stem-loop" EXACT []
+xref: http://en.wikipedia.org/wiki/Stem_loop "wiki"
+is_a: SO:0000122 ! RNA_sequence_secondary_structure
+
+[Term]
+id: SO:0000314
+name: direct_repeat
+def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke]
+subset: SOFA
+synonym: "direct repeat" EXACT []
+xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki"
+is_a: SO:0000657 ! repeat_region
+
+[Term]
+id: SO:0000315
+name: TSS
+def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]
+subset: SOFA
+synonym: "transcription start site" EXACT []
+synonym: "transcription_start_site" EXACT []
+is_a: SO:0000835 ! primary_transcript_region
+
+[Term]
+id: SO:0000316
+name: CDS
+def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]
+subset: SOFA
+synonym: "coding sequence" EXACT []
+synonym: "coding_sequence" EXACT []
+is_a: SO:0000836 ! mRNA_region
+
+[Term]
+id: SO:0000317
+name: cDNA_clone
+def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "cDNA clone" EXACT []
+is_a: SO:0000151 ! clone
+relationship: has_quality SO:0000756 ! cDNA
+
+[Term]
+id: SO:0000318
+name: start_codon
+def: "First codon to be translated by a ribosome." [SO:ke]
+subset: SOFA
+synonym: "initiation codon" EXACT []
+synonym: "start codon" EXACT []
+xref: http://en.wikipedia.org/wiki/Start_codon "wiki"
+is_a: SO:0000360 ! codon
+
+[Term]
+id: SO:0000319
+name: stop_codon
+def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]
+subset: SOFA
+synonym: "stop codon" EXACT []
+xref: http://en.wikipedia.org/wiki/Stop_codon "wiki"
+is_a: SO:0000360 ! codon
+
+[Term]
+id: SO:0000320
+name: intronic_splice_enhancer
+def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke]
+synonym: "intronic splice enhancer" EXACT []
+is_a: SO:0000344 ! splice_enhancer
+relationship: part_of SO:0000841 ! spliceosomal_intron_region
+
+[Term]
+id: SO:0000321
+name: mRNA_with_plus_1_frameshift
+def: "An mRNA with a plus 1 frameshift." [SO:ke]
+synonym: "mRNA with plus 1 frameshift" EXACT []
+is_a: SO:0000108 ! mRNA_with_frameshift
+relationship: has_quality SO:0000868 ! plus_1_frameshift
+
+[Term]
+id: SO:0000322
+name: nuclease_hypersensitive_site
+synonym: "nuclease hypersensitive site" EXACT []
+is_a: SO:0000684 ! nuclease_sensitive_site
+
+[Term]
+id: SO:0000323
+name: coding_start
+def: "The first base to be translated into protein." [SO:ke]
+synonym: "coding start" EXACT []
+synonym: "translation initiation site" EXACT []
+synonym: "translation start" RELATED []
+is_a: SO:0000851 ! CDS_region
+
+[Term]
+id: SO:0000324
+name: tag
+def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]
+subset: SOFA
+is_a: SO:0000696 ! oligo
+
+[Term]
+id: SO:0000325
+name: rRNA_large_subunit_primary_transcript
+def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]
+subset: SOFA
+synonym: "35S rRNA primary transcript" EXACT []
+synonym: "rRNA large subunit primary transcript" EXACT []
+is_a: SO:0000209 ! rRNA_primary_transcript
+
+[Term]
+id: SO:0000326
+name: SAGE_tag
+def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]
+subset: SOFA
+synonym: "SAGE tag" EXACT []
+is_a: SO:0000324 ! tag
+
+[Term]
+id: SO:0000327
+name: coding_end
+def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke]
+synonym: "coding end" EXACT []
+synonym: "translation termination site" EXACT []
+synonym: "translation_end" EXACT []
+is_a: SO:0000851 ! CDS_region
+
+[Term]
+id: SO:0000328
+name: microarray_oligo
+synonym: "microarray oligo" EXACT []
+synonym: "microarray oligonucleotide" EXACT []
+is_a: SO:0000051 ! probe
+
+[Term]
+id: SO:0000329
+name: mRNA_with_plus_2_frameshift
+def: "An mRNA with a plus 2 frameshift." [SO:xp]
+synonym: "mRNA with plus 2 frameshift" EXACT []
+is_a: SO:0000108 ! mRNA_with_frameshift
+relationship: has_quality SO:0000869 ! plus_2_framshift
+
+[Term]
+id: SO:0000330
+name: conserved_region
+def: "Region of sequence similarity by descent from a common ancestor." [SO:ke]
+subset: SOFA
+synonym: "conserved region" EXACT []
+xref: http://en.wikipedia.org/wiki/Conserved_region "wiki"
+is_a: SO:0001410 ! experimental_feature
+
+[Term]
+id: SO:0000331
+name: STS
+def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]
+subset: SOFA
+synonym: "sequence tag site" EXACT []
+is_a: SO:0000324 ! tag
+
+[Term]
+id: SO:0000332
+name: coding_conserved_region
+def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke]
+subset: SOFA
+synonym: "coding conserved region" EXACT []
+is_a: SO:0000330 ! conserved_region
+
+[Term]
+id: SO:0000333
+name: exon_junction
+def: "The boundary between two exons in a processed transcript." [SO:ke]
+subset: SOFA
+synonym: "exon junction" EXACT []
+is_a: SO:0000699 ! junction
+relationship: part_of SO:0000233 ! mature_transcript
+
+[Term]
+id: SO:0000334
+name: nc_conserved_region
+def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]
+subset: SOFA
+synonym: "nc conserved region" EXACT []
+synonym: "noncoding conserved region" EXACT []
+is_a: SO:0000330 ! conserved_region
+
+[Term]
+id: SO:0000335
+name: mRNA_with_minus_2_frameshift
+def: "A mRNA with a minus 2 frameshift." [SO:ke]
+synonym: "mRNA with minus 2 frameshift" EXACT []
+is_a: SO:0000108 ! mRNA_with_frameshift
+relationship: has_quality SO:0000867 ! minus_2_frameshift
+
+[Term]
+id: SO:0000336
+name: pseudogene
+def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Pseudogene "wiki"
+is_a: SO:0001411 ! biological_region
+relationship: non_functional_homolog_of SO:0000704 ! gene
+
+[Term]
+id: SO:0000337
+name: RNAi_reagent
+def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]
+subset: SOFA
+synonym: "RNAi reagent" EXACT []
+is_a: SO:0000442 ! ds_oligo
+
+[Term]
+id: SO:0000338
+name: MITE
+def: "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]
+synonym: "miniature inverted repeat transposable element" EXACT []
+is_a: SO:0000208 ! terminal_inverted_repeat_element
+
+[Term]
+id: SO:0000339
+name: recombination_hotspot
+def: "A region in a genome which promotes recombination." [SO:rd]
+synonym: "recombination hotspot" EXACT []
+xref: http://en.wikipedia.org/wiki/Recombination_hotspot "wiki"
+is_a: SO:0000298 ! recombination_feature
+
+[Term]
+id: SO:0000340
+name: chromosome
+def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Chromosome "wiki"
+is_a: SO:0001235 ! replicon
+
+[Term]
+id: SO:0000341
+name: chromosome_band
+def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]
+subset: SOFA
+synonym: "chromosome band" EXACT []
+synonym: "cytoband" EXACT []
+synonym: "cytological band" EXACT []
+xref: http://en.wikipedia.org/wiki/Cytological_band "wiki"
+is_a: SO:0000830 ! chromosome_part
+
+[Term]
+id: SO:0000342
+name: site_specific_recombination_target_region
+synonym: "site specific recombination target region" EXACT []
+is_a: SO:0000299 ! specific_recombination_site
+
+[Term]
+id: SO:0000343
+name: match
+def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]
+subset: SOFA
+is_a: SO:0001410 ! experimental_feature
+
+[Term]
+id: SO:0000344
+name: splice_enhancer
+def: "Region of a transcript that regulates splicing." [SO:ke]
+subset: SOFA
+synonym: "splice enhancer" EXACT []
+is_a: SO:0000165 ! enhancer
+is_a: SO:0001056 ! splicing_regulatory_region
+
+[Term]
+id: SO:0000345
+name: EST
+def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+synonym: "expressed sequence tag" EXACT []
+is_a: SO:0000324 ! tag
+relationship: derives_from SO:0000234 ! mRNA
+
+[Term]
+id: SO:0000346
+name: loxP_site
+synonym: "Cre-recombination target region" RELATED []
+synonym: "loxP site" EXACT []
+is_a: SO:0000947 ! resolution_site
+
+[Term]
+id: SO:0000347
+name: nucleotide_match
+def: "A match against a nucleotide sequence." [SO:ke]
+subset: SOFA
+synonym: "nucleotide match" EXACT []
+is_a: SO:0000343 ! match
+
+[Term]
+id: SO:0000348
+name: nucleic_acid
+def: "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]
+synonym: "nucleic acid" EXACT []
+xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki"
+is_a: SO:0000443 ! polymer_attribute
+
+[Term]
+id: SO:0000349
+name: protein_match
+def: "A match against a protein sequence." [SO:ke]
+subset: SOFA
+synonym: "protein match" EXACT []
+is_a: SO:0000343 ! match
+
+[Term]
+id: SO:0000350
+name: FRT_site
+def: "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]
+synonym: "FLP recombination target region" EXACT []
+synonym: "FRT site" EXACT []
+is_a: SO:0000948 ! inversion_site
+
+[Term]
+id: SO:0000351
+name: synthetic_sequence
+def: "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]
+synonym: "synthetic sequence" EXACT []
+is_a: SO:0000443 ! polymer_attribute
+
+[Term]
+id: SO:0000352
+name: DNA
+def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]
+is_a: SO:0000348 ! nucleic_acid
+
+[Term]
+id: SO:0000353
+name: sequence_assembly
+def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]
+subset: SOFA
+synonym: "sequence assembly" EXACT []
+xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki"
+is_a: SO:0001248 ! assembly
+
+[Term]
+id: SO:0000354
+name: group_1_intron_homing_endonuclease_target_region
+def: "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]
+synonym: "group 1 intron homing endonuclease target region" EXACT []
+is_a: SO:0000684 ! nuclease_sensitive_site
+
+[Term]
+id: SO:0000355
+name: haplotype_block
+def: "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]
+synonym: "haplotype block" EXACT []
+is_a: SO:0000298 ! recombination_feature
+
+[Term]
+id: SO:0000356
+name: RNA
+def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+is_a: SO:0000348 ! nucleic_acid
+
+[Term]
+id: SO:0000357
+name: flanked
+def: "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000359
+name: floxed
+def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Floxed "wiki"
+is_a: SO:0000357 ! flanked
+
+[Term]
+id: SO:0000360
+name: codon
+def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Codon "wiki"
+is_a: SO:0000851 ! CDS_region
+
+[Term]
+id: SO:0000361
+name: FRT_flanked
+def: "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]
+synonym: "FRT flanked" EXACT []
+is_a: SO:0000357 ! flanked
+
+[Term]
+id: SO:0000362
+name: invalidated_by_chimeric_cDNA
+def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]
+synonym: "invalidated by chimeric cDNA" EXACT []
+is_a: SO:0000790 ! invalidated
+
+[Term]
+id: SO:0000363
+name: floxed_gene
+def: "A transgene that is floxed." [SO:xp]
+synonym: "floxed gene" EXACT []
+is_a: SO:0000902 ! transgene
+relationship: has_quality SO:0000359 ! floxed
+
+[Term]
+id: SO:0000364
+name: transposable_element_flanking_region
+def: "The region of sequence surrounding a transposable element." [SO:ke]
+synonym: "transposable element flanking region" EXACT []
+is_a: SO:0000239 ! flanking_region
+
+[Term]
+id: SO:0000365
+name: integron
+def: "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]
+xref: http://en.wikipedia.org/wiki/Integron "wiki"
+is_a: SO:0001039 ! integrated_mobile_genetic_element
+
+[Term]
+id: SO:0000366
+name: insertion_site
+def: "The junction where an insertion occurred." [SO:ke]
+subset: SOFA
+synonym: "insertion site" EXACT []
+is_a: SO:0000699 ! junction
+
+[Term]
+id: SO:0000367
+name: attI_site
+def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]
+synonym: "attI site" EXACT []
+is_a: SO:0000946 ! integration_excision_site
+relationship: part_of SO:0000365 ! integron
+
+[Term]
+id: SO:0000368
+name: transposable_element_insertion_site
+def: "The junction in a genome where a transposable_element has inserted." [SO:ke]
+subset: SOFA
+synonym: "transposable element insertion site" EXACT []
+is_a: SO:0000366 ! insertion_site
+
+[Term]
+id: SO:0000369
+name: integrase_coding_region
+is_obsolete: true
+
+[Term]
+id: SO:0000370
+name: small_regulatory_ncRNA
+def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
+subset: SOFA
+synonym: "small regulatory ncRNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000371
+name: conjugative_transposon
+def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]
+synonym: "conjugative transposon" EXACT []
+is_a: SO:0000182 ! DNA_transposon
+
+[Term]
+id: SO:0000372
+name: enzymatic_RNA
+def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
+comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.
+subset: SOFA
+synonym: "enzymatic RNA" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: has_quality SO:0001185 ! enzymatic
+
+[Term]
+id: SO:0000373
+name: recombinationally_inverted_gene
+def: "A recombinationally rearranged gene by inversion." [SO:xp]
+synonym: "recombinationally inverted gene" EXACT []
+is_a: SO:0000456 ! recombinationally_rearranged_gene
+relationship: has_quality SO:1000036 ! inversion
+
+[Term]
+id: SO:0000374
+name: ribozyme
+def: "An RNA with catalytic activity." [SO:ma]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Ribozyme "wiki"
+is_a: SO:0000372 ! enzymatic_RNA
+relationship: has_quality SO:0001186 ! ribozymic
+
+[Term]
+id: SO:0000375
+name: rRNA_5_8S
+def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]
+subset: SOFA
+synonym: "5.8S LSU rRNA" EXACT []
+synonym: "5.8S ribosomal RNA" EXACT []
+synonym: "5.8S rRNA" EXACT []
+synonym: "rRNA 5 8S" EXACT []
+xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki"
+is_a: SO:0000651 ! large_subunit_rRNA
+
+[Term]
+id: SO:0000376
+name: RNA_6S
+def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]
+synonym: "6S RNA" EXACT []
+synonym: "RNA 6S" EXACT []
+xref: http://en.wikipedia.org/wiki/6S_RNA "wiki"
+is_a: SO:0000370 ! small_regulatory_ncRNA
+
+[Term]
+id: SO:0000377
+name: CsrB_RsmB_RNA
+def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]
+synonym: "CsrB RsmB RNA" EXACT []
+synonym: "CsrB-RsmB RNA" EXACT []
+is_a: SO:0000370 ! small_regulatory_ncRNA
+
+[Term]
+id: SO:0000378
+name: DsrA_RNA
+def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]
+synonym: "DsrA RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki"
+is_a: SO:0000370 ! small_regulatory_ncRNA
+
+[Term]
+id: SO:0000379
+name: GcvB_RNA
+def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]
+synonym: "GcvB RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/GcvB_RNA "wiki"
+is_a: SO:0000378 ! DsrA_RNA
+
+[Term]
+id: SO:0000380
+name: hammerhead_ribozyme
+def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]
+subset: SOFA
+synonym: "hammerhead ribozyme" EXACT []
+xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki"
+is_a: SO:0000715 ! RNA_motif
+relationship: has_quality SO:0001186 ! ribozymic
+
+[Term]
+id: SO:0000381
+name: group_IIA_intron
+synonym: "group IIA intron" EXACT []
+is_a: SO:0000603 ! group_II_intron
+
+[Term]
+id: SO:0000382
+name: group_IIB_intron
+synonym: "group IIB intron" EXACT []
+is_a: SO:0000603 ! group_II_intron
+
+[Term]
+id: SO:0000383
+name: MicF_RNA
+def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]
+synonym: "MicF RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/MicF_RNA "wiki"
+is_a: SO:0000644 ! antisense_RNA
+
+[Term]
+id: SO:0000384
+name: OxyS_RNA
+def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]
+synonym: "OxyS RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki"
+is_a: SO:0000370 ! small_regulatory_ncRNA
+
+[Term]
+id: SO:0000385
+name: RNase_MRP_RNA
+def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]
+subset: SOFA
+synonym: "RNase MRP RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000386
+name: RNase_P_RNA
+def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]
+subset: SOFA
+synonym: "RNase P RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000387
+name: RprA_RNA
+def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]
+synonym: "RprA RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki"
+is_a: SO:0000370 ! small_regulatory_ncRNA
+
+[Term]
+id: SO:0000388
+name: RRE_RNA
+def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]
+synonym: "RRE RNA" EXACT []
+is_a: SO:0000370 ! small_regulatory_ncRNA
+
+[Term]
+id: SO:0000389
+name: spot_42_RNA
+def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]
+synonym: "spot-42 RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki"
+is_a: SO:0000370 ! small_regulatory_ncRNA
+
+[Term]
+id: SO:0000390
+name: telomerase_RNA
+def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
+subset: SOFA
+synonym: "telomerase RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki"
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000391
+name: U1_snRNA
+def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]
+subset: SOFA
+synonym: "small nuclear RNA U1" EXACT [RSC:cb]
+synonym: "snRNA U1" EXACT [RSC:cb]
+synonym: "U1 small nuclear RNA" EXACT [RSC:cb]
+synonym: "U1 snRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki"
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000392
+name: U2_snRNA
+def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]
+subset: SOFA
+synonym: "small nuclear RNA U2" EXACT [RSC:CB]
+synonym: "snRNA U2" EXACT [RSC:CB]
+synonym: "U2 small nuclear RNA" EXACT [RSC:CB]
+synonym: "U2 snRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki"
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000393
+name: U4_snRNA
+def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
+subset: SOFA
+synonym: "small nuclear RNA U4" EXACT [RSC:cb]
+synonym: "snRNA U4" EXACT [RSC:cb]
+synonym: "U4 small nuclear RNA" EXACT [RSC:cb]
+synonym: "U4 snRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki"
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000394
+name: U4atac_snRNA
+def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]
+subset: SOFA
+synonym: "small nuclear RNA U4atac" EXACT [RSC:cb]
+synonym: "snRNA U4atac" EXACT [RSC:cb]
+synonym: "U4atac small nuclear RNA" EXACT [RSC:cb]
+synonym: "U4atac snRNA" EXACT []
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000395
+name: U5_snRNA
+def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]
+subset: SOFA
+synonym: "small nuclear RNA U5" EXACT [RSC:cb]
+synonym: "snRNA U5" EXACT [RSC:cb]
+synonym: "U5 small nuclear RNA" EXACT [RSC:cb]
+synonym: "U5 snRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki"
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000396
+name: U6_snRNA
+def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
+subset: SOFA
+synonym: "small nuclear RNA U6" EXACT [RSC:cb]
+synonym: "snRNA U6" EXACT [RSC:cb]
+synonym: "U6 small nuclear RNA" EXACT [RSC:cb]
+synonym: "U6 snRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki"
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000397
+name: U6atac_snRNA
+def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]
+subset: SOFA
+synonym: "snRNA U6atac" EXACT [RSC:cb]
+synonym: "U6atac small nuclear RNA" EXACT [RSC:cb]
+synonym: "U6atac snRNA" EXACT [RSC:cb]
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000398
+name: U11_snRNA
+def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]
+subset: SOFA
+synonym: "small nuclear RNA U11" EXACT [RSC:cb]
+synonym: "snRNA U11" EXACT [RSC:cb]
+synonym: "U11 small nuclear RNA" EXACT [RSC:cb]
+synonym: "U11 snRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki"
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000399
+name: U12_snRNA
+def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]
+subset: SOFA
+synonym: "small nuclear RNA U12" EXACT [RSC:cb]
+synonym: "snRNA U12" EXACT [RSC:cb]
+synonym: "U12 small nuclear RNA" EXACT [RSC:cb]
+synonym: "U12 snRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki"
+is_a: SO:0000274 ! snRNA
+
+[Term]
+id: SO:0000400
+name: sequence_attribute
+def: "An attribute describes a quality of sequence." [SO:ke]
+synonym: "sequence attribute" EXACT []
+
+[Term]
+id: SO:0000401
+name: gene_attribute
+synonym: "gene attribute" EXACT []
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000402
+name: enhancer_attribute
+is_obsolete: true
+
+[Term]
+id: SO:0000403
+name: U14_snoRNA
+alt_id: SO:0005839
+def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]
+comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
+subset: SOFA
+synonym: "small nucleolar RNA U14" EXACT []
+synonym: "snoRNA U14" EXACT []
+synonym: "U14 small nucleolar RNA" EXACT []
+synonym: "U14 snoRNA" EXACT []
+is_a: SO:0000593 ! C_D_box_snoRNA
+relationship: derives_from SO:0005837 ! U14_snoRNA_primary_transcript
+
+[Term]
+id: SO:0000404
+name: vault_RNA
+def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]
+subset: SOFA
+synonym: "vault RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki"
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000405
+name: Y_RNA
+def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]
+subset: SOFA
+synonym: "Y RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Y_RNA "wiki"
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000406
+name: twintron
+def: "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]
+xref: http://en.wikipedia.org/wiki/Twintron "wiki"
+is_a: SO:0000188 ! intron
+
+[Term]
+id: SO:0000407
+name: rRNA_18S
+def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]
+subset: SOFA
+synonym: "18S ribosomal RNA" EXACT []
+synonym: "18S rRNA" EXACT []
+synonym: "rRNA 18S" EXACT []
+xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki"
+is_a: SO:0000650 ! small_subunit_rRNA
+
+[Term]
+id: SO:0000408
+name: site
+def: "The interbase position where something (eg an aberration) occurred." [SO:ke]
+is_obsolete: true
+
+[Term]
+id: SO:0000409
+name: binding_site
+alt_id: BS:00033
+def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]
+comment: See GO:0005488 : binding.
+subset: biosapiens
+subset: SOFA
+synonym: "binding_or_interaction_site" EXACT []
+synonym: "site" RELATED []
+xref: http://en.wikipedia.org/wiki/Binding_site "wiki"
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000410
+name: protein_binding_site
+def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]
+comment: See GO:0042277 : peptide binding.
+subset: SOFA
+synonym: "protein binding site" EXACT []
+is_a: SO:0000409 ! binding_site
+
+[Term]
+id: SO:0000411
+name: rescue_region
+def: "A region that rescues." [SO:xp]
+synonym: "rescue fragment" EXACT []
+synonym: "rescue region" EXACT []
+synonym: "rescue segment" RELATED []
+is_a: SO:0000695 ! reagent
+relationship: has_quality SO:0000814 ! rescue
+
+[Term]
+id: SO:0000412
+name: restriction_fragment
+def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]
+subset: SOFA
+synonym: "restriction fragment" EXACT []
+xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki"
+is_a: SO:0000143 ! assembly_component
+
+[Term]
+id: SO:0000413
+name: sequence_difference
+def: "A region where the sequence differs from that of a specified sequence." [SO:ke]
+subset: SOFA
+synonym: "sequence difference" EXACT []
+is_a: SO:0000700 ! remark
+
+[Term]
+id: SO:0000414
+name: invalidated_by_genomic_contamination
+def: "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]
+synonym: "invalidated by genomic contamination" EXACT []
+is_a: SO:0000790 ! invalidated
+
+[Term]
+id: SO:0000415
+name: invalidated_by_genomic_polyA_primed_cDNA
+def: "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]
+synonym: "invalidated by genomic polyA primed cDNA" EXACT []
+is_a: SO:0000790 ! invalidated
+
+[Term]
+id: SO:0000416
+name: invalidated_by_partial_processing
+def: "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]
+synonym: "invalidated by partial processing" EXACT []
+is_a: SO:0000790 ! invalidated
+
+[Term]
+id: SO:0000417
+name: polypeptide_domain
+alt_id: BS:00012
+alt_id: BS:00134
+alt_id: SO:0001069
+def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]
+comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
+subset: biosapiens
+synonym: "domain" BROAD BS [uniprot:feature_type]
+synonym: "polypeptide domain" EXACT []
+synonym: "polypeptide_structural_domain" EXACT BS []
+synonym: "structural domain" BROAD BS []
+is_a: SO:0001070 ! polypeptide_structural_region
+is_a: SO:0100021 ! polypeptide_conserved_region
+
+[Term]
+id: SO:0000418
+name: signal_peptide
+alt_id: BS:00159
+def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
+subset: biosapiens
+subset: SOFA
+synonym: "signal" RELATED [uniprot:feature_type]
+synonym: "signal peptide" EXACT []
+synonym: "signal peptide coding sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki"
+is_a: SO:0001527 ! peptide_localization_signal
+relationship: part_of SO:0001062 ! propeptide
+
+[Term]
+id: SO:0000419
+name: mature_protein_region
+alt_id: BS:00149
+def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]
+comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
+subset: biosapiens
+subset: SOFA
+synonym: "chain" RELATED [uniprot:feature_type]
+synonym: "mature peptide" RELATED []
+synonym: "mature protein region" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+relationship: part_of SO:0001063 ! immature_peptide_region
+
+[Term]
+id: SO:0000420
+name: five_prime_terminal_inverted_repeat
+synonym: "5' TIR" EXACT []
+synonym: "five prime terminal inverted repeat" EXACT []
+is_a: SO:0000481 ! terminal_inverted_repeat
+
+[Term]
+id: SO:0000421
+name: three_prime_terminal_inverted_repeat
+synonym: "3' TIR" EXACT []
+synonym: "three prime terminal inverted repeat" EXACT []
+is_a: SO:0000481 ! terminal_inverted_repeat
+
+[Term]
+id: SO:0000422
+name: U5_LTR_region
+synonym: "U5 long terminal repeat region" EXACT []
+synonym: "U5 LTR region" EXACT []
+is_a: SO:0000848 ! LTR_component
+
+[Term]
+id: SO:0000423
+name: R_LTR_region
+synonym: "R long terminal repeat region" EXACT []
+synonym: "R LTR region" EXACT []
+is_a: SO:0000848 ! LTR_component
+
+[Term]
+id: SO:0000424
+name: U3_LTR_region
+synonym: "U3 long terminal repeat region" EXACT []
+synonym: "U3 LTR region" EXACT []
+is_a: SO:0000848 ! LTR_component
+
+[Term]
+id: SO:0000425
+name: five_prime_LTR
+synonym: "5' long terminal repeat" EXACT []
+synonym: "5' LTR" EXACT []
+synonym: "five prime LTR" EXACT []
+is_a: SO:0000286 ! long_terminal_repeat
+
+[Term]
+id: SO:0000426
+name: three_prime_LTR
+synonym: "3' long terminal repeat" EXACT []
+synonym: "3' LTR" EXACT []
+synonym: "three prime LTR" EXACT []
+is_a: SO:0000286 ! long_terminal_repeat
+
+[Term]
+id: SO:0000427
+name: R_five_prime_LTR_region
+synonym: "R 5' long term repeat region" EXACT []
+synonym: "R five prime LTR region" EXACT []
+is_a: SO:0000423 ! R_LTR_region
+is_a: SO:0000850 ! five_prime_LTR_component
+
+[Term]
+id: SO:0000428
+name: U5_five_prime_LTR_region
+synonym: "U5 5' long terminal repeat region" EXACT []
+synonym: "U5 five prime LTR region" EXACT []
+is_a: SO:0000422 ! U5_LTR_region
+is_a: SO:0000850 ! five_prime_LTR_component
+
+[Term]
+id: SO:0000429
+name: U3_five_prime_LTR_region
+synonym: "U3 5' long term repeat region" EXACT []
+synonym: "U3 five prime LTR region" EXACT []
+is_a: SO:0000424 ! U3_LTR_region
+is_a: SO:0000850 ! five_prime_LTR_component
+
+[Term]
+id: SO:0000430
+name: R_three_prime_LTR_region
+synonym: "R 3' long terminal repeat region" EXACT []
+synonym: "R three prime LTR region" EXACT []
+is_a: SO:0000849 ! three_prime_LTR_component
+
+[Term]
+id: SO:0000431
+name: U3_three_prime_LTR_region
+synonym: "U3 3' long terminal repeat region" EXACT []
+synonym: "U3 three prime LTR region" EXACT []
+is_a: SO:0000849 ! three_prime_LTR_component
+
+[Term]
+id: SO:0000432
+name: U5_three_prime_LTR_region
+synonym: "U5 3' long terminal repeat region" EXACT []
+synonym: "U5 three prime LTR region" EXACT []
+is_a: SO:0000849 ! three_prime_LTR_component
+
+[Term]
+id: SO:0000433
+name: non_LTR_retrotransposon_polymeric_tract
+def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]
+synonym: "non LTR retrotransposon polymeric tract" EXACT []
+is_a: SO:0000657 ! repeat_region
+is_a: SO:0000840 ! repeat_component
+relationship: part_of SO:0000189 ! non_LTR_retrotransposon
+
+[Term]
+id: SO:0000434
+name: target_site_duplication
+def: "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]
+synonym: "target site duplication" EXACT []
+is_a: SO:0000314 ! direct_repeat
+relationship: derives_from SO:0000101 ! transposable_element
+
+[Term]
+id: SO:0000435
+name: RR_tract
+def: "A polypurine tract within an LTR_retrotransposon." [SO:ke]
+synonym: "LTR retrotransposon poly purine tract" RELATED []
+synonym: "RR tract" EXACT []
+is_a: SO:0000330 ! conserved_region
+relationship: part_of SO:0000186 ! LTR_retrotransposon
+
+[Term]
+id: SO:0000436
+name: ARS
+def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]
+subset: SOFA
+synonym: "autonomously replicating sequence" EXACT []
+is_a: SO:0000296 ! origin_of_replication
+
+[Term]
+id: SO:0000437
+name: assortment_derived_duplication
+is_obsolete: true
+
+[Term]
+id: SO:0000438
+name: gene_not_polyadenylated
+is_obsolete: true
+
+[Term]
+id: SO:0000439
+name: inverted_ring_chromosome
+synonym: "inverted ring chromosome" EXACT []
+is_a: SO:1000030 ! chromosomal_inversion
+is_a: SO:1000045 ! ring_chromosome
+
+[Term]
+id: SO:0000440
+name: vector_replicon
+def: "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "vector" EXACT []
+synonym: "vector replicon" EXACT []
+xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology) "wiki"
+is_a: SO:0001235 ! replicon
+relationship: part_of SO:0000151 ! clone
+
+[Term]
+id: SO:0000441
+name: ss_oligo
+def: "A single stranded oligonucleotide." [SO:ke]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+synonym: "single strand oligo" EXACT []
+synonym: "single strand oligonucleotide" EXACT []
+synonym: "single stranded oligonucleotide" EXACT []
+synonym: "ss oligo" EXACT []
+synonym: "ss oligonucleotide" EXACT []
+is_a: SO:0000696 ! oligo
+
+[Term]
+id: SO:0000442
+name: ds_oligo
+def: "A double stranded oligonucleotide." [SO:ke]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+synonym: "double stranded oligonucleotide" EXACT []
+synonym: "ds oligo" EXACT []
+synonym: "ds-oligonucleotide" EXACT []
+is_a: SO:0000696 ! oligo
+
+[Term]
+id: SO:0000443
+name: polymer_attribute
+def: "An attribute to describe the kind of biological sequence." [SO:ke]
+synonym: "polymer attribute" EXACT []
+is_a: SO:0000400 ! sequence_attribute
+
+[Term]
+id: SO:0000444
+name: three_prime_noncoding_exon
+def: "Non-coding exon in the 3' UTR." [SO:ke]
+synonym: "three prime noncoding exon" EXACT []
+is_a: SO:0000198 ! noncoding_exon
+
+[Term]
+id: SO:0000445
+name: five_prime_noncoding_exon
+def: "Non-coding exon in the 5' UTR." [SO:ke]
+synonym: "5' nc exon" EXACT []
+synonym: "5' non coding exon" EXACT []
+synonym: "five prime noncoding exon" EXACT []
+is_a: SO:0000198 ! noncoding_exon
+
+[Term]
+id: SO:0000446
+name: UTR_intron
+def: "Intron located in the untranslated region." [SO:ke]
+synonym: "UTR intron" EXACT []
+is_a: SO:0000188 ! intron
+
+[Term]
+id: SO:0000447
+name: five_prime_UTR_intron
+def: "An intron located in the 5' UTR." [SO:ke]
+synonym: "five prime UTR intron" EXACT []
+is_a: SO:0000446 ! UTR_intron
+
+[Term]
+id: SO:0000448
+name: three_prime_UTR_intron
+def: "An intron located in the 3' UTR." [SO:ke]
+synonym: "three prime UTR intron" EXACT []
+is_a: SO:0000446 ! UTR_intron
+
+[Term]
+id: SO:0000449
+name: random_sequence
+def: "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components." [SO:ma]
+synonym: "random sequence" EXACT []
+is_a: SO:0000351 ! synthetic_sequence
+
+[Term]
+id: SO:0000450
+name: interband
+def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma]
+synonym: "chromosome interband" RELATED []
+is_a: SO:0000830 ! chromosome_part
+
+[Term]
+id: SO:0000451
+name: gene_with_polyadenylated_mRNA
+def: "A gene that encodes a polyadenylated mRNA." [SO:xp]
+synonym: "gene with polyadenylated mRNA" EXACT []
+is_a: SO:0001217 ! protein_coding_gene
+relationship: transcribed_to SO:0000871 ! polyadenylated_mRNA
+
+[Term]
+id: SO:0000452
+name: transgene_attribute
+is_obsolete: true
+
+[Term]
+id: SO:0000453
+name: chromosomal_transposition
+def: "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]
+synonym: "chromosomal transposition" EXACT []
+synonym: "transposition" NARROW []
+is_a: SO:1000183 ! chromosome_structure_variation
+
+[Term]
+id: SO:0000454
+name: rasiRNA
+def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]
+subset: SOFA
+synonym: "repeat associated small interfering RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/RasiRNA "wiki"
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000455
+name: gene_with_mRNA_with_frameshift
+def: "A gene that encodes an mRNA with a frameshift." [SO:xp]
+synonym: "gene with mRNA with frameshift" EXACT []
+is_a: SO:0001217 ! protein_coding_gene
+relationship: has_quality SO:0000865 ! frameshift
+
+[Term]
+id: SO:0000456
+name: recombinationally_rearranged_gene
+def: "A gene that is recombinationally rearranged." [SO:ke]
+synonym: "recombinationally rearranged gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000940 ! recombinationally_rearranged
+
+[Term]
+id: SO:0000457
+name: interchromosomal_duplication
+def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke]
+synonym: "interchromosomal duplication" EXACT []
+is_a: SO:1000037 ! chromosomal_duplication
+
+[Term]
+id: SO:0000458
+name: D_gene_segment
+def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D gene" EXACT []
+synonym: "D-GENE" EXACT []
+is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
+
+[Term]
+id: SO:0000459
+name: gene_with_trans_spliced_transcript
+def: "A gene with a transcript that is trans-spliced." [SO:xp]
+synonym: "gene with trans spliced transcript" EXACT []
+is_a: SO:0000704 ! gene
+relationship: transcribed_to SO:0000479 ! trans_spliced_transcript
+
+[Term]
+id: SO:0000460
+name: vertebrate_immunoglobulin_T_cell_receptor_segment
+comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
+synonym: "vertebrate immunoglobulin T cell receptor segment" EXACT []
+synonym: "vertebrate_immunoglobulin/T-cell receptor gene" EXACT []
+is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
+
+[Term]
+id: SO:0000461
+name: inversion_derived_bipartite_deficiency
+def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]
+synonym: "inversion derived bipartite deficiency" EXACT []
+is_a: SO:1000029 ! chromosomal_deletion
+
+[Term]
+id: SO:0000462
+name: pseudogenic_region
+def: "A non-functional descendant of a functional entity." [SO:cjm]
+subset: SOFA
+synonym: "pseudogenic region" EXACT []
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000463
+name: encodes_alternately_spliced_transcripts
+def: "A gene that encodes more than one transcript." [SO:ke]
+synonym: "encodes alternately spliced transcripts" EXACT []
+is_a: SO:0000401 ! gene_attribute
+
+[Term]
+id: SO:0000464
+name: decayed_exon
+def: "A non-functional descendant of an exon." [SO:ke]
+subset: SOFA
+synonym: "decayed exon" EXACT []
+is_a: SO:0000462 ! pseudogenic_region
+relationship: non_functional_homolog_of SO:0000147 ! exon
+
+[Term]
+id: SO:0000465
+name: inversion_derived_deficiency_plus_duplication
+def: "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]
+synonym: "inversion derived deficiency plus duplication" EXACT []
+is_a: SO:1000029 ! chromosomal_deletion
+is_a: SO:1000038 ! intrachromosomal_duplication
+
+[Term]
+id: SO:0000466
+name: V_gene_segment
+def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V gene" EXACT []
+synonym: "V-GENE" EXACT []
+synonym: "variable_gene" EXACT []
+is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
+
+[Term]
+id: SO:0000467
+name: post_translationally_regulated_by_protein_stability
+def: "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]
+synonym: "post translationally regulated by protein stability" EXACT []
+synonym: "post-translationally regulated by protein stability" EXACT []
+is_a: SO:0000130 ! post_translationally_regulated
+
+[Term]
+id: SO:0000468
+name: golden_path_fragment
+def: "One of the pieces of sequence that make up a golden path." [SO:rd]
+subset: SOFA
+synonym: "golden path fragment" EXACT []
+is_a: SO:0000143 ! assembly_component
+relationship: part_of SO:0000688 ! golden_path
+
+[Term]
+id: SO:0000469
+name: post_translationally_regulated_by_protein_modification
+def: "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]
+synonym: "post translationally regulated by protein modification" EXACT []
+synonym: "post-translationally regulated by protein modification" EXACT []
+is_a: SO:0000130 ! post_translationally_regulated
+
+[Term]
+id: SO:0000470
+name: J_gene_segment
+def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "J gene" EXACT []
+synonym: "J-GENE" EXACT []
+is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
+
+[Term]
+id: SO:0000471
+name: autoregulated
+def: "The gene product is involved in its own transcriptional regulation." [SO:ke]
+is_a: SO:0000123 ! transcriptionally_regulated
+
+[Term]
+id: SO:0000472
+name: tiling_path
+def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]
+subset: SOFA
+synonym: "tiling path" EXACT []
+is_a: SO:0000353 ! sequence_assembly
+
+[Term]
+id: SO:0000473
+name: negatively_autoregulated
+def: "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]
+synonym: "negatively autoregulated" EXACT []
+is_a: SO:0000126 ! transcriptionally_repressed
+is_a: SO:0000471 ! autoregulated
+
+[Term]
+id: SO:0000474
+name: tiling_path_fragment
+def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]
+subset: SOFA
+synonym: "tiling path fragment" EXACT []
+is_a: SO:0000143 ! assembly_component
+relationship: part_of SO:0000472 ! tiling_path
+
+[Term]
+id: SO:0000475
+name: positively_autoregulated
+def: "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]
+synonym: "positively autoregulated" EXACT []
+is_a: SO:0000125 ! transcriptionally_induced
+is_a: SO:0000471 ! autoregulated
+
+[Term]
+id: SO:0000476
+name: contig_read
+def: "A DNA sequencer read which is part of a contig." [SO:ke]
+synonym: "contig read" EXACT []
+is_a: SO:0000150 ! read
+
+[Term]
+id: SO:0000477
+name: polycistronic_gene
+def: "A gene that is polycistronic." [SO:ke]
+is_obsolete: true
+
+[Term]
+id: SO:0000478
+name: C_gene_segment
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "C gene" EXACT []
+synonym: "C_GENE" EXACT []
+synonym: "constant gene" EXACT []
+is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
+
+[Term]
+id: SO:0000479
+name: trans_spliced_transcript
+def: "A transcript that is trans-spliced." [SO:xp]
+synonym: "trans spliced transcript" EXACT []
+synonym: "trans-spliced transcript" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: has_quality SO:0000870 ! trans_spliced
+
+[Term]
+id: SO:0000480
+name: tiling_path_clone
+def: "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]
+synonym: "tiling path clone" EXACT []
+is_a: SO:0000151 ! clone
+is_a: SO:0000474 ! tiling_path_fragment
+
+[Term]
+id: SO:0000481
+name: terminal_inverted_repeat
+def: "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]
+synonym: "terminal inverted repeat" EXACT []
+synonym: "TIR" EXACT []
+is_a: SO:0000294 ! inverted_repeat
+relationship: part_of SO:0000208 ! terminal_inverted_repeat_element
+
+[Term]
+id: SO:0000482
+name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+synonym: "vertebrate immunoglobulin T cell receptor gene cluster" EXACT []
+synonym: "vertebrate_immunoglobulin/T-cell receptor gene cluster" EXACT []
+is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
+
+[Term]
+id: SO:0000483
+name: nc_primary_transcript
+def: "A primary transcript that is never translated into a protein." [SO:ke]
+subset: SOFA
+synonym: "nc primary transcript" EXACT []
+synonym: "noncoding primary transcript" EXACT []
+is_a: SO:0000185 ! primary_transcript
+
+[Term]
+id: SO:0000484
+name: three_prime_coding_exon_noncoding_region
+def: "The sequence of the 3' exon that is not coding." [SO:ke]
+subset: SOFA
+synonym: "three prime coding exon noncoding region" EXACT []
+synonym: "three_prime_exon_noncoding_region" EXACT []
+is_a: SO:0001214 ! noncoding_region_of_exon
+relationship: part_of SO:0000202 ! three_prime_coding_exon
+
+[Term]
+id: SO:0000485
+name: DJ_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(DJ)-J-CLUSTER" EXACT []
+synonym: "DJ J cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000486
+name: five_prime_coding_exon_noncoding_region
+def: "The sequence of the 5' exon preceding the start codon." [SO:ke]
+subset: SOFA
+synonym: "five prime coding exon noncoding region" EXACT []
+synonym: "five_prime_exon_noncoding_region" EXACT []
+is_a: SO:0001214 ! noncoding_region_of_exon
+relationship: part_of SO:0000200 ! five_prime_coding_exon
+
+[Term]
+id: SO:0000487
+name: VDJ_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(VDJ)-J-C-CLUSTER" EXACT []
+synonym: "VDJ J C cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000574 ! VDJ_gene_segment
+
+[Term]
+id: SO:0000488
+name: VDJ_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(VDJ)-J-CLUSTER" EXACT []
+synonym: "VDJ J cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000574 ! VDJ_gene_segment
+
+[Term]
+id: SO:0000489
+name: VJ_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(VJ)-C-CLUSTER" RELATED []
+synonym: "VJ C cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000576 ! VJ_gene_segment
+
+[Term]
+id: SO:0000490
+name: VJ_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(VJ)-J-C-CLUSTER" EXACT []
+synonym: "VJ J C cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000576 ! VJ_gene_segment
+
+[Term]
+id: SO:0000491
+name: VJ_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(VJ)-J-CLUSTER" EXACT []
+synonym: "VJ J cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000576 ! VJ_gene_segment
+
+[Term]
+id: SO:0000492
+name: D_gene_recombination_feature
+synonym: "D gene recombination feature" EXACT []
+is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
+
+[Term]
+id: SO:0000493
+name: three_prime_D_heptamer
+def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "3'D-HEPTAMER" EXACT []
+synonym: "three prime D heptamer" EXACT []
+is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
+relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
+
+[Term]
+id: SO:0000494
+name: three_prime_D_nonamer
+def: "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "3'D-NOMAMER" EXACT []
+synonym: "three prime D nonamer" EXACT []
+is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
+relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
+
+[Term]
+id: SO:0000495
+name: three_prime_D_spacer
+def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "3'D-SPACER" EXACT []
+synonym: "three prime D spacer" EXACT []
+is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
+relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
+
+[Term]
+id: SO:0000496
+name: five_prime_D_heptamer
+def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "5'D-HEPTAMER" EXACT []
+synonym: "five prime D heptamer" EXACT []
+is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
+relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
+
+[Term]
+id: SO:0000497
+name: five_prime_D_nonamer
+def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "5'D-NONAMER" EXACT []
+synonym: "five prime D nonamer" EXACT []
+is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
+relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
+
+[Term]
+id: SO:0000498
+name: five_prime_D_spacer
+def: "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "5'-SPACER" EXACT []
+synonym: "five prime D spacer" EXACT []
+synonym: "five prime D-spacer" EXACT []
+is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
+relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
+
+[Term]
+id: SO:0000499
+name: virtual_sequence
+def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]
+subset: SOFA
+synonym: "virtual sequence" EXACT []
+is_a: SO:0000353 ! sequence_assembly
+
+[Term]
+id: SO:0000500
+name: Hoogsteen_base_pair
+def: "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]
+synonym: "Hoogsteen base pair" EXACT []
+xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair "wiki"
+is_a: SO:0000028 ! base_pair
+
+[Term]
+id: SO:0000501
+name: reverse_Hoogsteen_base_pair
+def: "A type of non-canonical base-pairing." [SO:ke]
+synonym: "reverse Hoogsteen base pair" EXACT []
+is_a: SO:0000028 ! base_pair
+
+[Term]
+id: SO:0000502
+name: transcribed_region
+def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke]
+comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
+subset: SOFA
+is_obsolete: true
+
+[Term]
+id: SO:0000503
+name: alternately_spliced_gene_encodeing_one_transcript
+is_obsolete: true
+
+[Term]
+id: SO:0000504
+name: D_DJ_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D DJ C cluster" EXACT []
+synonym: "D-(DJ)-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000505
+name: D_DJ_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D DJ cluster" EXACT []
+synonym: "D-(DJ)-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000506
+name: D_DJ_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D DJ J C cluster" EXACT []
+synonym: "D-(DJ)-J-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000507
+name: pseudogenic_exon
+def: "A non functional descendant of an exon, part of a pseudogene." [SO:ke]
+comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
+synonym: "pseudogenic exon" EXACT []
+is_a: SO:0000462 ! pseudogenic_region
+relationship: non_functional_homolog_of SO:0000147 ! exon
+relationship: part_of SO:0000516 ! pseudogenic_transcript
+
+[Term]
+id: SO:0000508
+name: D_DJ_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D DJ J cluster" EXACT []
+synonym: "D-(DJ)-J-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000509
+name: D_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D J C cluster" EXACT []
+synonym: "D-J-C-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+
+[Term]
+id: SO:0000510
+name: VD_gene_segment
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V_D_GENE" EXACT []
+synonym: "VD gene" EXACT []
+is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
+
+[Term]
+id: SO:0000511
+name: J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "J C cluster" EXACT []
+synonym: "J-C-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+
+[Term]
+id: SO:0000512
+name: inversion_derived_deficiency_plus_aneuploid
+def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
+synonym: "inversion derived deficiency plus aneuploid" EXACT []
+is_a: SO:1000029 ! chromosomal_deletion
+
+[Term]
+id: SO:0000513
+name: J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "J cluster" EXACT []
+synonym: "J-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000470 ! J_gene_segment
+
+[Term]
+id: SO:0000514
+name: J_nonamer
+def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "J nonamer" EXACT []
+synonym: "J-NONAMER" EXACT []
+is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
+relationship: part_of SO:0000302 ! J_gene_recombination_feature
+
+[Term]
+id: SO:0000515
+name: J_heptamer
+def: "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "J heptamer" EXACT []
+synonym: "J-HEPTAMER" EXACT []
+is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
+relationship: part_of SO:0000302 ! J_gene_recombination_feature
+
+[Term]
+id: SO:0000516
+name: pseudogenic_transcript
+def: "A non functional descendant of a transcript, part of a pseudogene." [SO:ke]
+comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
+synonym: "pseudogenic transcript" EXACT []
+is_a: SO:0000462 ! pseudogenic_region
+relationship: non_functional_homolog_of SO:0000673 ! transcript
+relationship: part_of SO:0000336 ! pseudogene
+
+[Term]
+id: SO:0000517
+name: J_spacer
+def: "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "J spacer" EXACT []
+synonym: "J-SPACER" EXACT []
+is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
+relationship: part_of SO:0000302 ! J_gene_recombination_feature
+
+[Term]
+id: SO:0000518
+name: V_DJ_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V DJ cluster" EXACT []
+synonym: "V-(DJ)-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000519
+name: V_DJ_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V DJ J cluster" EXACT []
+synonym: "V-(DJ)-J-CLUSTER" RELATED []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000520
+name: V_VDJ_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V VDJ C cluster" EXACT []
+synonym: "V-(VDJ)-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000574 ! VDJ_gene_segment
+
+[Term]
+id: SO:0000521
+name: V_VDJ_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V VDJ cluster" EXACT []
+synonym: "V-(VDJ)-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000574 ! VDJ_gene_segment
+
+[Term]
+id: SO:0000522
+name: V_VDJ_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V VDJ J cluster" EXACT []
+synonym: "V-(VDJ)-J-CLUSTER" RELATED []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000574 ! VDJ_gene_segment
+
+[Term]
+id: SO:0000523
+name: V_VJ_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V VJ C cluster" EXACT []
+synonym: "V-(VJ)-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000576 ! VJ_gene_segment
+
+[Term]
+id: SO:0000524
+name: V_VJ_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V VJ cluster" EXACT []
+synonym: "V-(VJ)-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000576 ! VJ_gene_segment
+
+[Term]
+id: SO:0000525
+name: V_VJ_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V VJ J cluster" EXACT []
+synonym: "V-(VJ)-J-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000576 ! VJ_gene_segment
+
+[Term]
+id: SO:0000526
+name: V_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V cluster" EXACT []
+synonym: "V-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+
+[Term]
+id: SO:0000527
+name: V_D_DJ_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V D DJ C cluster" EXACT []
+synonym: "V-D-(DJ)-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000528
+name: V_D_DJ_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V D DJ cluster" EXACT []
+synonym: "V-D-(DJ)-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000529
+name: V_D_DJ_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V D DJ J C cluster" EXACT []
+synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000530
+name: V_D_DJ_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V D DJ J cluster" EXACT []
+synonym: "V-D-(DJ)-J-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000531
+name: V_D_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V D J C cluster" EXACT []
+synonym: "V-D-J-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+
+[Term]
+id: SO:0000532
+name: V_D_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V D J cluster" EXACT []
+synonym: "V-D-J-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+
+[Term]
+id: SO:0000533
+name: V_heptamer
+def: "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V heptamer" EXACT []
+synonym: "V-HEPTAMER" EXACT []
+is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
+relationship: part_of SO:0000538 ! V_gene_recombination_feature
+
+[Term]
+id: SO:0000534
+name: V_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V J cluster" EXACT []
+synonym: "V-J-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+
+[Term]
+id: SO:0000535
+name: V_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V J C cluster" EXACT []
+synonym: "V-J-C-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+
+[Term]
+id: SO:0000536
+name: V_nonamer
+def: "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V nonamer" EXACT []
+synonym: "V-NONAMER" EXACT []
+is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
+relationship: part_of SO:0000538 ! V_gene_recombination_feature
+
+[Term]
+id: SO:0000537
+name: V_spacer
+def: "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V spacer" EXACT []
+synonym: "V-SPACER" EXACT []
+is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
+relationship: part_of SO:0000538 ! V_gene_recombination_feature
+
+[Term]
+id: SO:0000538
+name: V_gene_recombination_feature
+def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V gene recombination feature" EXACT []
+synonym: "V-RS" EXACT []
+is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
+
+[Term]
+id: SO:0000539
+name: DJ_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(DJ)-C-CLUSTER" EXACT []
+synonym: "DJ C cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000540
+name: DJ_J_C_cluster
+def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(DJ)-J-C-CLUSTER" EXACT []
+synonym: "DJ J C cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000541
+name: VDJ_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "(VDJ)-C-CLUSTER" EXACT []
+synonym: "VDJ C cluster" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000574 ! VDJ_gene_segment
+
+[Term]
+id: SO:0000542
+name: V_DJ_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V DJ C cluster" EXACT []
+synonym: "V-(DJ)-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000543
+name: alternately_spliced_gene_encoding_greater_than_one_transcript
+is_obsolete: true
+
+[Term]
+id: SO:0000544
+name: helitron
+def: "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]
+synonym: "ISCR" RELATED []
+xref: http://en.wikipedia.org/wiki/Helitron "wiki"
+is_a: SO:0000182 ! DNA_transposon
+
+[Term]
+id: SO:0000545
+name: recoding_pseudoknot
+def: "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]
+synonym: "recoding pseudoknot" EXACT []
+is_a: SO:0000591 ! pseudoknot
+relationship: part_of SO:1001268 ! recoding_stimulatory_region
+
+[Term]
+id: SO:0000546
+name: designed_sequence
+synonym: "designed sequence" EXACT []
+is_a: SO:0000351 ! synthetic_sequence
+
+[Term]
+id: SO:0000547
+name: inversion_derived_bipartite_duplication
+def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]
+synonym: "inversion derived bipartite duplication" EXACT []
+is_a: SO:1000038 ! intrachromosomal_duplication
+
+[Term]
+id: SO:0000548
+name: gene_with_edited_transcript
+def: "A gene that encodes a transcript that is edited." [SO:xp]
+synonym: "gene with edited transcript" EXACT []
+is_a: SO:0001217 ! protein_coding_gene
+relationship: transcribed_to SO:0000873 ! edited_transcript
+
+[Term]
+id: SO:0000549
+name: inversion_derived_duplication_plus_aneuploid
+def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
+synonym: "inversion derived duplication plus aneuploid" EXACT []
+is_a: SO:1000038 ! intrachromosomal_duplication
+
+[Term]
+id: SO:0000550
+name: aneuploid_chromosome
+def: "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]
+comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
+synonym: "aneuploid chromosome" EXACT []
+is_a: SO:1000183 ! chromosome_structure_variation
+
+[Term]
+id: SO:0000551
+name: polyA_signal_sequence
+def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+subset: SOFA
+synonym: "poly(A) signal" EXACT []
+synonym: "polyA signal sequence" EXACT []
+synonym: "polyadenylation termination signal" EXACT []
+is_a: SO:0001679 ! transcription_regulatory_region
+
+[Term]
+id: SO:0000552
+name: Shine_Dalgarno_sequence
+def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]
+comment: Not found in Eukaryotic sequence.
+synonym: "five prime ribosome binding site" EXACT []
+synonym: "RBS" RELATED []
+synonym: "Shine Dalgarno sequence" EXACT []
+synonym: "Shine-Dalgarno sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki"
+is_a: SO:0000139 ! ribosome_entry_site
+
+[Term]
+id: SO:0000553
+name: polyA_site
+alt_id: SO:0001430
+def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+subset: SOFA
+synonym: "polyA cleavage site" EXACT []
+synonym: "polyA junction" EXACT []
+synonym: "polyA site" EXACT []
+synonym: "polyA_junction" EXACT []
+synonym: "polyadenylation site" RELATED []
+is_a: SO:0000699 ! junction
+relationship: part_of SO:0000205 ! three_prime_UTR
+relationship: part_of SO:0000233 ! mature_transcript
+
+[Term]
+id: SO:0000554
+name: assortment_derived_deficiency_plus_duplication
+is_obsolete: true
+
+[Term]
+id: SO:0000555
+name: five_prime_clip
+def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "5' clip" RELATED []
+synonym: "five prime clip" EXACT []
+is_a: SO:0000303 ! clip
+
+[Term]
+id: SO:0000556
+name: five_prime_D_recombination_signal_sequence
+def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "5'RS" EXACT []
+synonym: "five prime D recombination signal sequence" EXACT []
+synonym: "five prime D-recombination signal sequence" EXACT []
+is_a: SO:0000492 ! D_gene_recombination_feature
+
+[Term]
+id: SO:0000557
+name: three_prime_clip
+def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "3'-clip" EXACT []
+synonym: "three prime clip" EXACT []
+is_a: SO:0000303 ! clip
+
+[Term]
+id: SO:0000558
+name: C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "C cluster" EXACT []
+synonym: "C-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000478 ! C_gene_segment
+
+[Term]
+id: SO:0000559
+name: D_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D cluster" EXACT []
+synonym: "D-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+
+[Term]
+id: SO:0000560
+name: D_J_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D J cluster" EXACT []
+synonym: "D-J-CLUSTER" EXACT []
+is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
+relationship: has_part SO:0000458 ! D_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+
+[Term]
+id: SO:0000561
+name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
+def: "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "HEPTAMER" RELATED []
+synonym: "heptamer of recombination feature of vertebrate immune system gene" EXACT []
+is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
+
+[Term]
+id: SO:0000562
+name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
+synonym: "nonamer of recombination feature of vertebrate immune system gene" EXACT []
+is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
+
+[Term]
+id: SO:0000563
+name: vertebrate_immune_system_gene_recombination_spacer
+synonym: "vertebrate immune system gene recombination spacer" EXACT []
+is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
+
+[Term]
+id: SO:0000564
+name: V_DJ_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V DJ J C cluster" EXACT []
+synonym: "V-(DJ)-J-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000572 ! DJ_gene_segment
+
+[Term]
+id: SO:0000565
+name: V_VDJ_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V VDJ J C cluster" EXACT []
+synonym: "V-(VDJ)-J-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000574 ! VDJ_gene_segment
+
+[Term]
+id: SO:0000566
+name: V_VJ_J_C_cluster
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V VJ J C cluster" EXACT []
+synonym: "V-(VJ)-J-C-CLUSTER" EXACT []
+is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+relationship: has_part SO:0000466 ! V_gene_segment
+relationship: has_part SO:0000470 ! J_gene_segment
+relationship: has_part SO:0000478 ! C_gene_segment
+relationship: has_part SO:0000576 ! VJ_gene_segment
+
+[Term]
+id: SO:0000567
+name: inversion_derived_aneuploid_chromosome
+def: "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]
+synonym: "inversion derived aneuploid chromosome" EXACT []
+is_a: SO:0000550 ! aneuploid_chromosome
+
+[Term]
+id: SO:0000568
+name: bidirectional_promoter
+def: "An unregulated promoter that allows continuous expression." [SO:ke]
+synonym: "bidirectional promoter" EXACT []
+is_a: SO:0000167 ! promoter
+
+[Term]
+id: SO:0000569
+name: retrotransposed
+alt_id: SO:0100042
+def: "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke]
+comment: GO:0003964 RNA-directed DNA polymerase activity.
+xref: http://en.wikipedia.org/wiki/Retrotransposed "wiki"
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000570
+name: three_prime_D_recombination_signal_sequence
+def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "3'D-RS" EXACT []
+synonym: "three prime D recombination signal sequence" EXACT []
+synonym: "three_prime_D-recombination_signal_sequence" EXACT []
+is_a: SO:0000492 ! D_gene_recombination_feature
+
+[Term]
+id: SO:0000571
+name: miRNA_encoding
+synonym: "miRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000572
+name: DJ_gene_segment
+def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "D-J-GENE" EXACT []
+synonym: "DJ gene" EXACT []
+is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
+
+[Term]
+id: SO:0000573
+name: rRNA_encoding
+synonym: "rRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000574
+name: VDJ_gene_segment
+def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V-D-J-GENE" EXACT []
+synonym: "VDJ gene" EXACT []
+is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
+
+[Term]
+id: SO:0000575
+name: scRNA_encoding
+synonym: "scRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000576
+name: VJ_gene_segment
+def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
+synonym: "V-J-GENE" EXACT []
+synonym: "VJ gene" EXACT []
+is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
+
+[Term]
+id: SO:0000577
+name: centromere
+def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Centromere "wiki"
+is_a: SO:0000628 ! chromosomal_structural_element
+
+[Term]
+id: SO:0000578
+name: snoRNA_encoding
+synonym: "snoRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000579
+name: edited_transcript_feature
+def: "A locatable feature on a transcript that is edited." [SO:ma]
+synonym: "edited transcript feature" EXACT []
+is_a: SO:0000833 ! transcript_region
+
+[Term]
+id: SO:0000580
+name: methylation_guide_snoRNA_primary_transcript
+def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]
+synonym: "methylation guide snoRNA primary transcript" EXACT []
+is_a: SO:0000232 ! snoRNA_primary_transcript
+
+[Term]
+id: SO:0000581
+name: cap
+def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/5%27_cap "wiki"
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000582
+name: rRNA_cleavage_snoRNA_primary_transcript
+def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]
+synonym: "rRNA cleavage snoRNA primary transcript" EXACT []
+is_a: SO:0000232 ! snoRNA_primary_transcript
+
+[Term]
+id: SO:0000583
+name: pre_edited_region
+def: "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]
+synonym: "pre edited region" EXACT []
+synonym: "pre-edited region" EXACT []
+is_a: SO:0000579 ! edited_transcript_feature
+
+[Term]
+id: SO:0000584
+name: tmRNA
+def: "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]
+synonym: "10Sa RNA" RELATED []
+synonym: "ssrA" RELATED []
+xref: http://en.wikipedia.org/wiki/TmRNA "wiki"
+is_a: SO:0000370 ! small_regulatory_ncRNA
+
+[Term]
+id: SO:0000585
+name: C_D_box_snoRNA_encoding
+synonym: "C/D box snoRNA encoding" EXACT []
+is_a: SO:0000578 ! snoRNA_encoding
+
+[Term]
+id: SO:0000586
+name: tmRNA_primary_transcript
+def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]
+synonym: "10Sa RNA primary transcript" RELATED []
+synonym: "ssrA RNA primary transcript" RELATED []
+synonym: "tmRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+
+[Term]
+id: SO:0000587
+name: group_I_intron
+def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]
+comment: GO:0000372.
+subset: SOFA
+synonym: "group I intron" EXACT []
+xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki"
+is_a: SO:0000588 ! autocatalytically_spliced_intron
+
+[Term]
+id: SO:0000588
+name: autocatalytically_spliced_intron
+def: "A self spliced intron." [SO:ke]
+subset: SOFA
+synonym: "autocatalytically spliced intron" EXACT []
+is_a: SO:0000188 ! intron
+relationship: has_quality SO:0001186 ! ribozymic
+
+[Term]
+id: SO:0000589
+name: SRP_RNA_primary_transcript
+def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke]
+synonym: "SRP RNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+
+[Term]
+id: SO:0000590
+name: SRP_RNA
+def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]
+subset: SOFA
+synonym: "7S RNA" RELATED []
+synonym: "signal recognition particle RNA" RELATED []
+synonym: "SRP RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0000589 ! SRP_RNA_primary_transcript
+
+[Term]
+id: SO:0000591
+name: pseudoknot
+def: "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]
+xref: http://en.wikipedia.org/wiki/Pseudoknot "wiki"
+is_a: SO:0000002 ! sequence_secondary_structure
+
+[Term]
+id: SO:0000592
+name: H_pseudoknot
+def: "A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]
+synonym: "classical pseudoknot" EXACT []
+synonym: "H pseudoknot" EXACT []
+synonym: "H-pseudoknot" EXACT []
+synonym: "H-type pseudoknot" EXACT []
+synonym: "hairpin-type pseudoknot" EXACT []
+is_a: SO:0000591 ! pseudoknot
+
+[Term]
+id: SO:0000593
+name: C_D_box_snoRNA
+def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
+subset: SOFA
+synonym: "box C/D snoRNA" EXACT []
+synonym: "C D box snoRNA" EXACT []
+synonym: "C/D box snoRNA" EXACT []
+is_a: SO:0000275 ! snoRNA
+relationship: derives_from SO:0000595 ! C_D_box_snoRNA_primary_transcript
+
+[Term]
+id: SO:0000594
+name: H_ACA_box_snoRNA
+def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
+synonym: "box H/ACA snoRNA" EXACT []
+synonym: "H ACA box snoRNA" EXACT []
+synonym: "H/ACA box snoRNA" EXACT []
+is_a: SO:0000275 ! snoRNA
+relationship: derives_from SO:0000596 ! H_ACA_box_snoRNA_primary_transcript
+
+[Term]
+id: SO:0000595
+name: C_D_box_snoRNA_primary_transcript
+def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]
+synonym: "C/D box snoRNA primary transcript" EXACT []
+is_a: SO:0000232 ! snoRNA_primary_transcript
+
+[Term]
+id: SO:0000596
+name: H_ACA_box_snoRNA_primary_transcript
+def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]
+synonym: "H ACA box snoRNA primary transcript" EXACT []
+is_a: SO:0000232 ! snoRNA_primary_transcript
+
+[Term]
+id: SO:0000597
+name: transcript_edited_by_U_insertion/deletion
+def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html]
+is_obsolete: true
+
+[Term]
+id: SO:0000598
+name: edited_by_C_insertion_and_dinucleotide_insertion
+synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0000599
+name: edited_by_C_to_U_substitution
+is_obsolete: true
+
+[Term]
+id: SO:0000600
+name: edited_by_A_to_I_substitution
+is_obsolete: true
+
+[Term]
+id: SO:0000601
+name: edited_by_G_addition
+is_obsolete: true
+
+[Term]
+id: SO:0000602
+name: guide_RNA
+def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]
+subset: SOFA
+synonym: "gRNA" EXACT []
+synonym: "guide RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki"
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000603
+name: group_II_intron
+def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]
+comment: GO:0000373.
+subset: SOFA
+synonym: "group II intron" EXACT []
+xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki"
+is_a: SO:0000588 ! autocatalytically_spliced_intron
+
+[Term]
+id: SO:0000604
+name: editing_block
+def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]
+synonym: "editing block" EXACT []
+is_a: SO:0000579 ! edited_transcript_feature
+
+[Term]
+id: SO:0000605
+name: intergenic_region
+def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+subset: SOFA
+synonym: "intergenic region" EXACT []
+xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki"
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000606
+name: editing_domain
+def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]
+synonym: "editing domain" EXACT []
+is_a: SO:0000579 ! edited_transcript_feature
+
+[Term]
+id: SO:0000607
+name: unedited_region
+def: "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]
+synonym: "unedited region" EXACT []
+is_a: SO:0000579 ! edited_transcript_feature
+
+[Term]
+id: SO:0000608
+name: H_ACA_box_snoRNA_encoding
+synonym: "H ACA box snoRNA encoding" EXACT []
+is_a: SO:0000578 ! snoRNA_encoding
+
+[Term]
+id: SO:0000609
+name: oligo_U_tail
+def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]
+synonym: "oligo U tail" EXACT []
+is_a: SO:0001411 ! biological_region
+relationship: adjacent_to SO:0000602 ! guide_RNA
+
+[Term]
+id: SO:0000610
+name: polyA_sequence
+def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]
+subset: SOFA
+synonym: "polyA sequence" EXACT []
+is_a: SO:0001411 ! biological_region
+relationship: adjacent_to SO:0000234 ! mRNA
+
+[Term]
+id: SO:0000611
+name: branch_site
+def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]
+subset: SOFA
+synonym: "branch point" EXACT []
+synonym: "branch site" EXACT []
+synonym: "branch_point" EXACT []
+is_a: SO:0000841 ! spliceosomal_intron_region
+
+[Term]
+id: SO:0000612
+name: polypyrimidine_tract
+def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]
+subset: SOFA
+synonym: "polypyrimidine tract" EXACT []
+xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki"
+is_a: SO:0000841 ! spliceosomal_intron_region
+
+[Term]
+id: SO:0000613
+name: bacterial_RNApol_promoter
+def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]
+synonym: "bacterial RNApol promoter" EXACT []
+is_a: SO:0000752 ! gene_group_regulatory_region
+is_a: SO:0001203 ! RNA_polymerase_promoter
+
+[Term]
+id: SO:0000614
+name: bacterial_terminator
+def: "A terminator signal for bacterial transcription." [SO:ke]
+synonym: "bacterial terminator" EXACT []
+is_a: SO:0000141 ! terminator
+is_a: SO:0000752 ! gene_group_regulatory_region
+
+[Term]
+id: SO:0000615
+name: terminator_of_type_2_RNApol_III_promoter
+def: "A terminator signal for RNA polymerase III transcription." [SO:ke]
+synonym: "terminator of type 2 RNApol III promoter" EXACT []
+is_a: SO:0000951 ! eukaryotic_terminator
+
+[Term]
+id: SO:0000616
+name: transcription_end_site
+def: "The base where transcription ends." [SO:ke]
+subset: SOFA
+synonym: "transcription end site" EXACT []
+is_a: SO:0000835 ! primary_transcript_region
+
+[Term]
+id: SO:0000617
+name: RNApol_III_promoter_type_1
+synonym: "RNApol III promoter type 1" EXACT []
+is_a: SO:0000171 ! RNApol_III_promoter
+
+[Term]
+id: SO:0000618
+name: RNApol_III_promoter_type_2
+synonym: "RNApol III promoter type 2" EXACT []
+synonym: "tRNA promoter" RELATED []
+is_a: SO:0000171 ! RNApol_III_promoter
+
+[Term]
+id: SO:0000619
+name: A_box
+def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]
+comment: Binds TFIIIC.
+synonym: "A-box" EXACT []
+xref: http://en.wikipedia.org/wiki/A-box "wiki"
+is_a: SO:0001660 ! core_promoter_element
+
+[Term]
+id: SO:0000620
+name: B_box
+def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]
+comment: Binds TFIIIC.
+synonym: "B-box" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2
+
+[Term]
+id: SO:0000621
+name: RNApol_III_promoter_type_3
+synonym: "RNApol III promoter type 3" EXACT []
+is_a: SO:0000171 ! RNApol_III_promoter
+
+[Term]
+id: SO:0000622
+name: C_box
+def: "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]
+synonym: "C-box" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
+
+[Term]
+id: SO:0000623
+name: snRNA_encoding
+synonym: "snRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000624
+name: telomere
+def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]
+subset: SOFA
+synonym: "telomeric DNA" EXACT []
+synonym: "telomeric sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Telomere "wiki"
+is_a: SO:0000628 ! chromosomal_structural_element
+
+[Term]
+id: SO:0000625
+name: silencer
+def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki"
+is_a: SO:0000727 ! CRM
+
+[Term]
+id: SO:0000626
+name: chromosomal_regulatory_element
+synonym: "chromosomal regulatory element" EXACT []
+is_a: SO:0000830 ! chromosome_part
+
+[Term]
+id: SO:0000627
+name: insulator
+def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]
+subset: SOFA
+synonym: "insulator element" EXACT []
+xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki"
+is_a: SO:0001055 ! transcriptional_cis_regulatory_region
+
+[Term]
+id: SO:0000628
+name: chromosomal_structural_element
+subset: SOFA
+synonym: "chromosomal structural element" EXACT []
+is_a: SO:0000830 ! chromosome_part
+
+[Term]
+id: SO:0000629
+name: five_prime_open_reading_frame
+synonym: "five prime open reading frame" EXACT []
+is_a: SO:0000836 ! mRNA_region
+relationship: part_of SO:0000204 ! five_prime_UTR
+
+[Term]
+id: SO:0000630
+name: upstream_AUG_codon
+def: "A start codon upstream of the ORF." [SO:ke]
+synonym: "upstream AUG codon" EXACT []
+is_a: SO:0000837 ! UTR_region
+relationship: part_of SO:0000203 ! UTR
+
+[Term]
+id: SO:0000631
+name: polycistronic_primary_transcript
+def: "A primary transcript encoding for more than one gene product." [SO:ke]
+synonym: "polycistronic primary transcript" EXACT []
+is_a: SO:0000078 ! polycistronic_transcript
+is_a: SO:0000185 ! primary_transcript
+relationship: has_quality SO:0000880 ! polycistronic
+
+[Term]
+id: SO:0000632
+name: monocistronic_primary_transcript
+def: "A primary transcript encoding for one gene product." [SO:ke]
+synonym: "monocistronic primary transcript" EXACT []
+is_a: SO:0000185 ! primary_transcript
+is_a: SO:0000665 ! monocistronic_transcript
+relationship: has_quality SO:0000878 ! monocistronic
+
+[Term]
+id: SO:0000633
+name: monocistronic_mRNA
+def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]
+synonym: "monocistronic mRNA" EXACT []
+synonym: "monocistronic processed transcript" EXACT []
+xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki"
+is_a: SO:0000234 ! mRNA
+is_a: SO:0000665 ! monocistronic_transcript
+relationship: has_quality SO:0000878 ! monocistronic
+
+[Term]
+id: SO:0000634
+name: polycistronic_mRNA
+def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]
+synonym: "polycistronic mRNA" EXACT []
+synonym: "polycistronic processed transcript" RELATED []
+xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki"
+is_a: SO:0000078 ! polycistronic_transcript
+is_a: SO:0000234 ! mRNA
+relationship: has_quality SO:0000880 ! polycistronic
+
+[Term]
+id: SO:0000635
+name: mini_exon_donor_RNA
+def: "A primary transcript that donates the spliced leader to other mRNA." [SO:ke]
+synonym: "mini exon donor RNA" EXACT []
+synonym: "mini-exon donor RNA" EXACT []
+is_a: SO:0000185 ! primary_transcript
+
+[Term]
+id: SO:0000636
+name: spliced_leader_RNA
+synonym: "mini-exon" RELATED []
+synonym: "spliced leader RNA" EXACT []
+is_a: SO:0000835 ! primary_transcript_region
+relationship: part_of SO:0000635 ! mini_exon_donor_RNA
+
+[Term]
+id: SO:0000637
+name: engineered_plasmid
+def: "A plasmid that is engineered." [SO:xp]
+synonym: "engineered plasmid" EXACT []
+synonym: "engineered plasmid gene" RELATED []
+is_a: SO:0000155 ! plasmid
+is_a: SO:0000804 ! engineered_region
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000638
+name: transcribed_spacer_region
+def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]
+synonym: "transcribed spacer region" EXACT []
+is_a: SO:0000838 ! rRNA_primary_transcript_region
+
+[Term]
+id: SO:0000639
+name: internal_transcribed_spacer_region
+def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]
+synonym: "internal transcribed spacer region" EXACT []
+is_a: SO:0000638 ! transcribed_spacer_region
+
+[Term]
+id: SO:0000640
+name: external_transcribed_spacer_region
+def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]
+synonym: "external transcribed spacer region" EXACT []
+is_a: SO:0000638 ! transcribed_spacer_region
+
+[Term]
+id: SO:0000641
+name: tetranucleotide_repeat_microsatellite_feature
+synonym: "tetranucleotide repeat microsatellite feature" EXACT []
+is_a: SO:0000289 ! microsatellite
+
+[Term]
+id: SO:0000642
+name: SRP_RNA_encoding
+synonym: "SRP RNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000643
+name: minisatellite
+def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Minisatellite "wiki"
+is_a: SO:0000005 ! satellite_DNA
+
+[Term]
+id: SO:0000644
+name: antisense_RNA
+def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]
+subset: SOFA
+synonym: "antisense RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki"
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0000645 ! antisense_primary_transcript
+
+[Term]
+id: SO:0000645
+name: antisense_primary_transcript
+def: "The reverse complement of the primary transcript." [SO:ke]
+subset: SOFA
+synonym: "antisense primary transcript" EXACT []
+is_a: SO:0000185 ! primary_transcript
+
+[Term]
+id: SO:0000646
+name: siRNA
+def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]
+subset: SOFA
+synonym: "small interfering RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/SiRNA "wiki"
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000647
+name: miRNA_primary_transcript
+alt_id: SO:0000648
+def: "A primary transcript encoding a micro RNA." [SO:ke]
+synonym: "micro RNA primary transcript" EXACT []
+synonym: "miRNA primary transcript" EXACT []
+synonym: "small temporal RNA primary transcript" EXACT []
+synonym: "stRNA primary transcript" EXACT []
+synonym: "stRNA_primary_transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+relationship: has_part SO:0001244 ! pre_miRNA
+
+[Term]
+id: SO:0000650
+name: small_subunit_rRNA
+def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]
+subset: SOFA
+synonym: "small subunit rRNA" EXACT []
+synonym: "SSU RNA" EXACT [RSC:cb]
+synonym: "SSU rRNA" EXACT [RSC:cb]
+is_a: SO:0000252 ! rRNA
+relationship: derives_from SO:0000255 ! rRNA_small_subunit_primary_transcript
+
+[Term]
+id: SO:0000651
+name: large_subunit_rRNA
+def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]
+subset: SOFA
+synonym: "large subunit rRNA" EXACT []
+synonym: "LSU RNA" EXACT [RSC:cb]
+synonym: "LSU rRNA" EXACT [RSC:cb]
+is_a: SO:0000252 ! rRNA
+relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript
+
+[Term]
+id: SO:0000652
+name: rRNA_5S
+def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]
+subset: SOFA
+synonym: "5S LSU rRNA" EXACT []
+synonym: "5S ribosomal RNA" EXACT []
+synonym: "5S rRNA" EXACT []
+synonym: "rRNA 5S" EXACT []
+xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki"
+is_a: SO:0000651 ! large_subunit_rRNA
+
+[Term]
+id: SO:0000653
+name: rRNA_28S
+def: "A component of the large ribosomal subunit." [SO:ke]
+subset: SOFA
+synonym: "28S LSU rRNA" EXACT []
+synonym: "28S ribosomal RNA" EXACT []
+synonym: "28S rRNA" EXACT []
+synonym: "rRNA 28S" EXACT []
+xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki"
+is_a: SO:0000651 ! large_subunit_rRNA
+
+[Term]
+id: SO:0000654
+name: maxicircle_gene
+def: "A mitochondrial gene located in a maxicircle." [SO:xp]
+synonym: "maxi-circle gene" EXACT []
+synonym: "maxicircle gene" EXACT []
+is_a: SO:0000089 ! kinetoplast_gene
+relationship: part_of SO:0000742 ! maxicircle
+
+[Term]
+id: SO:0000655
+name: ncRNA
+def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]
+comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
+subset: SOFA
+synonym: "noncoding RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/NcRNA "wiki"
+is_a: SO:0000233 ! mature_transcript
+
+[Term]
+id: SO:0000656
+name: stRNA_encoding
+synonym: "stRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000657
+name: repeat_region
+def: "A region of sequence containing one or more repeat units." [SO:ke]
+subset: SOFA
+synonym: "repeat region" EXACT []
+is_a: SO:0001411 ! biological_region
+relationship: has_part SO:0000726 ! repeat_unit
+
+[Term]
+id: SO:0000658
+name: dispersed_repeat
+def: "A repeat that is located at dispersed sites in the genome." [SO:ke]
+subset: SOFA
+synonym: "dispersed repeat" EXACT []
+synonym: "interspersed repeat" EXACT []
+xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki"
+is_a: SO:0000657 ! repeat_region
+
+[Term]
+id: SO:0000659
+name: tmRNA_encoding
+synonym: "tmRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000660
+name: DNA_invertase_target_sequence
+is_obsolete: true
+
+[Term]
+id: SO:0000661
+name: intron_attribute
+is_obsolete: true
+
+[Term]
+id: SO:0000662
+name: spliceosomal_intron
+def: "An intron which is spliced by the spliceosome." [SO:ke]
+comment: GO:0000398.
+subset: SOFA
+synonym: "spliceosomal intron" EXACT []
+is_a: SO:0000188 ! intron
+
+[Term]
+id: SO:0000663
+name: tRNA_encoding
+synonym: "tRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000664
+name: introgressed_chromosome_region
+synonym: "introgressed chromosome region" EXACT []
+is_a: SO:0000830 ! chromosome_part
+
+[Term]
+id: SO:0000665
+name: monocistronic_transcript
+def: "A transcript that is monocistronic." [SO:xp]
+synonym: "monocistronic transcript" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: has_quality SO:0000878 ! monocistronic
+
+[Term]
+id: SO:0000666
+name: mobile_intron
+def: "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]
+synonym: "mobile intron" EXACT []
+is_a: SO:0000188 ! intron
+is_a: SO:0001037 ! mobile_genetic_element
+relationship: has_quality SO:0001234 ! mobile
+
+[Term]
+id: SO:0000667
+name: insertion
+alt_id: SO:1000034
+def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]
+subset: DBVAR
+subset: SOFA
+synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
+synonym: "nucleotide insertion" EXACT []
+synonym: "nucleotide_insertion" EXACT []
+xref: loinc:LA6687-3 "Insertion"
+is_a: SO:0001059 ! sequence_alteration
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000668
+name: EST_match
+def: "A match against an EST sequence." [SO:ke]
+subset: SOFA
+synonym: "EST match" EXACT []
+is_a: SO:0000102 ! expressed_sequence_match
+
+[Term]
+id: SO:0000669
+name: sequence_rearrangement_feature
+synonym: "sequence rearrangement feature" EXACT []
+is_a: SO:0000298 ! recombination_feature
+
+[Term]
+id: SO:0000670
+name: chromosome_breakage_sequence
+def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]
+synonym: "chromosome breakage sequence" EXACT []
+is_a: SO:0000669 ! sequence_rearrangement_feature
+
+[Term]
+id: SO:0000671
+name: internal_eliminated_sequence
+def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]
+synonym: "internal eliminated sequence" EXACT []
+is_a: SO:0000669 ! sequence_rearrangement_feature
+
+[Term]
+id: SO:0000672
+name: macronucleus_destined_segment
+def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]
+synonym: "macronucleus destined segment" EXACT []
+is_a: SO:0000669 ! sequence_rearrangement_feature
+
+[Term]
+id: SO:0000673
+name: transcript
+def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/RNA "wiki"
+is_a: SO:0000831 ! gene_member_region
+
+[Term]
+id: SO:0000674
+name: non_canonical_splice_site
+def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke]
+synonym: "non canonical splice site" EXACT []
+synonym: "non-canonical splice site" EXACT []
+is_obsolete: true
+consider: SO:0000678
+consider: SO:0000679
+
+[Term]
+id: SO:0000675
+name: canonical_splice_site
+def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke]
+synonym: "canonical splice site" EXACT []
+is_obsolete: true
+consider: SO:0000676
+consider: SO:0000677
+
+[Term]
+id: SO:0000676
+name: canonical_three_prime_splice_site
+def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke]
+synonym: "canonical 3' splice site" EXACT []
+synonym: "canonical three prime splice site" EXACT []
+is_a: SO:0000164 ! three_prime_cis_splice_site
+
+[Term]
+id: SO:0000677
+name: canonical_five_prime_splice_site
+def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke]
+synonym: "canonical 5' splice site" EXACT []
+synonym: "canonical five prime splice site" EXACT []
+is_a: SO:0000163 ! five_prime_cis_splice_site
+
+[Term]
+id: SO:0000678
+name: non_canonical_three_prime_splice_site
+def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke]
+synonym: "non canonical 3' splice site" RELATED []
+synonym: "non canonical three prime splice site" EXACT []
+synonym: "non-canonical three prime splice site" EXACT []
+is_a: SO:0000164 ! three_prime_cis_splice_site
+
+[Term]
+id: SO:0000679
+name: non_canonical_five_prime_splice_site
+def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke]
+synonym: "non canonical 5' splice site" EXACT []
+synonym: "non canonical five prime splice site" EXACT []
+synonym: "non-canonical five prime splice site" EXACT []
+is_a: SO:0000163 ! five_prime_cis_splice_site
+
+[Term]
+id: SO:0000680
+name: non_canonical_start_codon
+def: "A start codon that is not the usual AUG sequence." [SO:ke]
+synonym: "non ATG start codon" EXACT []
+synonym: "non canonical start codon" EXACT []
+synonym: "non-canonical start codon" EXACT []
+is_a: SO:0000318 ! start_codon
+
+[Term]
+id: SO:0000681
+name: aberrant_processed_transcript
+def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke]
+synonym: "aberrant processed transcript" EXACT []
+is_a: SO:0000673 ! transcript
+
+[Term]
+id: SO:0000682
+name: splicing_feature
+is_obsolete: true
+
+[Term]
+id: SO:0000683
+name: exonic_splice_enhancer
+def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]
+synonym: "exonic splice enhancer" EXACT []
+is_a: SO:0000344 ! splice_enhancer
+
+[Term]
+id: SO:0000684
+name: nuclease_sensitive_site
+def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]
+subset: SOFA
+synonym: "nuclease sensitive site" EXACT []
+is_a: SO:0000059 ! nuclease_binding_site
+
+[Term]
+id: SO:0000685
+name: DNAseI_hypersensitive_site
+synonym: "DHS" EXACT []
+synonym: "DNAseI hypersensitive site" EXACT []
+is_a: SO:0000322 ! nuclease_hypersensitive_site
+
+[Term]
+id: SO:0000686
+name: translocation_element
+def: "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]
+synonym: "translocation element" EXACT []
+is_a: SO:1000044 ! chromosomal_translocation
+
+[Term]
+id: SO:0000687
+name: deletion_junction
+def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]
+subset: SOFA
+synonym: "deletion junction" EXACT []
+is_a: SO:0000699 ! junction
+
+[Term]
+id: SO:0000688
+name: golden_path
+def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]
+subset: SOFA
+synonym: "golden path" EXACT []
+is_a: SO:0000353 ! sequence_assembly
+
+[Term]
+id: SO:0000689
+name: cDNA_match
+def: "A match against cDNA sequence." [SO:ke]
+subset: SOFA
+synonym: "cDNA match" EXACT []
+is_a: SO:0000102 ! expressed_sequence_match
+
+[Term]
+id: SO:0000690
+name: gene_with_polycistronic_transcript
+def: "A gene that encodes a polycistronic transcript." [SO:xp]
+synonym: "gene with polycistronic transcript" EXACT []
+is_a: SO:0000704 ! gene
+relationship: transcribed_to SO:0000078 ! polycistronic_transcript
+
+[Term]
+id: SO:0000691
+name: cleaved_initiator_methionine
+alt_id: BS:00067
+def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]
+subset: biosapiens
+synonym: "cleaved initiator methionine" EXACT []
+synonym: "init_met" RELATED [uniprot:feature_type]
+synonym: "initiator methionine" RELATED []
+is_a: SO:0100011 ! cleaved_peptide_region
+
+[Term]
+id: SO:0000692
+name: gene_with_dicistronic_transcript
+def: "A gene that encodes a dicistronic transcript." [SO:xp]
+synonym: "gene with dicistronic transcript" EXACT []
+is_a: SO:0000690 ! gene_with_polycistronic_transcript
+relationship: transcribed_to SO:0000079 ! dicistronic_transcript
+
+[Term]
+id: SO:0000693
+name: gene_with_recoded_mRNA
+def: "A gene that encodes an mRNA that is recoded." [SO:xp]
+synonym: "gene with recoded mRNA" EXACT []
+is_a: SO:0001217 ! protein_coding_gene
+relationship: has_quality SO:0000881 ! recoded
+
+[Term]
+id: SO:0000694
+name: SNP
+def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]
+subset: SOFA
+synonym: "single nucleotide polymorphism" EXACT []
+is_a: SO:0001483 ! SNV
+
+[Term]
+id: SO:0000695
+name: reagent
+def: "A sequence used in experiment." [SO:ke]
+comment: Requested by Lynn Crosby, jan 2006.
+subset: SOFA
+is_a: SO:0001409 ! biomaterial_region
+
+[Term]
+id: SO:0000696
+name: oligo
+def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]
+subset: SOFA
+synonym: "oligonucleotide" EXACT []
+xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki"
+is_a: SO:0000695 ! reagent
+
+[Term]
+id: SO:0000697
+name: gene_with_stop_codon_read_through
+def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp]
+synonym: "gene with stop codon read through" EXACT []
+is_a: SO:0000693 ! gene_with_recoded_mRNA
+relationship: has_part SO:0000883 ! stop_codon_read_through
+
+[Term]
+id: SO:0000698
+name: gene_with_stop_codon_redefined_as_pyrrolysine
+def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]
+synonym: "gene with stop codon redefined as pyrrolysine" EXACT []
+is_a: SO:0000697 ! gene_with_stop_codon_read_through
+relationship: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine
+
+[Term]
+id: SO:0000699
+name: junction
+def: "A sequence_feature with an extent of zero." [SO:ke]
+comment: A junction is a boundary between regions. A boundary has an extent of zero.
+subset: SOFA
+synonym: "boundary" EXACT []
+synonym: "breakpoint" EXACT []
+is_a: SO:0000110 ! sequence_feature
+
+[Term]
+id: SO:0000700
+name: remark
+def: "A comment about the sequence." [SO:ke]
+subset: SOFA
+is_a: SO:0001410 ! experimental_feature
+
+[Term]
+id: SO:0000701
+name: possible_base_call_error
+def: "A region of sequence where the validity of the base calling is questionable." [SO:ke]
+subset: SOFA
+synonym: "possible base call error" EXACT []
+is_a: SO:0000413 ! sequence_difference
+
+[Term]
+id: SO:0000702
+name: possible_assembly_error
+def: "A region of sequence where there may have been an error in the assembly." [SO:ke]
+subset: SOFA
+synonym: "possible assembly error" EXACT []
+is_a: SO:0000413 ! sequence_difference
+
+[Term]
+id: SO:0000703
+name: experimental_result_region
+def: "A region of sequence implicated in an experimental result." [SO:ke]
+subset: SOFA
+synonym: "experimental result region" EXACT []
+is_a: SO:0000700 ! remark
+
+[Term]
+id: SO:0000704
+name: gene
+def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Gene "wiki"
+is_a: SO:0001411 ! biological_region
+relationship: member_of SO:0005855 ! gene_group
+
+[Term]
+id: SO:0000705
+name: tandem_repeat
+def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]
+subset: SOFA
+synonym: "tandem repeat" EXACT []
+xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki"
+xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
+is_a: SO:0000657 ! repeat_region
+
+[Term]
+id: SO:0000706
+name: trans_splice_acceptor_site
+def: "The 3' splice site of the acceptor primary transcript." [SO:ke]
+comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
+subset: SOFA
+synonym: "3' trans splice site" RELATED []
+synonym: "trans splice acceptor site" EXACT []
+is_a: SO:0001420 ! trans_splice_site
+
+[Term]
+id: SO:0000707
+name: trans_splice_donor_site
+def: "The 5' five prime splice site region of the donor RNA." [SO:ke]
+comment: SL RNA contains a donor site.
+synonym: "5 prime trans splice site" RELATED []
+synonym: "trans splice donor site" EXACT []
+synonym: "trans-splice donor site" EXACT []
+is_a: SO:0001420 ! trans_splice_site
+
+[Term]
+id: SO:0000708
+name: SL1_acceptor_site
+def: "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]
+synonym: "SL1 acceptor site" EXACT []
+is_a: SO:0000706 ! trans_splice_acceptor_site
+
+[Term]
+id: SO:0000709
+name: SL2_acceptor_site
+def: "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL2 acceptor site" EXACT []
+is_a: SO:0000706 ! trans_splice_acceptor_site
+
+[Term]
+id: SO:0000710
+name: gene_with_stop_codon_redefined_as_selenocysteine
+def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]
+synonym: "gene with stop codon redefined as selenocysteine" EXACT []
+is_a: SO:0000697 ! gene_with_stop_codon_read_through
+relationship: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine
+
+[Term]
+id: SO:0000711
+name: gene_with_mRNA_recoded_by_translational_bypass
+def: "A gene with mRNA recoded by translational bypass." [SO:xp]
+synonym: "gene with mRNA recoded by translational bypass" EXACT []
+is_a: SO:0000693 ! gene_with_recoded_mRNA
+relationship: has_quality SO:0000886 ! recoded_by_translational_bypass
+
+[Term]
+id: SO:0000712
+name: gene_with_transcript_with_translational_frameshift
+def: "A gene encoding a transcript that has a translational frameshift." [SO:xp]
+synonym: "gene with transcript with translational frameshift" EXACT []
+is_a: SO:0000693 ! gene_with_recoded_mRNA
+relationship: has_quality SO:0000887 ! translationally_frameshifted
+
+[Term]
+id: SO:0000713
+name: DNA_motif
+def: "A motif that is active in the DNA form of the sequence." [SO:ke]
+synonym: "DNA motif" EXACT []
+xref: http://en.wikipedia.org/wiki/DNA_motif "wiki"
+is_a: SO:0000714 ! nucleotide_motif
+
+[Term]
+id: SO:0000714
+name: nucleotide_motif
+def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke]
+subset: SOFA
+synonym: "nucleotide motif" EXACT []
+is_a: SO:0001683 ! sequence_motif
+
+[Term]
+id: SO:0000715
+name: RNA_motif
+def: "A motif that is active in RNA sequence." [SO:ke]
+subset: SOFA
+synonym: "RNA motif" EXACT []
+is_a: SO:0000714 ! nucleotide_motif
+
+[Term]
+id: SO:0000716
+name: dicistronic_mRNA
+def: "An mRNA that has the quality dicistronic." [SO:ke]
+synonym: "dicistronic mRNA" EXACT []
+synonym: "dicistronic processed transcript" RELATED []
+is_a: SO:0000079 ! dicistronic_transcript
+is_a: SO:0000634 ! polycistronic_mRNA
+relationship: has_quality SO:0000879 ! dicistronic
+
+[Term]
+id: SO:0000717
+name: reading_frame
+def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]
+comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
+subset: SOFA
+synonym: "reading frame" EXACT []
+xref: http://en.wikipedia.org/wiki/Reading_frame "wiki"
+is_a: SO:0001410 ! experimental_feature
+
+[Term]
+id: SO:0000718
+name: blocked_reading_frame
+def: "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]
+comment: Term requested by Rama from SGD.
+synonym: "blocked reading frame" EXACT []
+is_a: SO:0000717 ! reading_frame
+
+[Term]
+id: SO:0000719
+name: ultracontig
+def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]
+subset: SOFA
+synonym: "superscaffold" RELATED []
+is_a: SO:0001876 ! partial_genomic_sequence_assembly
+
+[Term]
+id: SO:0000720
+name: foreign_transposable_element
+def: "A transposable element that is foreign." [SO:ke]
+comment: requested by Michael on 19 Nov 2004.
+synonym: "foreign transposable element" EXACT []
+is_a: SO:0000101 ! transposable_element
+relationship: has_quality SO:0000784 ! foreign
+
+[Term]
+id: SO:0000721
+name: gene_with_dicistronic_primary_transcript
+def: "A gene that encodes a dicistronic primary transcript." [SO:xp]
+comment: Requested by Michael, 19 nov 2004.
+synonym: "gene with dicistronic primary transcript" EXACT []
+is_a: SO:0000692 ! gene_with_dicistronic_transcript
+relationship: transcribed_to SO:1001197 ! dicistronic_primary_transcript
+
+[Term]
+id: SO:0000722
+name: gene_with_dicistronic_mRNA
+def: "A gene that encodes a polycistronic mRNA." [SO:xp]
+comment: Requested by MA nov 19 2004.
+synonym: "gene with dicistronic mRNA" EXACT []
+synonym: "gene with dicistronic processed transcript" EXACT []
+is_a: SO:0000692 ! gene_with_dicistronic_transcript
+relationship: transcribed_to SO:0000716 ! dicistronic_mRNA
+
+[Term]
+id: SO:0000723
+name: iDNA
+def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]
+synonym: "intervening DNA" EXACT []
+xref: http://en.wikipedia.org/wiki/IDNA "wiki"
+is_a: SO:0000298 ! recombination_feature
+
+[Term]
+id: SO:0000724
+name: oriT
+def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+subset: SOFA
+synonym: "origin of transfer" EXACT []
+xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki"
+is_a: SO:0000296 ! origin_of_replication
+
+[Term]
+id: SO:0000725
+name: transit_peptide
+alt_id: BS:00055
+def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
+subset: biosapiens
+subset: SOFA
+synonym: "signal" RELATED []
+synonym: "transit" RELATED [uniprot:feature_type]
+synonym: "transit peptide" EXACT []
+is_a: SO:0001527 ! peptide_localization_signal
+
+[Term]
+id: SO:0000726
+name: repeat_unit
+def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke]
+comment: Added to comply with the feature table. A single repeat.
+synonym: "repeat unit" EXACT []
+xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000727
+name: CRM
+def: "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]
+comment: Requested by Stephen Grossmann Dec 2004.
+subset: SOFA
+synonym: "cis regulatory module" EXACT []
+synonym: "TF module" EXACT []
+synonym: "transcription factor module" EXACT []
+is_a: SO:0001055 ! transcriptional_cis_regulatory_region
+relationship: has_part SO:0000235 ! TF_binding_site
+
+[Term]
+id: SO:0000728
+name: intein
+def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]
+comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
+synonym: "protein intron" RELATED []
+xref: http://en.wikipedia.org/wiki/Intein "wiki"
+is_a: SO:0100011 ! cleaved_peptide_region
+
+[Term]
+id: SO:0000729
+name: intein_containing
+def: "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]
+synonym: "intein containing" EXACT []
+is_a: SO:0000010 ! protein_coding
+
+[Term]
+id: SO:0000730
+name: gap
+def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]
+subset: SOFA
+is_a: SO:0000143 ! assembly_component
+relationship: part_of SO:0000353 ! sequence_assembly
+
+[Term]
+id: SO:0000731
+name: fragmentary
+def: "An attribute to describe a feature that is incomplete." [SO:ke]
+comment: Term added because of request by MO people.
+synonym: "fragment" EXACT []
+is_a: SO:0000905 ! status
+
+[Term]
+id: SO:0000732
+name: predicted
+def: "An attribute describing an unverified region." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Predicted "wiki"
+is_a: SO:0000905 ! status
+
+[Term]
+id: SO:0000733
+name: feature_attribute
+def: "An attribute describing a located_sequence_feature." [SO:ke]
+synonym: "feature attribute" EXACT []
+is_a: SO:0000400 ! sequence_attribute
+
+[Term]
+id: SO:0000734
+name: exemplar_mRNA
+def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
+comment: Added for the MO people.
+synonym: "exemplar mRNA" EXACT []
+is_a: SO:0000234 ! mRNA
+relationship: has_quality SO:0000864 ! exemplar
+
+[Term]
+id: SO:0000735
+name: sequence_location
+synonym: "sequence location" EXACT []
+is_a: SO:0000400 ! sequence_attribute
+
+[Term]
+id: SO:0000736
+name: organelle_sequence
+synonym: "organelle sequence" EXACT []
+is_a: SO:0000735 ! sequence_location
+
+[Term]
+id: SO:0000737
+name: mitochondrial_sequence
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "mitochondrial sequence" EXACT []
+is_a: SO:0000736 ! organelle_sequence
+
+[Term]
+id: SO:0000738
+name: nuclear_sequence
+synonym: "nuclear sequence" EXACT []
+is_a: SO:0000736 ! organelle_sequence
+
+[Term]
+id: SO:0000739
+name: nucleomorphic_sequence
+synonym: "nucleomorphic sequence" EXACT []
+is_a: SO:0000736 ! organelle_sequence
+
+[Term]
+id: SO:0000740
+name: plastid_sequence
+synonym: "plastid sequence" EXACT []
+is_a: SO:0000736 ! organelle_sequence
+
+[Term]
+id: SO:0000741
+name: kinetoplast
+alt_id: SO:0000826
+def: "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055]
+synonym: "kinetoplast_chromosome" EXACT []
+xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki"
+is_a: SO:0001026 ! genome
+relationship: has_part SO:0000742 ! maxicircle
+relationship: has_part SO:0000980 ! minicircle
+
+[Term]
+id: SO:0000742
+name: maxicircle
+alt_id: SO:0000827
+def: "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]
+synonym: "maxicircle_chromosome" EXACT []
+is_a: SO:0001235 ! replicon
+
+[Term]
+id: SO:0000743
+name: apicoplast_sequence
+synonym: "apicoplast sequence" EXACT []
+is_a: SO:0000740 ! plastid_sequence
+
+[Term]
+id: SO:0000744
+name: chromoplast_sequence
+synonym: "chromoplast sequence" EXACT []
+is_a: SO:0000740 ! plastid_sequence
+
+[Term]
+id: SO:0000745
+name: chloroplast_sequence
+synonym: "chloroplast sequence" EXACT []
+is_a: SO:0000740 ! plastid_sequence
+
+[Term]
+id: SO:0000746
+name: cyanelle_sequence
+synonym: "cyanelle sequence" EXACT []
+is_a: SO:0000740 ! plastid_sequence
+
+[Term]
+id: SO:0000747
+name: leucoplast_sequence
+synonym: "leucoplast sequence" EXACT []
+is_a: SO:0000740 ! plastid_sequence
+
+[Term]
+id: SO:0000748
+name: proplastid_sequence
+synonym: "proplastid sequence" EXACT []
+is_a: SO:0000740 ! plastid_sequence
+
+[Term]
+id: SO:0000749
+name: plasmid_location
+synonym: "plasmid location" EXACT []
+is_a: SO:0000735 ! sequence_location
+
+[Term]
+id: SO:0000750
+name: amplification_origin
+def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]
+synonym: "amplification origin" EXACT []
+is_a: SO:0000296 ! origin_of_replication
+
+[Term]
+id: SO:0000751
+name: proviral_location
+synonym: "proviral location" EXACT []
+is_a: SO:0000735 ! sequence_location
+
+[Term]
+id: SO:0000752
+name: gene_group_regulatory_region
+subset: SOFA
+synonym: "gene group regulatory region" EXACT []
+is_a: SO:0001679 ! transcription_regulatory_region
+relationship: member_of SO:0005855 ! gene_group
+
+[Term]
+id: SO:0000753
+name: clone_insert
+def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]
+subset: SOFA
+synonym: "clone insert" EXACT []
+is_a: SO:0000695 ! reagent
+relationship: part_of SO:0000151 ! clone
+
+[Term]
+id: SO:0000754
+name: lambda_vector
+def: "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]
+synonym: "lambda vector" EXACT []
+is_a: SO:0000440 ! vector_replicon
+
+[Term]
+id: SO:0000755
+name: plasmid_vector
+synonym: "plasmid vector" EXACT []
+xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors "wiki"
+is_a: SO:0000440 ! vector_replicon
+relationship: derives_from SO:0000155 ! plasmid
+
+[Term]
+id: SO:0000756
+name: cDNA
+def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]
+synonym: "complementary DNA" EXACT []
+xref: http://en.wikipedia.org/wiki/CDNA "wiki"
+is_a: SO:0000352 ! DNA
+
+[Term]
+id: SO:0000757
+name: single_stranded_cDNA
+synonym: "single strand cDNA" EXACT []
+synonym: "single stranded cDNA" EXACT []
+synonym: "single-strand cDNA" RELATED []
+is_a: SO:0000756 ! cDNA
+
+[Term]
+id: SO:0000758
+name: double_stranded_cDNA
+synonym: "double strand cDNA" RELATED []
+synonym: "double stranded cDNA" EXACT []
+synonym: "double-strand cDNA" RELATED []
+is_a: SO:0000756 ! cDNA
+
+[Term]
+id: SO:0000759
+name: plasmid_clone
+is_obsolete: true
+
+[Term]
+id: SO:0000760
+name: YAC_clone
+is_obsolete: true
+
+[Term]
+id: SO:0000761
+name: phagemid_clone
+is_obsolete: true
+
+[Term]
+id: SO:0000762
+name: PAC_clone
+synonym: "P1_clone" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0000763
+name: fosmid_clone
+is_obsolete: true
+
+[Term]
+id: SO:0000764
+name: BAC_clone
+is_obsolete: true
+
+[Term]
+id: SO:0000765
+name: cosmid_clone
+is_obsolete: true
+
+[Term]
+id: SO:0000766
+name: pyrrolysyl_tRNA
+def: "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]
+synonym: "pyrrolysyl tRNA" EXACT []
+synonym: "pyrrolysyl-transfer ribonucleic acid" EXACT []
+synonym: "pyrrolysyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0001178 ! pyrrolysine_tRNA_primary_transcript
+
+[Term]
+id: SO:0000767
+name: clone_insert_start
+is_obsolete: true
+
+[Term]
+id: SO:0000768
+name: episome
+def: "A plasmid that may integrate with a chromosome." [SO:ma]
+is_a: SO:0000155 ! plasmid
+
+[Term]
+id: SO:0000769
+name: tmRNA_coding_piece
+def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]
+comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005.
+synonym: "tmRNA coding piece" EXACT []
+is_a: SO:0000847 ! tmRNA_region
+
+[Term]
+id: SO:0000770
+name: tmRNA_acceptor_piece
+def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]
+comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005.
+synonym: "tmRNA acceptor piece" EXACT []
+is_a: SO:0000847 ! tmRNA_region
+
+[Term]
+id: SO:0000771
+name: QTL
+def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]
+comment: Added in respose to request by Simon Twigger November 14th 2005.
+synonym: "quantitative trait locus" EXACT []
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0000772
+name: genomic_island
+def: "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]
+comment: Genomic islands are transmissible elements characterized by large size (>10kb).
+synonym: "genomic island" EXACT []
+xref: http://en.wikipedia.org/wiki/Genomic_island "wiki"
+is_a: SO:0001039 ! integrated_mobile_genetic_element
+
+[Term]
+id: SO:0000773
+name: pathogenic_island
+def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]
+comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
+synonym: "pathogenic island" EXACT []
+is_a: SO:0000772 ! genomic_island
+
+[Term]
+id: SO:0000774
+name: metabolic_island
+def: "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
+comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
+synonym: "metabolic island" EXACT []
+is_a: SO:0000772 ! genomic_island
+
+[Term]
+id: SO:0000775
+name: adaptive_island
+def: "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]
+comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
+synonym: "adaptive island" EXACT []
+is_a: SO:0000772 ! genomic_island
+
+[Term]
+id: SO:0000776
+name: symbiosis_island
+def: "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
+comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.
+synonym: "symbiosis island" EXACT []
+is_a: SO:0000772 ! genomic_island
+
+[Term]
+id: SO:0000777
+name: pseudogenic_rRNA
+def: "A non functional descendant of an rRNA." [SO:ke]
+comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
+subset: SOFA
+synonym: "pseudogenic rRNA" EXACT []
+is_a: SO:0000462 ! pseudogenic_region
+
+[Term]
+id: SO:0000778
+name: pseudogenic_tRNA
+def: "A non functional descendent of a tRNA." [SO:ke]
+comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
+subset: SOFA
+synonym: "pseudogenic tRNA" EXACT []
+is_a: SO:0000462 ! pseudogenic_region
+
+[Term]
+id: SO:0000779
+name: engineered_episome
+def: "An episome that is engineered." [SO:xp]
+comment: Requested by Lynn Crosby Jan 2006.
+synonym: "engineered episome" EXACT []
+is_a: SO:0000637 ! engineered_plasmid
+is_a: SO:0000768 ! episome
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000780
+name: transposable_element_attribute
+comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs
+is_obsolete: true
+
+[Term]
+id: SO:0000781
+name: transgenic
+def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke]
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000782
+name: natural
+def: "An attribute describing a feature that occurs in nature." [SO:ke]
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000783
+name: engineered
+def: "An attribute to describe a region that was modified in vitro." [SO:ke]
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000784
+name: foreign
+def: "An attribute to describe a region from another species." [SO:ke]
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000785
+name: cloned_region
+comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
+synonym: "cloned region" EXACT []
+synonym: "cloned segment" EXACT []
+is_a: SO:0000695 ! reagent
+relationship: part_of SO:0000753 ! clone_insert
+
+[Term]
+id: SO:0000786
+name: reagent_attribute
+comment: Added jan 2006 by KE.
+synonym: "reagent attribute" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000787
+name: clone_attribute
+is_obsolete: true
+
+[Term]
+id: SO:0000788
+name: cloned
+is_obsolete: true
+
+[Term]
+id: SO:0000789
+name: validated
+def: "An attribute to describe a feature that has been proven." [SO:ke]
+is_a: SO:0000905 ! status
+
+[Term]
+id: SO:0000790
+name: invalidated
+def: "An attribute describing a feature that is invalidated." [SO:ke]
+is_a: SO:0000905 ! status
+
+[Term]
+id: SO:0000791
+name: cloned_genomic
+is_obsolete: true
+
+[Term]
+id: SO:0000792
+name: cloned_cDNA
+is_obsolete: true
+
+[Term]
+id: SO:0000793
+name: engineered_DNA
+is_obsolete: true
+
+[Term]
+id: SO:0000794
+name: engineered_rescue_region
+def: "A rescue region that is engineered." [SO:xp]
+synonym: "engineered rescue fragment" EXACT []
+synonym: "engineered rescue region" EXACT []
+synonym: "engineered rescue segment" EXACT []
+is_a: SO:0000411 ! rescue_region
+is_a: SO:0000804 ! engineered_region
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000795
+name: rescue_mini_gene
+def: "A mini_gene that rescues." [SO:xp]
+synonym: "rescue mini gene" EXACT []
+synonym: "rescue mini-gene" EXACT []
+is_a: SO:0000815 ! mini_gene
+relationship: has_quality SO:0000814 ! rescue
+
+[Term]
+id: SO:0000796
+name: transgenic_transposable_element
+def: "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]
+comment: Modified as requested by Lynn - FB. May 2007.
+synonym: "transgenic transposable element" EXACT []
+is_a: SO:0000101 ! transposable_element
+relationship: derives_from SO:0000151 ! clone
+relationship: has_quality SO:0000781 ! transgenic
+
+[Term]
+id: SO:0000797
+name: natural_transposable_element
+def: "TE that exists (or existed) in nature." [FB:mc]
+synonym: "natural transposable element" EXACT []
+is_a: SO:0000101 ! transposable_element
+is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
+relationship: has_quality SO:0000782 ! natural
+
+[Term]
+id: SO:0000798
+name: engineered_transposable_element
+def: "TE that has been modified by manipulations in vitro." [FB:mc]
+synonym: "engineered transposable element" EXACT []
+is_a: SO:0000101 ! transposable_element
+is_a: SO:0000804 ! engineered_region
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000799
+name: engineered_foreign_transposable_element
+def: "A transposable_element that is engineered and foreign." [FB:mc]
+synonym: "engineered foreign transposable element" EXACT []
+is_a: SO:0000720 ! foreign_transposable_element
+is_a: SO:0000798 ! engineered_transposable_element
+is_a: SO:0000805 ! engineered_foreign_region
+relationship: has_quality SO:0000783 ! engineered
+relationship: has_quality SO:0000784 ! foreign
+
+[Term]
+id: SO:0000800
+name: assortment_derived_duplication
+def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]
+synonym: "assortment derived duplication" EXACT []
+is_a: SO:0001504 ! assortment_derived_variation
+
+[Term]
+id: SO:0000801
+name: assortment_derived_deficiency_plus_duplication
+def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]
+synonym: "assortment derived deficiency plus duplication" EXACT []
+is_a: SO:0001504 ! assortment_derived_variation
+
+[Term]
+id: SO:0000802
+name: assortment_derived_deficiency
+def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]
+synonym: "assortment-derived deficiency" EXACT []
+is_a: SO:0001504 ! assortment_derived_variation
+
+[Term]
+id: SO:0000803
+name: assortment_derived_aneuploid
+def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]
+synonym: "assortment derived aneuploid" EXACT []
+is_a: SO:0001504 ! assortment_derived_variation
+
+[Term]
+id: SO:0000804
+name: engineered_region
+def: "A region that is engineered." [SO:xp]
+synonym: "construct" EXACT []
+synonym: "engineered region" EXACT []
+synonym: "engineered sequence" EXACT []
+is_a: SO:0001409 ! biomaterial_region
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000805
+name: engineered_foreign_region
+def: "A region that is engineered and foreign." [SO:xp]
+synonym: "engineered foreign region" EXACT []
+is_a: SO:0000804 ! engineered_region
+relationship: has_quality SO:0000783 ! engineered
+relationship: has_quality SO:0000784 ! foreign
+
+[Term]
+id: SO:0000806
+name: fusion
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000807
+name: engineered_tag
+def: "A tag that is engineered." [SO:xp]
+synonym: "engineered tag" EXACT []
+is_a: SO:0000324 ! tag
+is_a: SO:0000804 ! engineered_region
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000808
+name: validated_cDNA_clone
+def: "A cDNA clone that has been validated." [SO:xp]
+synonym: "validated cDNA clone" EXACT []
+is_a: SO:0000317 ! cDNA_clone
+relationship: has_quality SO:0000789 ! validated
+
+[Term]
+id: SO:0000809
+name: invalidated_cDNA_clone
+def: "A cDNA clone that is invalid." [SO:xp]
+synonym: "invalidated cDNA clone" EXACT []
+is_a: SO:0000317 ! cDNA_clone
+relationship: has_quality SO:0000790 ! invalidated
+
+[Term]
+id: SO:0000810
+name: chimeric_cDNA_clone
+def: "A cDNA clone invalidated because it is chimeric." [SO:xp]
+synonym: "chimeric cDNA clone" EXACT []
+is_a: SO:0000809 ! invalidated_cDNA_clone
+relationship: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA
+
+[Term]
+id: SO:0000811
+name: genomically_contaminated_cDNA_clone
+def: "A cDNA clone invalidated by genomic contamination." [SO:xp]
+synonym: "genomically contaminated cDNA clone" EXACT []
+is_a: SO:0000809 ! invalidated_cDNA_clone
+relationship: has_quality SO:0000414 ! invalidated_by_genomic_contamination
+
+[Term]
+id: SO:0000812
+name: polyA_primed_cDNA_clone
+def: "A cDNA clone invalidated by polyA priming." [SO:xp]
+synonym: "polyA primed cDNA clone" EXACT []
+is_a: SO:0000809 ! invalidated_cDNA_clone
+relationship: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA
+
+[Term]
+id: SO:0000813
+name: partially_processed_cDNA_clone
+def: "A cDNA invalidated clone by partial processing." [SO:xp]
+synonym: "partially processed cDNA clone" EXACT []
+is_a: SO:0000809 ! invalidated_cDNA_clone
+relationship: has_quality SO:0000416 ! invalidated_by_partial_processing
+
+[Term]
+id: SO:0000814
+name: rescue
+def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000815
+name: mini_gene
+def: "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]
+synonym: "mini gene" EXACT []
+is_a: SO:0000236 ! ORF
+
+[Term]
+id: SO:0000816
+name: rescue_gene
+def: "A gene that rescues." [SO:xp]
+synonym: "rescue gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000814 ! rescue
+
+[Term]
+id: SO:0000817
+name: wild_type
+def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]
+synonym: "wild type" EXACT []
+xref: http://en.wikipedia.org/wiki/Wild_type "wiki"
+xref: loinc:LA9658-1 "wild type"
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000818
+name: wild_type_rescue_gene
+def: "A gene that rescues." [SO:xp]
+synonym: "wild type rescue gene" EXACT []
+is_a: SO:0000816 ! rescue_gene
+relationship: has_quality SO:0000817 ! wild_type
+
+[Term]
+id: SO:0000819
+name: mitochondrial_chromosome
+def: "A chromosome originating in a mitochondria." [SO:xp]
+synonym: "mitochondrial chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000737 ! mitochondrial_sequence
+
+[Term]
+id: SO:0000820
+name: chloroplast_chromosome
+def: "A chromosome originating in a chloroplast." [SO:xp]
+synonym: "chloroplast chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000745 ! chloroplast_sequence
+
+[Term]
+id: SO:0000821
+name: chromoplast_chromosome
+def: "A chromosome originating in a chromoplast." [SO:xp]
+synonym: "chromoplast chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000744 ! chromoplast_sequence
+
+[Term]
+id: SO:0000822
+name: cyanelle_chromosome
+def: "A chromosome originating in a cyanelle." [SO:xp]
+synonym: "cyanelle chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000746 ! cyanelle_sequence
+
+[Term]
+id: SO:0000823
+name: leucoplast_chromosome
+def: "A chromosome with origin in a leucoplast." [SO:xp]
+synonym: "leucoplast chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000747 ! leucoplast_sequence
+
+[Term]
+id: SO:0000824
+name: macronuclear_chromosome
+def: "A chromosome originating in a macronucleus." [SO:xp]
+synonym: "macronuclear chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000083 ! macronuclear_sequence
+
+[Term]
+id: SO:0000825
+name: micronuclear_chromosome
+def: "A chromosome originating in a micronucleus." [SO:xp]
+synonym: "micronuclear chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000084 ! micronuclear_sequence
+
+[Term]
+id: SO:0000828
+name: nuclear_chromosome
+def: "A chromosome originating in a nucleus." [SO:xp]
+synonym: "nuclear chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000738 ! nuclear_sequence
+
+[Term]
+id: SO:0000829
+name: nucleomorphic_chromosome
+def: "A chromosome originating in a nucleomorph." [SO:xp]
+synonym: "nucleomorphic chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000739 ! nucleomorphic_sequence
+
+[Term]
+id: SO:0000830
+name: chromosome_part
+def: "A region of a chromosome." [SO:ke]
+comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
+subset: SOFA
+synonym: "chromosome part" EXACT []
+is_a: SO:0001411 ! biological_region
+relationship: part_of SO:0000340 ! chromosome
+
+[Term]
+id: SO:0000831
+name: gene_member_region
+def: "A region of a gene." [SO:ke]
+comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.
+subset: SOFA
+synonym: "gene member region" EXACT []
+is_a: SO:0001411 ! biological_region
+relationship: member_of SO:0000704 ! gene
+
+[Term]
+id: SO:0000832
+name: promoter_region
+def: "A region of sequence which is part of a promoter." [SO:ke]
+comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
+is_obsolete: true
+
+[Term]
+id: SO:0000833
+name: transcript_region
+def: "A region of a transcript." [SO:ke]
+comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
+subset: SOFA
+synonym: "transcript region" EXACT []
+is_a: SO:0001411 ! biological_region
+relationship: part_of SO:0000673 ! transcript
+
+[Term]
+id: SO:0000834
+name: mature_transcript_region
+def: "A region of a mature transcript." [SO:ke]
+comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
+subset: SOFA
+synonym: "mature transcript region" EXACT []
+is_a: SO:0000833 ! transcript_region
+
+[Term]
+id: SO:0000835
+name: primary_transcript_region
+def: "A part of a primary transcript." [SO:ke]
+comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
+subset: SOFA
+synonym: "primary transcript region" EXACT []
+is_a: SO:0000833 ! transcript_region
+relationship: part_of SO:0000185 ! primary_transcript
+
+[Term]
+id: SO:0000836
+name: mRNA_region
+def: "A region of an mRNA." [SO:cb]
+comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
+subset: SOFA
+synonym: "mRNA region" EXACT []
+is_a: SO:0000834 ! mature_transcript_region
+relationship: part_of SO:0000234 ! mRNA
+
+[Term]
+id: SO:0000837
+name: UTR_region
+def: "A region of UTR." [SO:ke]
+comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
+subset: SOFA
+synonym: "UTR region" EXACT []
+is_a: SO:0000836 ! mRNA_region
+
+[Term]
+id: SO:0000838
+name: rRNA_primary_transcript_region
+def: "A region of an rRNA primary transcript." [SO:ke]
+comment: To allow transcribed_spacer_region to have a path to the root.
+synonym: "rRNA primary transcript region" EXACT []
+is_a: SO:0000835 ! primary_transcript_region
+relationship: part_of SO:0000209 ! rRNA_primary_transcript
+
+[Term]
+id: SO:0000839
+name: polypeptide_region
+alt_id: BS:00124
+alt_id: BS:00331
+def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]
+comment: Added to allow the polypeptide regions to have is_a paths back to the root.
+subset: biosapiens
+subset: SOFA
+synonym: "positional" RELATED []
+synonym: "positional polypeptide feature" RELATED []
+synonym: "region" NARROW [uniprot:feature_type]
+synonym: "region or site annotation" RELATED []
+synonym: "site" NARROW [uniprot:feature_type]
+is_a: SO:0001411 ! biological_region
+relationship: part_of SO:0000104 ! polypeptide
+
+[Term]
+id: SO:0000840
+name: repeat_component
+def: "A region of a repeated sequence." [SO:ke]
+comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root.
+synonym: "repeat component" EXACT []
+is_a: SO:0001412 ! topologically_defined_region
+
+[Term]
+id: SO:0000841
+name: spliceosomal_intron_region
+def: "A region within an intron." [SO:ke]
+comment: A terms added to allow the parts of introns to have is_a paths to the root.
+subset: SOFA
+synonym: "spliceosomal intron region" EXACT []
+is_a: SO:0000835 ! primary_transcript_region
+relationship: part_of SO:0000662 ! spliceosomal_intron
+
+[Term]
+id: SO:0000842
+name: gene_component_region
+subset: SOFA
+synonym: "gene component region" EXACT []
+is_a: SO:0001411 ! biological_region
+relationship: part_of SO:0000704 ! gene
+
+[Term]
+id: SO:0000843
+name: bacterial_RNApol_promoter_region
+def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke]
+comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
+is_obsolete: true
+
+[Term]
+id: SO:0000844
+name: RNApol_II_promoter_region
+def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke]
+comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
+is_obsolete: true
+
+[Term]
+id: SO:0000845
+name: RNApol_III_promoter_type_1_region
+def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke]
+comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.
+is_obsolete: true
+
+[Term]
+id: SO:0000846
+name: RNApol_III_promoter_type_2_region
+def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke]
+comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.
+is_obsolete: true
+
+[Term]
+id: SO:0000847
+name: tmRNA_region
+def: "A region of a tmRNA." [SO:cb]
+comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
+synonym: "tmRNA region" EXACT []
+is_a: SO:0000834 ! mature_transcript_region
+relationship: part_of SO:0000584 ! tmRNA
+
+[Term]
+id: SO:0000848
+name: LTR_component
+synonym: "long term repeat component" EXACT []
+synonym: "LTR component" EXACT []
+is_a: SO:0000840 ! repeat_component
+relationship: part_of SO:0000286 ! long_terminal_repeat
+
+[Term]
+id: SO:0000849
+name: three_prime_LTR_component
+synonym: "3' long terminal repeat component" EXACT []
+synonym: "three prime LTR component" EXACT []
+is_a: SO:0000848 ! LTR_component
+relationship: part_of SO:0000426 ! three_prime_LTR
+
+[Term]
+id: SO:0000850
+name: five_prime_LTR_component
+synonym: "5' long term repeat component" EXACT []
+synonym: "five prime LTR component" EXACT []
+is_a: SO:0000848 ! LTR_component
+relationship: part_of SO:0000425 ! five_prime_LTR
+
+[Term]
+id: SO:0000851
+name: CDS_region
+def: "A region of a CDS." [SO:cb]
+subset: SOFA
+synonym: "CDS region" EXACT []
+is_a: SO:0000836 ! mRNA_region
+relationship: part_of SO:0000316 ! CDS
+
+[Term]
+id: SO:0000852
+name: exon_region
+def: "A region of an exon." [RSC:cb]
+subset: SOFA
+synonym: "exon region" EXACT []
+is_a: SO:0000833 ! transcript_region
+relationship: part_of SO:0000147 ! exon
+
+[Term]
+id: SO:0000853
+name: homologous_region
+def: "A region that is homologous to another region." [SO:ke]
+synonym: "homolog" EXACT []
+synonym: "homologous region" EXACT []
+synonym: "homologue" EXACT []
+xref: http://en.wikipedia.org/wiki/Homology_(biology) "wiki"
+is_a: SO:0000330 ! conserved_region
+relationship: has_quality SO:0000857 ! homologous
+
+[Term]
+id: SO:0000854
+name: paralogous_region
+def: "A homologous_region that is paralogous to another region." [SO:ke]
+comment: A term to be used in conjunction with the paralogous_to relationship.
+synonym: "paralog" EXACT []
+synonym: "paralogous region" EXACT []
+synonym: "paralogue" EXACT []
+xref: http://en.wikipedia.org/wiki/Paralog#Paralogy "wiki"
+is_a: SO:0000853 ! homologous_region
+relationship: has_quality SO:0000859 ! paralogous
+
+[Term]
+id: SO:0000855
+name: orthologous_region
+def: "A homologous_region that is orthologous to another region." [SO:ke]
+comment: This term should be used in conjunction with the similarity relationships defined in SO.
+synonym: "ortholog" EXACT []
+synonym: "orthologous region" EXACT []
+synonym: "orthologue" EXACT []
+xref: http://en.wikipedia.org/wiki/Ortholog#Orthology "wiki"
+is_a: SO:0000853 ! homologous_region
+relationship: has_quality SO:0000858 ! orthologous
+
+[Term]
+id: SO:0000856
+name: conserved
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000857
+name: homologous
+def: "Similarity due to common ancestry." [SO:ke]
+is_a: SO:0000856 ! conserved
+
+[Term]
+id: SO:0000858
+name: orthologous
+def: "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]
+is_a: SO:0000857 ! homologous
+
+[Term]
+id: SO:0000859
+name: paralogous
+def: "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]
+is_a: SO:0000857 ! homologous
+
+[Term]
+id: SO:0000860
+name: syntenic
+def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Syntenic "wiki"
+is_a: SO:0000856 ! conserved
+
+[Term]
+id: SO:0000861
+name: capped_primary_transcript
+def: "A primary transcript that is capped." [SO:xp]
+synonym: "capped primary transcript" EXACT []
+is_a: SO:0000185 ! primary_transcript
+relationship: adjacent_to SO:0000581 ! cap
+relationship: has_quality SO:0000146 ! capped
+
+[Term]
+id: SO:0000862
+name: capped_mRNA
+def: "An mRNA that is capped." [SO:xp]
+synonym: "capped mRNA" EXACT []
+is_a: SO:0000234 ! mRNA
+relationship: adjacent_to SO:0000581 ! cap
+relationship: has_quality SO:0000146 ! capped
+
+[Term]
+id: SO:0000863
+name: mRNA_attribute
+def: "An attribute describing an mRNA feature." [SO:ke]
+synonym: "mRNA attribute" EXACT []
+is_a: SO:0000237 ! transcript_attribute
+
+[Term]
+id: SO:0000864
+name: exemplar
+def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]
+is_a: SO:0000863 ! mRNA_attribute
+
+[Term]
+id: SO:0000865
+name: frameshift
+def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Frameshift "wiki"
+is_a: SO:0000863 ! mRNA_attribute
+
+[Term]
+id: SO:0000866
+name: minus_1_frameshift
+def: "A frameshift caused by deleting one base." [SO:ke]
+synonym: "minus 1 frameshift" EXACT []
+is_a: SO:0000865 ! frameshift
+
+[Term]
+id: SO:0000867
+name: minus_2_frameshift
+def: "A frameshift caused by deleting two bases." [SO:ke]
+synonym: "minus 2 frameshift" EXACT []
+is_a: SO:0000865 ! frameshift
+
+[Term]
+id: SO:0000868
+name: plus_1_frameshift
+def: "A frameshift caused by inserting one base." [SO:ke]
+synonym: "plus 1 frameshift" EXACT []
+is_a: SO:0000865 ! frameshift
+
+[Term]
+id: SO:0000869
+name: plus_2_framshift
+def: "A frameshift caused by inserting two bases." [SO:ke]
+synonym: "plus 2 framshift" EXACT []
+is_a: SO:0000865 ! frameshift
+
+[Term]
+id: SO:0000870
+name: trans_spliced
+def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]
+synonym: "trans-spliced" EXACT []
+is_a: SO:0000237 ! transcript_attribute
+
+[Term]
+id: SO:0000871
+name: polyadenylated_mRNA
+def: "An mRNA that is polyadenylated." [SO:xp]
+synonym: "polyadenylated mRNA" EXACT []
+is_a: SO:0000234 ! mRNA
+relationship: adjacent_to SO:0000610 ! polyA_sequence
+relationship: has_quality SO:0000246 ! polyadenylated
+
+[Term]
+id: SO:0000872
+name: trans_spliced_mRNA
+def: "An mRNA that is trans-spliced." [SO:xp]
+synonym: "trans-spliced mRNA" EXACT []
+is_a: SO:0000234 ! mRNA
+is_a: SO:0000479 ! trans_spliced_transcript
+relationship: adjacent_to SO:0000636 ! spliced_leader_RNA
+relationship: has_quality SO:0000870 ! trans_spliced
+
+[Term]
+id: SO:0000873
+name: edited_transcript
+def: "A transcript that is edited." [SO:ke]
+synonym: "edited transcript" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: guided_by SO:0000602 ! guide_RNA
+relationship: has_part SO:0000977 ! anchor_binding_site
+relationship: has_quality SO:0000116 ! edited
+
+[Term]
+id: SO:0000874
+name: edited_transcript_by_A_to_I_substitution
+def: "A transcript that has been edited by A to I substitution." [SO:ke]
+synonym: "edited transcript by A to I substitution" EXACT []
+is_a: SO:0000873 ! edited_transcript
+
+[Term]
+id: SO:0000875
+name: bound_by_protein
+def: "An attribute describing a sequence that is bound by a protein." [SO:ke]
+synonym: "bound by protein" EXACT []
+is_a: SO:0000277 ! bound_by_factor
+
+[Term]
+id: SO:0000876
+name: bound_by_nucleic_acid
+def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]
+synonym: "bound by nucleic acid" EXACT []
+is_a: SO:0000277 ! bound_by_factor
+
+[Term]
+id: SO:0000877
+name: alternatively_spliced
+def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]
+synonym: "alternatively spliced" EXACT []
+is_a: SO:0000237 ! transcript_attribute
+
+[Term]
+id: SO:0000878
+name: monocistronic
+def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke]
+is_a: SO:0000237 ! transcript_attribute
+
+[Term]
+id: SO:0000879
+name: dicistronic
+def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke]
+is_a: SO:0000880 ! polycistronic
+
+[Term]
+id: SO:0000880
+name: polycistronic
+def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]
+is_a: SO:0000237 ! transcript_attribute
+
+[Term]
+id: SO:0000881
+name: recoded
+def: "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]
+is_a: SO:0000863 ! mRNA_attribute
+
+[Term]
+id: SO:0000882
+name: codon_redefined
+def: "An attribute describing the alteration of codon meaning." [SO:ke]
+synonym: "codon redefined" EXACT []
+is_a: SO:0000881 ! recoded
+
+[Term]
+id: SO:0000883
+name: stop_codon_read_through
+def: "A stop codon redefined to be a new amino acid." [SO:ke]
+synonym: "stop codon read through" EXACT []
+synonym: "stop codon readthrough" RELATED []
+is_a: SO:0000145 ! recoded_codon
+
+[Term]
+id: SO:0000884
+name: stop_codon_redefined_as_pyrrolysine
+def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]
+synonym: "stop codon redefined as pyrrolysine" EXACT []
+is_a: SO:0000883 ! stop_codon_read_through
+
+[Term]
+id: SO:0000885
+name: stop_codon_redefined_as_selenocysteine
+def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]
+synonym: "stop codon redefined as selenocysteine" EXACT []
+is_a: SO:0000883 ! stop_codon_read_through
+
+[Term]
+id: SO:0000886
+name: recoded_by_translational_bypass
+def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke]
+synonym: "recoded by translational bypass" EXACT []
+is_a: SO:0000881 ! recoded
+
+[Term]
+id: SO:0000887
+name: translationally_frameshifted
+def: "Recoding by frameshifting a particular site." [SO:ke]
+synonym: "translationally frameshifted" EXACT []
+is_a: SO:0000881 ! recoded
+
+[Term]
+id: SO:0000888
+name: maternally_imprinted_gene
+def: "A gene that is maternally_imprinted." [SO:xp]
+synonym: "maternally imprinted gene" EXACT []
+is_a: SO:0000898 ! epigenetically_modified_gene
+relationship: has_quality SO:0000135 ! maternally_imprinted
+
+[Term]
+id: SO:0000889
+name: paternally_imprinted_gene
+def: "A gene that is paternally imprinted." [SO:xp]
+synonym: "paternally imprinted gene" EXACT []
+is_a: SO:0000898 ! epigenetically_modified_gene
+relationship: has_quality SO:0000136 ! paternally_imprinted
+
+[Term]
+id: SO:0000890
+name: post_translationally_regulated_gene
+def: "A gene that is post translationally regulated." [SO:xp]
+synonym: "post translationally regulated gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000130 ! post_translationally_regulated
+
+[Term]
+id: SO:0000891
+name: negatively_autoregulated_gene
+def: "A gene that is negatively autoreguated." [SO:xp]
+synonym: "negatively autoregulated gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000473 ! negatively_autoregulated
+
+[Term]
+id: SO:0000892
+name: positively_autoregulated_gene
+def: "A gene that is positively autoregulated." [SO:xp]
+synonym: "positively autoregulated gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000475 ! positively_autoregulated
+
+[Term]
+id: SO:0000893
+name: silenced
+def: "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Silenced "wiki"
+is_a: SO:0000126 ! transcriptionally_repressed
+
+[Term]
+id: SO:0000894
+name: silenced_by_DNA_modification
+def: "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]
+synonym: "silenced by DNA modification" EXACT []
+is_a: SO:0000893 ! silenced
+
+[Term]
+id: SO:0000895
+name: silenced_by_DNA_methylation
+def: "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]
+synonym: "silenced by DNA methylation" EXACT []
+is_a: SO:0000894 ! silenced_by_DNA_modification
+
+[Term]
+id: SO:0000896
+name: translationally_regulated_gene
+def: "A gene that is translationally regulated." [SO:xp]
+synonym: "translationally regulated gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000131 ! translationally_regulated
+
+[Term]
+id: SO:0000897
+name: allelically_excluded_gene
+def: "A gene that is allelically_excluded." [SO:xp]
+synonym: "allelically excluded gene" EXACT []
+is_a: SO:0000898 ! epigenetically_modified_gene
+relationship: has_quality SO:0000137 ! allelically_excluded
+
+[Term]
+id: SO:0000898
+name: epigenetically_modified_gene
+def: "A gene that is epigenetically modified." [SO:ke]
+synonym: "epigenetically modified gene" EXACT []
+is_a: SO:0000704 ! gene
+is_a: SO:0001720 ! epigenetically_modified_region
+relationship: has_quality SO:0000133 ! epigenetically_modified
+
+[Term]
+id: SO:0000899
+name: nuclear_mitochondrial
+def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke]
+synonym: "nuclear mitochondrial" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000900
+name: processed
+def: "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke]
+is_obsolete: true
+
+[Term]
+id: SO:0000901
+name: unequally_crossed_over
+def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke]
+synonym: "unequally crossed over" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000902
+name: transgene
+def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]
+xref: http://en.wikipedia.org/wiki/Transgene "wiki"
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000781 ! transgenic
+
+[Term]
+id: SO:0000903
+name: endogenous_retroviral_sequence
+synonym: "endogenous retroviral sequence" EXACT []
+is_a: SO:0000751 ! proviral_location
+
+[Term]
+id: SO:0000904
+name: rearranged_at_DNA_level
+def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]
+synonym: "rearranged at DNA level" EXACT []
+is_a: SO:0000133 ! epigenetically_modified
+
+[Term]
+id: SO:0000905
+name: status
+def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke]
+comment: This term is the hypernym of attributes and should not be annotated to.
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000906
+name: independently_known
+def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke]
+synonym: "independently known" EXACT []
+is_a: SO:0000905 ! status
+
+[Term]
+id: SO:0000907
+name: supported_by_sequence_similarity
+def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]
+synonym: "supported by sequence similarity" EXACT []
+is_a: SO:0000732 ! predicted
+
+[Term]
+id: SO:0000908
+name: supported_by_domain_match
+def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]
+synonym: "supported by domain match" EXACT []
+is_a: SO:0000907 ! supported_by_sequence_similarity
+
+[Term]
+id: SO:0000909
+name: supported_by_EST_or_cDNA
+def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]
+synonym: "supported by EST or cDNA" EXACT []
+is_a: SO:0000907 ! supported_by_sequence_similarity
+
+[Term]
+id: SO:0000910
+name: orphan
+is_a: SO:0000732 ! predicted
+
+[Term]
+id: SO:0000911
+name: predicted_by_ab_initio_computation
+def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]
+synonym: "predicted by ab initio computation" EXACT []
+is_a: SO:0000732 ! predicted
+
+[Term]
+id: SO:0000912
+name: asx_turn
+alt_id: BS:00203
+def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "asx turn" EXACT []
+is_a: SO:0001128 ! polypeptide_turn_motif
+
+[Term]
+id: SO:0000913
+name: cloned_cDNA_insert
+def: "A clone insert made from cDNA." [SO:xp]
+synonym: "cloned cDNA insert" EXACT []
+is_a: SO:0000753 ! clone_insert
+relationship: has_quality SO:0000756 ! cDNA
+
+[Term]
+id: SO:0000914
+name: cloned_genomic_insert
+def: "A clone insert made from genomic DNA." [SO:xp]
+synonym: "cloned genomic insert" EXACT []
+is_a: SO:0000753 ! clone_insert
+relationship: has_quality SO:0000991 ! genomic_DNA
+
+[Term]
+id: SO:0000915
+name: engineered_insert
+def: "A clone insert that is engineered." [SO:xp]
+synonym: "engineered insert" EXACT []
+is_a: SO:0000753 ! clone_insert
+is_a: SO:0000804 ! engineered_region
+relationship: has_quality SO:0000783 ! engineered
+
+[Term]
+id: SO:0000916
+name: edit_operation
+synonym: "edit operation" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000917
+name: insert_U
+def: "An edit to insert a U." [SO:ke]
+comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
+synonym: "insert U" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000918
+name: delete_U
+def: "An edit to delete a uridine." [SO:ke]
+comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
+synonym: "delete U" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000919
+name: substitute_A_to_I
+def: "An edit to substitute an I for an A." [SO:ke]
+synonym: "substitute A to I" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000920
+name: insert_C
+def: "An edit to insert a cytidine." [SO:ke]
+synonym: "insert C" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000921
+name: insert_dinucleotide
+def: "An edit to insert a dinucleotide." [SO:ke]
+synonym: "insert dinucleotide" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000922
+name: substitute_C_to_U
+def: "An edit to substitute an U for a C." [SO:ke]
+synonym: "substitute C to U" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000923
+name: insert_G
+def: "An edit to insert a G." [SO:ke]
+synonym: "insert G" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000924
+name: insert_GC
+def: "An edit to insert a GC dinucleotide." [SO:ke]
+comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
+synonym: "insert GC" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000925
+name: insert_GU
+def: "An edit to insert a GU dinucleotide." [SO:ke]
+comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
+synonym: "insert GU" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000926
+name: insert_CU
+def: "An edit to insert a CU dinucleotide." [SO:ke]
+comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
+synonym: "insert CU" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000927
+name: insert_AU
+def: "An edit to insert a AU dinucleotide." [SO:ke]
+comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
+synonym: "insert AU" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000928
+name: insert_AA
+def: "An edit to insert a AA dinucleotide." [SO:ke]
+comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
+synonym: "insert AA" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000929
+name: edited_mRNA
+def: "An mRNA that is edited." [SO:xp]
+synonym: "edited mRNA" EXACT []
+is_a: SO:0000234 ! mRNA
+is_a: SO:0000873 ! edited_transcript
+relationship: has_quality SO:0000116 ! edited
+
+[Term]
+id: SO:0000930
+name: guide_RNA_region
+def: "A region of guide RNA." [SO:ma]
+synonym: "guide RNA region" EXACT []
+is_a: SO:0000834 ! mature_transcript_region
+relationship: part_of SO:0000602 ! guide_RNA
+
+[Term]
+id: SO:0000931
+name: anchor_region
+def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]
+synonym: "anchor region" EXACT []
+is_a: SO:0000930 ! guide_RNA_region
+
+[Term]
+id: SO:0000932
+name: pre_edited_mRNA
+synonym: "pre-edited mRNA" EXACT []
+is_a: SO:0000120 ! protein_coding_primary_transcript
+
+[Term]
+id: SO:0000933
+name: intermediate
+def: "An attribute to describe a feature between stages of processing." [SO:ke]
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000934
+name: miRNA_target_site
+def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]
+synonym: "miRNA target site" EXACT []
+is_a: SO:0001655 ! nucleotide_binding_site
+
+[Term]
+id: SO:0000935
+name: edited_CDS
+def: "A CDS that is edited." [SO:xp]
+synonym: "edited CDS" EXACT []
+is_a: SO:0000316 ! CDS
+relationship: has_quality SO:0000116 ! edited
+
+[Term]
+id: SO:0000936
+name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
+synonym: "vertebrate immunoglobulin T cell receptor rearranged segment" EXACT []
+is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
+
+[Term]
+id: SO:0000937
+name: vertebrate_immune_system_feature
+is_obsolete: true
+
+[Term]
+id: SO:0000938
+name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
+synonym: "vertebrate immunoglobulin T cell receptor rearranged gene cluster" EXACT []
+is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
+
+[Term]
+id: SO:0000939
+name: vertebrate_immune_system_gene_recombination_signal_feature
+synonym: "vertebrate immune system gene recombination signal feature" EXACT []
+is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
+
+[Term]
+id: SO:0000940
+name: recombinationally_rearranged
+synonym: "recombinationally rearranged" EXACT []
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000941
+name: recombinationally_rearranged_vertebrate_immune_system_gene
+def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]
+synonym: "recombinationally rearranged vertebrate immune system gene" EXACT []
+is_a: SO:0000456 ! recombinationally_rearranged_gene
+
+[Term]
+id: SO:0000942
+name: attP_site
+def: "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]
+synonym: "attP site" EXACT []
+is_a: SO:0000946 ! integration_excision_site
+relationship: part_of SO:0001042 ! phage_sequence
+
+[Term]
+id: SO:0000943
+name: attB_site
+def: "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]
+synonym: "attB site" EXACT []
+is_a: SO:0000946 ! integration_excision_site
+
+[Term]
+id: SO:0000944
+name: attL_site
+def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]
+synonym: "attBP'" RELATED []
+synonym: "attL site" RELATED []
+is_a: SO:0000946 ! integration_excision_site
+
+[Term]
+id: SO:0000945
+name: attR_site
+def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]
+synonym: "attPB'" RELATED []
+synonym: "attR site" EXACT []
+is_a: SO:0000946 ! integration_excision_site
+
+[Term]
+id: SO:0000946
+name: integration_excision_site
+def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]
+synonym: "attachment site" RELATED []
+synonym: "integration excision site" EXACT []
+is_a: SO:0000342 ! site_specific_recombination_target_region
+
+[Term]
+id: SO:0000947
+name: resolution_site
+def: "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]
+synonym: "res site" EXACT []
+synonym: "resolution site" EXACT []
+is_a: SO:0000342 ! site_specific_recombination_target_region
+
+[Term]
+id: SO:0000948
+name: inversion_site
+def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]
+comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
+synonym: "inversion site" EXACT []
+is_a: SO:0000342 ! site_specific_recombination_target_region
+
+[Term]
+id: SO:0000949
+name: dif_site
+def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]
+synonym: "dif site" EXACT []
+is_a: SO:0000947 ! resolution_site
+
+[Term]
+id: SO:0000950
+name: attC_site
+def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]
+synonym: "attC site" EXACT []
+is_a: SO:0000946 ! integration_excision_site
+relationship: part_of SO:0000365 ! integron
+
+[Term]
+id: SO:0000951
+name: eukaryotic_terminator
+synonym: "eukaryotic terminator" EXACT []
+is_a: SO:0000141 ! terminator
+
+[Term]
+id: SO:0000952
+name: oriV
+def: "An origin of vegetative replication in plasmids and phages." [SO:as]
+synonym: "origin of vegetative replication" EXACT []
+is_a: SO:0000296 ! origin_of_replication
+
+[Term]
+id: SO:0000953
+name: oriC
+def: "An origin of bacterial chromosome replication." [SO:as]
+synonym: "origin of bacterial chromosome replication" EXACT []
+is_a: SO:0000296 ! origin_of_replication
+
+[Term]
+id: SO:0000954
+name: DNA_chromosome
+def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma]
+synonym: "DNA chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_quality SO:0000352 ! DNA
+
+[Term]
+id: SO:0000955
+name: double_stranded_DNA_chromosome
+def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]
+synonym: "double stranded DNA chromosome" EXACT []
+is_a: SO:0000954 ! DNA_chromosome
+relationship: has_quality SO:0000985 ! double
+
+[Term]
+id: SO:0000956
+name: single_stranded_DNA_chromosome
+def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]
+synonym: "single stranded DNA chromosome" EXACT []
+is_a: SO:0000954 ! DNA_chromosome
+relationship: has_quality SO:0000984 ! single
+
+[Term]
+id: SO:0000957
+name: linear_double_stranded_DNA_chromosome
+def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]
+synonym: "linear double stranded DNA chromosome" EXACT []
+is_a: SO:0000955 ! double_stranded_DNA_chromosome
+relationship: has_quality SO:0000987 ! linear
+
+[Term]
+id: SO:0000958
+name: circular_double_stranded_DNA_chromosome
+def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]
+synonym: "circular double stranded DNA chromosome" EXACT []
+is_a: SO:0000955 ! double_stranded_DNA_chromosome
+relationship: has_quality SO:0000988 ! circular
+
+[Term]
+id: SO:0000959
+name: linear_single_stranded_DNA_chromosome
+def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]
+synonym: "linear single stranded DNA chromosome" EXACT []
+is_a: SO:0000956 ! single_stranded_DNA_chromosome
+relationship: has_quality SO:0000987 ! linear
+
+[Term]
+id: SO:0000960
+name: circular_single_stranded_DNA_chromosome
+def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
+synonym: "circular single stranded DNA chromosome" EXACT []
+is_a: SO:0000956 ! single_stranded_DNA_chromosome
+relationship: has_quality SO:0000988 ! circular
+
+[Term]
+id: SO:0000961
+name: RNA_chromosome
+def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma]
+synonym: "RNA chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_quality SO:0000356 ! RNA
+
+[Term]
+id: SO:0000962
+name: single_stranded_RNA_chromosome
+def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]
+synonym: "single stranded RNA chromosome" EXACT []
+is_a: SO:0000961 ! RNA_chromosome
+relationship: has_quality SO:0000984 ! single
+
+[Term]
+id: SO:0000963
+name: linear_single_stranded_RNA_chromosome
+def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]
+synonym: "linear single stranded RNA chromosome" EXACT []
+is_a: SO:0000962 ! single_stranded_RNA_chromosome
+relationship: has_quality SO:0000987 ! linear
+
+[Term]
+id: SO:0000964
+name: linear_double_stranded_RNA_chromosome
+def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]
+synonym: "linear double stranded RNA chromosome" EXACT []
+is_a: SO:0000965 ! double_stranded_RNA_chromosome
+relationship: has_quality SO:0000987 ! linear
+
+[Term]
+id: SO:0000965
+name: double_stranded_RNA_chromosome
+def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]
+synonym: "double stranded RNA chromosome" EXACT []
+is_a: SO:0000961 ! RNA_chromosome
+relationship: has_quality SO:0000985 ! double
+
+[Term]
+id: SO:0000966
+name: circular_single_stranded_RNA_chromosome
+def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
+synonym: "circular single stranded RNA chromosome" EXACT []
+is_a: SO:0000962 ! single_stranded_RNA_chromosome
+relationship: has_quality SO:0000988 ! circular
+
+[Term]
+id: SO:0000967
+name: circular_double_stranded_RNA_chromosome
+def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]
+synonym: "circular double stranded RNA chromosome" EXACT []
+is_a: SO:0000965 ! double_stranded_RNA_chromosome
+relationship: has_quality SO:0000988 ! circular
+
+[Term]
+id: SO:0000968
+name: sequence_replication_mode
+comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
+synonym: "sequence replication mode" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000969
+name: rolling_circle
+comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581.
+synonym: "rolling circle" EXACT []
+xref: http://en.wikipedia.org/wiki/Rolling_circle "wiki"
+is_obsolete: true
+
+[Term]
+id: SO:0000970
+name: theta_replication
+comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582
+synonym: "theta replication" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000971
+name: DNA_replication_mode
+comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260.
+synonym: "DNA replication mode" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000972
+name: RNA_replication_mode
+comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
+synonym: "RNA replication mode" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0000973
+name: insertion_sequence
+def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]
+synonym: "insertion sequence" EXACT []
+synonym: "IS" RELATED []
+xref: http://en.wikipedia.org/wiki/Insertion_sequence "wiki"
+is_a: SO:0000208 ! terminal_inverted_repeat_element
+
+[Term]
+id: SO:0000975
+name: minicircle_gene
+synonym: "minicircle gene" EXACT []
+is_a: SO:0000089 ! kinetoplast_gene
+relationship: part_of SO:0000980 ! minicircle
+
+[Term]
+id: SO:0000976
+name: cryptic
+def: "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke]
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000977
+name: anchor_binding_site
+comment: Part of an edited transcript only.
+synonym: "anchor binding site" EXACT []
+is_a: SO:0000833 ! transcript_region
+
+[Term]
+id: SO:0000978
+name: template_region
+def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]
+synonym: "information region" EXACT []
+synonym: "template region" EXACT []
+is_a: SO:0000930 ! guide_RNA_region
+
+[Term]
+id: SO:0000979
+name: gRNA_encoding
+def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma]
+synonym: "gRNA encoding" EXACT []
+is_a: SO:0000011 ! non_protein_coding
+
+[Term]
+id: SO:0000980
+name: minicircle
+alt_id: SO:0000974
+def: "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]
+synonym: "minicircle_chromosome" EXACT []
+xref: http://en.wikipedia.org/wiki/Minicircle "wiki"
+is_a: SO:0001235 ! replicon
+
+[Term]
+id: SO:0000981
+name: rho_dependent_bacterial_terminator
+synonym: "rho dependent bacterial terminator" EXACT []
+is_a: SO:0000614 ! bacterial_terminator
+
+[Term]
+id: SO:0000982
+name: rho_independent_bacterial_terminator
+synonym: "rho independent bacterial terminator" EXACT []
+is_a: SO:0000614 ! bacterial_terminator
+
+[Term]
+id: SO:0000983
+name: strand_attribute
+comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
+synonym: "strand attribute" EXACT []
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0000984
+name: single
+comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
+is_a: SO:0000983 ! strand_attribute
+
+[Term]
+id: SO:0000985
+name: double
+comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
+is_a: SO:0000983 ! strand_attribute
+
+[Term]
+id: SO:0000986
+name: topology_attribute
+comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
+synonym: "topology attribute" EXACT []
+is_a: SO:0000443 ! polymer_attribute
+
+[Term]
+id: SO:0000987
+name: linear
+def: "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]
+comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
+synonym: "two-ended" RELATED []
+is_a: SO:0000986 ! topology_attribute
+disjoint_from: SO:0000988 ! circular
+
+[Term]
+id: SO:0000988
+name: circular
+def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]
+comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
+synonym: "zero-ended" RELATED []
+is_a: SO:0000986 ! topology_attribute
+
+[Term]
+id: SO:0000989
+name: class_II_RNA
+def: "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]
+synonym: "class II RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000990
+name: class_I_RNA
+def: "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]
+comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
+synonym: "class I RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0000991
+name: genomic_DNA
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "genomic DNA" EXACT []
+is_a: SO:0000352 ! DNA
+
+[Term]
+id: SO:0000992
+name: BAC_cloned_genomic_insert
+comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006.
+synonym: "BAC cloned genomic insert" EXACT []
+is_a: SO:0000914 ! cloned_genomic_insert
+relationship: derives_from SO:0000153 ! BAC
+
+[Term]
+id: SO:0000993
+name: consensus
+comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.
+is_a: SO:0000905 ! status
+
+[Term]
+id: SO:0000994
+name: consensus_region
+comment: DO not obsolete without considering MGED mapping.
+synonym: "consensus region" EXACT []
+is_a: SO:0001410 ! experimental_feature
+relationship: has_quality SO:0000993 ! consensus
+
+[Term]
+id: SO:0000995
+name: consensus_mRNA
+comment: DO not obsolete without considering MGED mapping.
+synonym: "consensus mRNA" EXACT []
+is_a: SO:0000234 ! mRNA
+is_a: SO:0000994 ! consensus_region
+relationship: has_quality SO:0000993 ! consensus
+
+[Term]
+id: SO:0000996
+name: predicted_gene
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "predicted gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000732 ! predicted
+
+[Term]
+id: SO:0000997
+name: gene_fragment
+comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
+synonym: "gene fragment" EXACT []
+is_a: SO:0000842 ! gene_component_region
+relationship: has_quality SO:0000731 ! fragmentary
+
+[Term]
+id: SO:0000998
+name: recursive_splice_site
+def: "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]
+synonym: "recursive splice site" EXACT []
+is_a: SO:0001419 ! cis_splice_site
+
+[Term]
+id: SO:0000999
+name: BAC_end
+def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]
+comment: Requested by Keith Boroevich December, 2006.
+synonym: "BAC end" EXACT []
+synonym: "BAC end sequence" EXACT []
+synonym: "BES" EXACT []
+is_a: SO:0000150 ! read
+relationship: part_of SO:0000153 ! BAC
+
+[Term]
+id: SO:0001000
+name: rRNA_16S
+def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]
+subset: SOFA
+synonym: "16S ribosomal RNA" EXACT []
+synonym: "16S rRNA" RELATED []
+synonym: "16S SSU RNA" EXACT []
+synonym: "rRNA 16S" EXACT []
+xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki"
+is_a: SO:0000650 ! small_subunit_rRNA
+
+[Term]
+id: SO:0001001
+name: rRNA_23S
+def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]
+subset: SOFA
+synonym: "23S LSU rRNA" EXACT []
+synonym: "23S ribosomal RNA" RELATED []
+synonym: "23S rRNA" EXACT []
+synonym: "rRNA 23S" EXACT []
+is_a: SO:0000651 ! large_subunit_rRNA
+
+[Term]
+id: SO:0001002
+name: rRNA_25S
+def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]
+subset: SOFA
+synonym: "25S LSU rRNA" EXACT []
+synonym: "25S ribosomal RNA" EXACT []
+synonym: "25S rRNA" EXACT []
+synonym: "rRNA 25S" EXACT []
+is_a: SO:0000651 ! large_subunit_rRNA
+
+[Term]
+id: SO:0001003
+name: solo_LTR
+def: "A recombination product between the 2 LTR of the same element." [SO:ke]
+comment: Requested by Hadi Quesneville January 2007.
+synonym: "solo LTR" EXACT []
+is_a: SO:0000286 ! long_terminal_repeat
+
+[Term]
+id: SO:0001004
+name: low_complexity
+synonym: "low complexity" EXACT []
+is_a: SO:0000905 ! status
+
+[Term]
+id: SO:0001005
+name: low_complexity_region
+synonym: "low complexity region" EXACT []
+is_a: SO:0001410 ! experimental_feature
+relationship: has_quality SO:0001004 ! low_complexity
+
+[Term]
+id: SO:0001006
+name: prophage
+def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." [GOC:jl]
+xref: http://en.wikipedia.org/wiki/Prophage "wiki"
+is_a: SO:0000113 ! proviral_region
+
+[Term]
+id: SO:0001007
+name: cryptic_prophage
+def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [GOC:jl]
+comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
+synonym: "cryptic prophage" EXACT []
+xref: http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w
+is_a: SO:0000772 ! genomic_island
+
+[Term]
+id: SO:0001008
+name: tetraloop
+def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Tetraloop "wiki"
+is_a: SO:0000313 ! stem_loop
+
+[Term]
+id: SO:0001009
+name: DNA_constraint_sequence
+def: "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\]&dispmax=50]
+synonym: "DNA constraint" EXACT []
+synonym: "DNA constraint sequence" EXACT []
+is_a: SO:0000442 ! ds_oligo
+
+[Term]
+id: SO:0001010
+name: i_motif
+def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]
+synonym: "i motif" EXACT []
+synonym: "short intercalated motif" EXACT []
+is_a: SO:0000142 ! DNA_sequence_secondary_structure
+
+[Term]
+id: SO:0001011
+name: PNA_oligo
+def: "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]
+synonym: "peptide nucleic acid" EXACT []
+synonym: "PNA oligo" EXACT []
+xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid "wiki"
+is_a: SO:0001247 ! synthetic_oligo
+relationship: has_quality SO:0001184 ! PNA
+
+[Term]
+id: SO:0001012
+name: DNAzyme
+def: "A DNA sequence with catalytic activity." [SO:cb]
+comment: Added by request from Colin Batchelor.
+synonym: "catalytic DNA" EXACT []
+synonym: "deoxyribozyme" RELATED []
+synonym: "DNA enzyme" EXACT []
+is_a: SO:0000696 ! oligo
+relationship: has_quality SO:0001185 ! enzymatic
+
+[Term]
+id: SO:0001013
+name: MNP
+def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]
+synonym: "multiple nucleotide polymorphism" RELATED []
+is_a: SO:0002007 ! MNV
+
+[Term]
+id: SO:0001014
+name: intron_domain
+comment: Requested by Colin Batchelor, Feb 2007.
+synonym: "intron domain" EXACT []
+is_a: SO:0000835 ! primary_transcript_region
+relationship: part_of SO:0000188 ! intron
+
+[Term]
+id: SO:0001015
+name: wobble_base_pair
+def: "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]
+synonym: "wobble base pair" EXACT []
+synonym: "wobble pair" EXACT []
+xref: http://en.wikipedia.org/wiki/Wobble_base_pair "wiki"
+is_a: SO:0000028 ! base_pair
+
+[Term]
+id: SO:0001016
+name: internal_guide_sequence
+def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]
+synonym: "IGS" EXACT []
+synonym: "internal guide sequence" EXACT []
+is_a: SO:0001014 ! intron_domain
+relationship: part_of SO:0000587 ! group_I_intron
+
+[Term]
+id: SO:0001017
+name: silent_mutation
+def: "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke]
+comment: Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.
+synonym: "silent mutation" EXACT []
+xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
+xref: loinc:LA6700-4 "Silent"
+is_a: SO:0001878 ! feature_variant
+
+[Term]
+id: SO:0001018
+name: epitope
+def: "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]
+comment: Requested by Trish Whetzel.
+xref: http://en.wikipedia.org/wiki/Epitope "wiki"
+is_a: SO:0000409 ! binding_site
+
+[Term]
+id: SO:0001019
+name: copy_number_variation
+def: "A variation that increases or decreases the copy number of a given region." [SO:ke]
+subset: SOFA
+synonym: "CNP" EXACT []
+synonym: "CNV" EXACT []
+synonym: "copy number polymorphism" EXACT []
+synonym: "copy number variation" EXACT []
+xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki"
+is_a: SO:0001059 ! sequence_alteration
+
+[Term]
+id: SO:0001020
+name: sequence_variant_affecting_copy_number
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting copy number" EXACT []
+synonym: "sequence variant affecting copy number" EXACT []
+is_obsolete: true
+replaced_by: SO:0001563
+
+[Term]
+id: SO:0001021
+name: chromosome_breakpoint
+alt_id: SO:0001242
+synonym: "aberration breakpoint" EXACT []
+synonym: "aberration_junction" EXACT []
+synonym: "chromosome breakpoint" EXACT []
+is_a: SO:0000699 ! junction
+relationship: part_of SO:0000340 ! chromosome
+
+[Term]
+id: SO:0001022
+name: inversion_breakpoint
+def: "The point within a chromosome where an inversion begins or ends." [SO:cb]
+synonym: "inversion breakpoint" EXACT []
+is_a: SO:0001021 ! chromosome_breakpoint
+
+[Term]
+id: SO:0001023
+name: allele
+def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]
+synonym: "allelomorph" EXACT []
+xref: http://en.wikipedia.org/wiki/Allele "wiki"
+is_a: SO:0001507 ! variant_collection
+relationship: variant_of SO:0000704 ! gene
+
+[Term]
+id: SO:0001024
+name: haplotype
+def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]
+xref: http://en.wikipedia.org/wiki/Haplotype "wiki"
+is_a: SO:0001507 ! variant_collection
+relationship: variant_of SO:0000355 ! haplotype_block
+
+[Term]
+id: SO:0001025
+name: polymorphic_sequence_variant
+def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]
+synonym: "polymorphic sequence variant" EXACT []
+is_a: SO:0001023 ! allele
+
+[Term]
+id: SO:0001026
+name: genome
+def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]
+xref: http://en.wikipedia.org/wiki/Genome "wiki"
+is_a: SO:0001260 ! sequence_collection
+relationship: has_part SO:0001235 ! replicon
+
+[Term]
+id: SO:0001027
+name: genotype
+def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]
+xref: http://en.wikipedia.org/wiki/Genotype "wiki"
+is_a: SO:0001507 ! variant_collection
+relationship: variant_of SO:0001026 ! genome
+
+[Term]
+id: SO:0001028
+name: diplotype
+def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]
+is_a: SO:0001507 ! variant_collection
+
+[Term]
+id: SO:0001029
+name: direction_attribute
+synonym: "direction attribute" EXACT []
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0001030
+name: forward
+def: "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]
+is_a: SO:0001029 ! direction_attribute
+
+[Term]
+id: SO:0001031
+name: reverse
+def: "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke]
+is_a: SO:0001029 ! direction_attribute
+
+[Term]
+id: SO:0001032
+name: mitochondrial_DNA
+comment: This terms is used by MO.
+synonym: "mitochondrial DNA" EXACT []
+synonym: "mtDNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA "wiki"
+is_a: SO:0000737 ! mitochondrial_sequence
+relationship: has_quality SO:0000352 ! DNA
+
+[Term]
+id: SO:0001033
+name: chloroplast_DNA
+comment: This term is used by MO.
+synonym: "chloroplast DNA" EXACT []
+is_a: SO:0000745 ! chloroplast_sequence
+relationship: has_quality SO:0000352 ! DNA
+
+[Term]
+id: SO:0001034
+name: miRtron
+def: "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]
+comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
+is_a: SO:0001014 ! intron_domain
+relationship: has_part SO:0001244 ! pre_miRNA
+
+[Term]
+id: SO:0001035
+name: piRNA
+def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]
+synonym: "piwi-associated RNA" EXACT []
+xref: http://en.wikipedia.org/wiki/PiRNA "wiki"
+is_a: SO:0000655 ! ncRNA
+
+[Term]
+id: SO:0001036
+name: arginyl_tRNA
+def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]
+synonym: "arginyl tRNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript
+
+[Term]
+id: SO:0001037
+name: mobile_genetic_element
+def: "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]
+subset: SOFA
+synonym: "MGE" EXACT []
+synonym: "mobile genetic element" EXACT []
+xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki"
+is_a: SO:0001411 ! biological_region
+relationship: has_quality SO:0001234 ! mobile
+
+[Term]
+id: SO:0001038
+name: extrachromosomal_mobile_genetic_element
+def: "An MGE that is not integrated into the host chromosome." [SO:ke]
+synonym: "extrachromosomal mobile genetic element" EXACT []
+is_a: SO:0001037 ! mobile_genetic_element
+
+[Term]
+id: SO:0001039
+name: integrated_mobile_genetic_element
+def: "An MGE that is integrated into the host chromosome." [SO:ke]
+subset: SOFA
+synonym: "integrated mobile genetic element" EXACT []
+is_a: SO:0001037 ! mobile_genetic_element
+
+[Term]
+id: SO:0001040
+name: integrated_plasmid
+def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke]
+synonym: "integrated plasmid" EXACT []
+is_a: SO:0001039 ! integrated_mobile_genetic_element
+relationship: derives_from SO:0000155 ! plasmid
+
+[Term]
+id: SO:0001041
+name: viral_sequence
+def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]
+comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
+synonym: "viral sequence" EXACT []
+synonym: "virus sequence" EXACT []
+is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
+is_a: SO:0001235 ! replicon
+
+[Term]
+id: SO:0001042
+name: phage_sequence
+def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke]
+synonym: "bacteriophage" EXACT []
+synonym: "phage" EXACT []
+synonym: "phage sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Bacteriophage "wiki"
+is_a: SO:0001041 ! viral_sequence
+
+[Term]
+id: SO:0001043
+name: attCtn_site
+def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]
+synonym: "attCtn site" EXACT []
+is_a: SO:0000946 ! integration_excision_site
+relationship: part_of SO:0000371 ! conjugative_transposon
+
+[Term]
+id: SO:0001044
+name: nuclear_mt_pseudogene
+def: "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]
+comment: Definition change requested by Val, 3172757.
+synonym: "nuclear mitochondrial pseudogene" EXACT []
+synonym: "nuclear mt pseudogene" EXACT []
+synonym: "NUMT" EXACT []
+xref: http://en.wikipedia.org/wiki/Numt "wikipedia"
+is_a: SO:0001760 ! non_processed_pseudogene
+
+[Term]
+id: SO:0001045
+name: cointegrated_plasmid
+def: "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]
+synonym: "cointegrated plasmid" EXACT []
+synonym: "cointegrated replicon" EXACT []
+is_a: SO:0001039 ! integrated_mobile_genetic_element
+
+[Term]
+id: SO:0001046
+name: IRLinv_site
+def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]
+synonym: "IRLinv site" EXACT []
+is_a: SO:0001048 ! inversion_site_part
+relationship: part_of SO:0000948 ! inversion_site
+
+[Term]
+id: SO:0001047
+name: IRRinv_site
+def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]
+synonym: "IRRinv site" EXACT []
+is_a: SO:0001048 ! inversion_site_part
+relationship: part_of SO:0000948 ! inversion_site
+
+[Term]
+id: SO:0001048
+name: inversion_site_part
+def: "A region located within an inversion site." [SO:ke]
+comment: A term created to allow the parts of an inversion site have an is_a path back to the root.
+synonym: "inversion site part" EXACT []
+is_a: SO:0000342 ! site_specific_recombination_target_region
+
+[Term]
+id: SO:0001049
+name: defective_conjugative_transposon
+def: "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]
+synonym: "defective conjugative transposon" EXACT []
+is_a: SO:0000772 ! genomic_island
+
+[Term]
+id: SO:0001050
+name: repeat_fragment
+def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke]
+comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
+synonym: "repeat fragment" EXACT []
+is_a: SO:0000840 ! repeat_component
+relationship: part_of SO:0001649 ! nested_repeat
+
+[Term]
+id: SO:0001051
+name: nested_region
+is_obsolete: true
+
+[Term]
+id: SO:0001052
+name: nested_repeat
+is_obsolete: true
+
+[Term]
+id: SO:0001053
+name: nested_transposon
+is_obsolete: true
+
+[Term]
+id: SO:0001054
+name: transposon_fragment
+def: "A portion of a transposon, interrupted by the insertion of another element." [SO:ke]
+synonym: "transposon fragment" EXACT []
+is_a: SO:0000840 ! repeat_component
+relationship: part_of SO:0001648 ! nested_transposon
+
+[Term]
+id: SO:0001055
+name: transcriptional_cis_regulatory_region
+def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]
+subset: SOFA
+synonym: "transcription-control region" EXACT []
+synonym: "transcriptional cis regulatory region" EXACT []
+is_a: SO:0001679 ! transcription_regulatory_region
+
+[Term]
+id: SO:0001056
+name: splicing_regulatory_region
+def: "A regulatory_region that modulates splicing." [SO:ke]
+subset: SOFA
+synonym: "splicing regulatory region" EXACT []
+is_a: SO:0001679 ! transcription_regulatory_region
+
+[Term]
+id: SO:0001057
+name: enhanceosome
+is_obsolete: true
+
+[Term]
+id: SO:0001058
+name: promoter_targeting_sequence
+def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]
+synonym: "promoter targeting sequence" EXACT []
+is_a: SO:0001055 ! transcriptional_cis_regulatory_region
+
+[Term]
+id: SO:0001059
+name: sequence_alteration
+alt_id: SO:1000004
+alt_id: SO:1000007
+def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]
+comment: Merged with partially characterized change in nucleotide sequence.
+subset: SOFA
+synonym: "partially characterised change in DNA sequence" NARROW []
+synonym: "partially_characterised_change_in_DNA_sequence" NARROW []
+synonym: "sequence alteration" EXACT []
+synonym: "sequence variation" RELATED []
+synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW []
+is_a: SO:0000110 ! sequence_feature
+
+[Term]
+id: SO:0001060
+name: sequence_variant
+def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
+synonym: "ANNOVAR:unknown" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "sequence variant" EXACT []
+synonym: "VAAST:sequence_variant" EXACT VAR []
+
+[Term]
+id: SO:0001061
+name: propeptide_cleavage_site
+alt_id: BS:00063
+def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]
+comment: Discrete.
+subset: biosapiens
+synonym: "propeptide cleavage site" EXACT []
+is_a: SO:0100011 ! cleaved_peptide_region
+relationship: part_of SO:0001062 ! propeptide
+
+[Term]
+id: SO:0001062
+name: propeptide
+alt_id: BS:00077
+def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "propep" RELATED [uniprot:feature_type]
+xref: http://en.wikipedia.org/wiki/Propeptide "wiki"
+is_a: SO:0100011 ! cleaved_peptide_region
+
+[Term]
+id: SO:0001063
+name: immature_peptide_region
+alt_id: BS:00129
+def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+subset: SOFA
+synonym: "immature peptide region" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+
+[Term]
+id: SO:0001064
+name: active_peptide
+alt_id: BS:00076
+def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]
+comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
+subset: biosapiens
+synonym: "active peptide" EXACT []
+synonym: "peptide" BROAD [uniprot:feature_type]
+xref: http://en.wikipedia.org/wiki/Peptide "wiki"
+is_a: SO:0000419 ! mature_protein_region
+
+[Term]
+id: SO:0001066
+name: compositionally_biased_region_of_peptide
+alt_id: BS:00068
+def: "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]
+comment: Range.
+subset: biosapiens
+synonym: "compbias" RELATED [uniprot:feature_type]
+synonym: "compositional bias" RELATED []
+synonym: "compositionally biased" RELATED []
+synonym: "compositionally biased region of peptide" RELATED []
+synonym: "compositionally_biased_region" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+
+[Term]
+id: SO:0001067
+name: polypeptide_motif
+alt_id: BS:00032
+def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]
+comment: Range.
+subset: biosapiens
+synonym: "motif" BROAD [uniprot:feature_type]
+synonym: "polypeptide motif" EXACT []
+is_a: SO:0100021 ! polypeptide_conserved_region
+
+[Term]
+id: SO:0001068
+name: polypeptide_repeat
+alt_id: BS:00070
+def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "polypeptide repeat" EXACT []
+synonym: "repeat" RELATED [uniprot:feature_type]
+is_a: SO:0100021 ! polypeptide_conserved_region
+
+[Term]
+id: SO:0001070
+name: polypeptide_structural_region
+alt_id: BS:00337
+def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]
+comment: Range.
+subset: biosapiens
+synonym: "polypeptide structural region" EXACT []
+synonym: "structural_region" RELATED []
+is_a: SO:0000839 ! polypeptide_region
+
+[Term]
+id: SO:0001071
+name: membrane_structure
+alt_id: BS:00128
+def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "membrane structure" EXACT []
+is_a: SO:0001070 ! polypeptide_structural_region
+
+[Term]
+id: SO:0001072
+name: extramembrane_polypeptide_region
+alt_id: BS:00154
+def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]
+comment: Range.
+subset: biosapiens
+synonym: "extramembrane" RELATED BS []
+synonym: "extramembrane polypeptide region" EXACT []
+synonym: "extramembrane_region" RELATED BS []
+synonym: "topo_dom" RELATED BS [uniprot:feature_type]
+is_a: SO:0001070 ! polypeptide_structural_region
+relationship: part_of SO:0001071 ! membrane_structure
+
+[Term]
+id: SO:0001073
+name: cytoplasmic_polypeptide_region
+alt_id: BS:00145
+def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "cytoplasm_location" EXACT BS []
+synonym: "cytoplasmic polypeptide region" EXACT []
+synonym: "inside" RELATED BS []
+is_a: SO:0001072 ! extramembrane_polypeptide_region
+
+[Term]
+id: SO:0001074
+name: non_cytoplasmic_polypeptide_region
+alt_id: BS:00144
+def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]
+comment: This could be inside an organelle within the cell.
+subset: biosapiens
+synonym: "non cytoplasmic polypeptide region" EXACT []
+synonym: "non_cytoplasm_location" EXACT BS []
+synonym: "outside" RELATED BS []
+is_a: SO:0001072 ! extramembrane_polypeptide_region
+
+[Term]
+id: SO:0001075
+name: intramembrane_polypeptide_region
+alt_id: BS:00156
+def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR]
+subset: biosapiens
+synonym: "intramembrane" RELATED BS []
+synonym: "intramembrane polypeptide region" EXACT []
+is_a: SO:0001070 ! polypeptide_structural_region
+relationship: part_of SO:0001071 ! membrane_structure
+
+[Term]
+id: SO:0001076
+name: membrane_peptide_loop
+alt_id: BS:00155
+def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "membrane peptide loop" EXACT []
+synonym: "membrane_loop" RELATED BS []
+is_a: SO:0001075 ! intramembrane_polypeptide_region
+
+[Term]
+id: SO:0001077
+name: transmembrane_polypeptide_region
+alt_id: BS:00158
+def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]
+subset: biosapiens
+synonym: "transmem" RELATED BS [uniprot:feature_type]
+synonym: "transmembrane" RELATED BS []
+synonym: "transmembrane polypeptide region" EXACT []
+is_a: SO:0001075 ! intramembrane_polypeptide_region
+
+[Term]
+id: SO:0001078
+name: polypeptide_secondary_structure
+alt_id: BS:00003
+def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]
+comment: Biosapien term was secondary_structure.
+subset: biosapiens
+synonym: "2nary structure" RELATED BS []
+synonym: "polypeptide secondary structure" EXACT []
+synonym: "secondary structure" RELATED BS []
+synonym: "secondary structure region" RELATED BS []
+synonym: "secondary_structure" RELATED BS []
+xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki"
+is_a: SO:0001070 ! polypeptide_structural_region
+
+[Term]
+id: SO:0001079
+name: polypeptide_structural_motif
+alt_id: BS:0000338
+def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]
+subset: biosapiens
+synonym: "polypeptide structural motif" RELATED []
+synonym: "structural_motif" RELATED BS []
+xref: http://en.wikipedia.org/wiki/Structural_motif "wiki"
+is_a: SO:0001070 ! polypeptide_structural_region
+
+[Term]
+id: SO:0001080
+name: coiled_coil
+alt_id: BS:00041
+def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]
+comment: Range.
+subset: biosapiens
+synonym: "coiled" RELATED BS [uniprot:feature_type]
+synonym: "coiled coil" EXACT []
+xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki"
+is_a: SO:0001079 ! polypeptide_structural_motif
+
+[Term]
+id: SO:0001081
+name: helix_turn_helix
+alt_id: BS:00147
+def: "A motif comprising two helices separated by a turn." [EBIBS:GAR]
+subset: biosapiens
+synonym: "helix turn helix" EXACT []
+synonym: "helix-turn-helix" EXACT []
+synonym: "HTH" RELATED BS []
+is_a: SO:0001079 ! polypeptide_structural_motif
+relationship: has_part SO:0001114 ! peptide_helix
+relationship: has_part SO:0001128 ! polypeptide_turn_motif
+
+[Term]
+id: SO:0001082
+name: polypeptide_sequencing_information
+alt_id: BS:00125
+def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "sequencing_information" EXACT []
+is_a: SO:0000700 ! remark
+
+[Term]
+id: SO:0001083
+name: non_adjacent_residues
+alt_id: BS:00182
+def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]
+subset: biosapiens
+synonym: "non consecutive" EXACT []
+synonym: "non_cons" EXACT [uniprot:feature_type]
+is_a: SO:0001082 ! polypeptide_sequencing_information
+
+[Term]
+id: SO:0001084
+name: non_terminal_residue
+alt_id: BS:00072
+def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]
+comment: Discrete.
+subset: biosapiens
+synonym: "non terminal" EXACT []
+synonym: "non_ter" EXACT [uniprot:feature_type]
+is_a: SO:0001082 ! polypeptide_sequencing_information
+
+[Term]
+id: SO:0001085
+name: sequence_conflict
+alt_id: BS:00069
+def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]
+comment: Discrete.
+subset: biosapiens
+synonym: "conflict" EXACT [uniprot:feature_type]
+is_a: SO:0001082 ! polypeptide_sequencing_information
+
+[Term]
+id: SO:0001086
+name: sequence_uncertainty
+alt_id: BS:00181
+def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]
+subset: biosapiens
+synonym: "unsure" EXACT [uniprot:feature_type]
+is_a: SO:0001082 ! polypeptide_sequencing_information
+
+[Term]
+id: SO:0001087
+name: cross_link
+alt_id: BS:00178
+def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual]
+subset: biosapiens
+synonym: "cross link" EXACT []
+synonym: "crosslink" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0001088
+name: disulfide_bond
+alt_id: BS:00028
+def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual]
+comment: 2 discreet & joined.
+subset: biosapiens
+synonym: "disulfid" RELATED []
+synonym: "disulfide" RELATED []
+synonym: "disulfide bond" RELATED []
+synonym: "disulphide" EXACT []
+synonym: "disulphide bond" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:0001089
+name: post_translationally_modified_region
+alt_id: BS:00052
+def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]
+comment: Discrete.
+subset: biosapiens
+synonym: "mod_res" EXACT [uniprot:feature_type]
+synonym: "modified residue" EXACT []
+synonym: "post_translational_modification" EXACT []
+xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki"
+is_a: SO:0100001 ! biochemical_region_of_peptide
+
+[Term]
+id: SO:0001090
+name: covalent_binding_site
+alt_id: BS:00246
+def: "Binding involving a covalent bond." [EBIBS:GAR]
+subset: biosapiens
+synonym: "covalent binding site" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0001091
+name: non_covalent_binding_site
+alt_id: BS:00029
+def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR]
+comment: Discrete.
+subset: biosapiens
+synonym: "binding" RELATED [uniprot:curation]
+synonym: "binding site" RELATED []
+synonym: "non covalent binding site" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0001092
+name: polypeptide_metal_contact
+alt_id: BS:00027
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]
+comment: Residue is part of a binding site for a metal ion.
+subset: biosapiens
+synonym: "metal_binding" RELATED []
+is_a: SO:0001656 ! metal_binding_site
+is_a: SO:0100002 ! molecular_contact_region
+
+[Term]
+id: SO:0001093
+name: protein_protein_contact
+alt_id: BS:00131
+def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]
+subset: biosapiens
+synonym: "protein protein contact" EXACT []
+synonym: "protein protein contact site" EXACT []
+synonym: "protein_protein_interaction" RELATED []
+xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki"
+is_a: SO:0000410 ! protein_binding_site
+is_a: SO:0100002 ! molecular_contact_region
+
+[Term]
+id: SO:0001094
+name: polypeptide_calcium_ion_contact_site
+alt_id: BS:00186
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]
+comment: Residue involved in contact with calcium.
+subset: biosapiens
+synonym: "ca bind" RELATED []
+synonym: "ca_bind" EXACT BS [uniprot:feature_type]
+synonym: "Ca_contact_site" EXACT []
+synonym: "polypeptide calcium ion contact site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001095
+name: polypeptide_cobalt_ion_contact_site
+alt_id: BS:00136
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "Co_contact_site" EXACT []
+synonym: "polypeptide cobalt ion contact site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001096
+name: polypeptide_copper_ion_contact_site
+alt_id: BS:00146
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "Cu_contact_site" EXACT []
+synonym: "polypeptide copper ion contact site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001097
+name: polypeptide_iron_ion_contact_site
+alt_id: BS:00137
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "Fe_contact_site" EXACT []
+synonym: "polypeptide iron ion contact site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001098
+name: polypeptide_magnesium_ion_contact_site
+alt_id: BS:00187
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "Mg_contact_site" EXACT []
+synonym: "polypeptide magnesium ion contact site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001099
+name: polypeptide_manganese_ion_contact_site
+alt_id: BS:00140
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "Mn_contact_site" EXACT []
+synonym: "polypeptide manganese ion contact site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001100
+name: polypeptide_molybdenum_ion_contact_site
+alt_id: BS:00141
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "Mo_contact_site" EXACT []
+synonym: "polypeptide molybdenum ion contact site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001101
+name: polypeptide_nickel_ion_contact_site
+alt_id: BS:00142
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]
+subset: biosapiens
+synonym: "Ni_contact_site" EXACT []
+synonym: "polypeptide nickel ion contact site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001102
+name: polypeptide_tungsten_ion_contact_site
+alt_id: BS:00143
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "polypeptide tungsten ion contact site" EXACT []
+synonym: "W_contact_site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001103
+name: polypeptide_zinc_ion_contact_site
+alt_id: BS:00185
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]
+subset: biosapiens
+synonym: "polypeptide zinc ion contact site" EXACT []
+synonym: "Zn_contact_site" EXACT []
+is_a: SO:0001092 ! polypeptide_metal_contact
+
+[Term]
+id: SO:0001104
+name: catalytic_residue
+alt_id: BS:00026
+def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]
+comment: Discrete.
+subset: biosapiens
+synonym: "act_site" RELATED [uniprot:feature_type]
+synonym: "active site residue" EXACT []
+synonym: "catalytic residue" EXACT []
+is_a: SO:0001237 ! amino_acid
+relationship: part_of SO:0100019 ! polypeptide_catalytic_motif
+
+[Term]
+id: SO:0001105
+name: polypeptide_ligand_contact
+alt_id: BS:00157
+def: "Residues which interact with a ligand." [EBIBS:GAR]
+subset: biosapiens
+synonym: "polypeptide ligand contact" EXACT []
+synonym: "protein-ligand interaction" RELATED []
+is_a: SO:0001657 ! ligand_binding_site
+is_a: SO:0100002 ! molecular_contact_region
+
+[Term]
+id: SO:0001106
+name: asx_motif
+alt_id: BS:00202
+def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "asx motif" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001107
+name: beta_bulge
+alt_id: BS:00208
+def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta bulge" EXACT []
+xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki"
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001108
+name: beta_bulge_loop
+alt_id: BS:00209
+def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta bulge loop" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001109
+name: beta_bulge_loop_five
+alt_id: BS:00210
+def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta bulge loop five" EXACT []
+is_a: SO:0001108 ! beta_bulge_loop
+
+[Term]
+id: SO:0001110
+name: beta_bulge_loop_six
+alt_id: BS:00211
+def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta bulge loop six" EXACT []
+is_a: SO:0001108 ! beta_bulge_loop
+
+[Term]
+id: SO:0001111
+name: beta_strand
+alt_id: BS:00042
+def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]
+comment: Range.
+subset: biosapiens
+synonym: "strand" RELATED BS [uniprot:feature_type]
+xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki"
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001112
+name: antiparallel_beta_strand
+alt_id: BS:0000341
+def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]
+comment: Range.
+subset: biosapiens
+synonym: "antiparallel beta strand" EXACT []
+is_a: SO:0001111 ! beta_strand
+
+[Term]
+id: SO:0001113
+name: parallel_beta_strand
+alt_id: BS:00151
+def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]
+comment: Range.
+subset: biosapiens
+synonym: "parallel beta strand" EXACT []
+is_a: SO:0001111 ! beta_strand
+
+[Term]
+id: SO:0001114
+name: peptide_helix
+alt_id: BS:00152
+def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "helix" RELATED BS []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001115
+name: left_handed_peptide_helix
+alt_id: BS:00222
+def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]
+subset: biosapiens
+synonym: "helix-l" RELATED []
+synonym: "left handed helix" EXACT []
+is_a: SO:0001114 ! peptide_helix
+
+[Term]
+id: SO:0001116
+name: right_handed_peptide_helix
+alt_id: BS:0000339
+def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]
+subset: biosapiens
+synonym: "helix" RELATED BS []
+synonym: "right handed helix" EXACT []
+is_a: SO:0001114 ! peptide_helix
+
+[Term]
+id: SO:0001117
+name: alpha_helix
+alt_id: BS:00040
+def: "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "a-helix" RELATED BS []
+synonym: "helix" RELATED BS [uniprot:feature_type]
+xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki"
+is_a: SO:0001116 ! right_handed_peptide_helix
+
+[Term]
+id: SO:0001118
+name: pi_helix
+alt_id: BS:00153
+def: "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "pi helix" EXACT []
+xref: http://en.wikipedia.org/wiki/Pi_helix "wiki"
+is_a: SO:0001116 ! right_handed_peptide_helix
+
+[Term]
+id: SO:0001119
+name: three_ten_helix
+alt_id: BS:0000340
+def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "3(10) helix" EXACT []
+synonym: "3-10 helix" EXACT []
+synonym: "310 helix" EXACT []
+synonym: "three ten helix" EXACT []
+xref: http://en.wikipedia.org/wiki/310_helix "wiki"
+is_a: SO:0001116 ! right_handed_peptide_helix
+
+[Term]
+id: SO:0001120
+name: polypeptide_nest_motif
+alt_id: BS:00223
+def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "nest" RELATED BS []
+synonym: "nest_motif" EXACT []
+synonym: "polypeptide nest motif" RELATED []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001121
+name: polypeptide_nest_left_right_motif
+alt_id: BS:00224
+def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "nest_left_right" EXACT []
+synonym: "nest_lr" EXACT []
+synonym: "polypeptide nest left right motif" EXACT []
+is_a: SO:0001120 ! polypeptide_nest_motif
+
+[Term]
+id: SO:0001122
+name: polypeptide_nest_right_left_motif
+alt_id: BS:00225
+def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "nest_right_left" EXACT []
+synonym: "nest_rl" EXACT []
+synonym: "polypeptide nest right left motif" EXACT []
+is_a: SO:0001120 ! polypeptide_nest_motif
+
+[Term]
+id: SO:0001123
+name: schellmann_loop
+alt_id: BS:00226
+def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "paperclip" RELATED BS []
+synonym: "paperclip loop" RELATED []
+synonym: "schellmann loop" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001124
+name: schellmann_loop_seven
+alt_id: BS:00228
+def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "schellmann loop seven" EXACT []
+synonym: "seven-residue schellmann loop" EXACT []
+is_a: SO:0001123 ! schellmann_loop
+
+[Term]
+id: SO:0001125
+name: schellmann_loop_six
+alt_id: BS:00227
+def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "schellmann loop six" EXACT []
+synonym: "six-residue schellmann loop" EXACT []
+is_a: SO:0001123 ! schellmann_loop
+
+[Term]
+id: SO:0001126
+name: serine_threonine_motif
+alt_id: BS:00229
+def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "serine/threonine motif" EXACT []
+synonym: "st motif" EXACT []
+synonym: "st_motif" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001127
+name: serine_threonine_staple_motif
+alt_id: BS:00230
+def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "serine threonine staple motif" EXACT []
+synonym: "st_staple" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001128
+name: polypeptide_turn_motif
+alt_id: BS:00148
+def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]
+comment: Range.
+subset: biosapiens
+synonym: "turn" RELATED BS []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0001129
+name: asx_turn_left_handed_type_one
+alt_id: BS:00206
+def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "asx turn left handed type one" EXACT []
+synonym: "asx_turn_il" RELATED []
+is_a: SO:0000912 ! asx_turn
+
+[Term]
+id: SO:0001130
+name: asx_turn_left_handed_type_two
+alt_id: BS:00204
+def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "asx turn left handed type two" EXACT []
+synonym: "asx_turn_iil" EXACT []
+is_a: SO:0000912 ! asx_turn
+
+[Term]
+id: SO:0001131
+name: asx_turn_right_handed_type_two
+alt_id: BS:00205
+def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "asx turn right handed type two" EXACT []
+synonym: "asx_turn_iir" EXACT []
+is_a: SO:0000912 ! asx_turn
+
+[Term]
+id: SO:0001132
+name: asx_turn_right_handed_type_one
+alt_id: BS:00207
+def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "asx turn type right handed type one" EXACT []
+synonym: "asx_turn_ir" EXACT []
+is_a: SO:0000912 ! asx_turn
+
+[Term]
+id: SO:0001133
+name: beta_turn
+alt_id: BS:00212
+def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta turn" EXACT []
+is_a: SO:0001128 ! polypeptide_turn_motif
+
+[Term]
+id: SO:0001134
+name: beta_turn_left_handed_type_one
+alt_id: BS:00215
+def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta turn left handed type one" EXACT []
+synonym: "beta_turn_il" EXACT []
+synonym: "type I' beta turn" EXACT []
+synonym: "type I' turn" EXACT []
+is_a: SO:0001133 ! beta_turn
+
+[Term]
+id: SO:0001135
+name: beta_turn_left_handed_type_two
+alt_id: BS:00213
+def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta turn left handed type two" EXACT []
+synonym: "beta_turn_iil" EXACT []
+synonym: "type II' beta turn" EXACT []
+synonym: "type II' turn" EXACT []
+is_a: SO:0001133 ! beta_turn
+
+[Term]
+id: SO:0001136
+name: beta_turn_right_handed_type_one
+alt_id: BS:00216
+def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta turn right handed type one" EXACT []
+synonym: "beta_turn_ir" EXACT []
+synonym: "type I beta turn" EXACT []
+synonym: "type I turn" EXACT []
+is_a: SO:0001133 ! beta_turn
+
+[Term]
+id: SO:0001137
+name: beta_turn_right_handed_type_two
+alt_id: BS:00214
+def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "beta turn right handed type two" EXACT []
+synonym: "beta_turn_iir" EXACT []
+synonym: "type II beta turn" EXACT []
+synonym: "type II turn" EXACT []
+is_a: SO:0001133 ! beta_turn
+
+[Term]
+id: SO:0001138
+name: gamma_turn
+alt_id: BS:00219
+def: "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "gamma turn" EXACT []
+is_a: SO:0001128 ! polypeptide_turn_motif
+
+[Term]
+id: SO:0001139
+name: gamma_turn_classic
+alt_id: BS:00220
+def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "classic gamma turn" EXACT []
+synonym: "gamma turn classic" EXACT []
+is_a: SO:0001138 ! gamma_turn
+
+[Term]
+id: SO:0001140
+name: gamma_turn_inverse
+alt_id: BS:00221
+def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "gamma turn inverse" EXACT []
+is_a: SO:0001138 ! gamma_turn
+
+[Term]
+id: SO:0001141
+name: serine_threonine_turn
+alt_id: BS:00231
+def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "serine/threonine turn" EXACT []
+synonym: "st_turn" EXACT []
+is_a: SO:0001128 ! polypeptide_turn_motif
+
+[Term]
+id: SO:0001142
+name: st_turn_left_handed_type_one
+alt_id: BS:00234
+def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "st turn left handed type one" EXACT []
+synonym: "st_turn_il" EXACT []
+is_a: SO:0001141 ! serine_threonine_turn
+
+[Term]
+id: SO:0001143
+name: st_turn_left_handed_type_two
+alt_id: BS:00232
+def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "st turn left handed type two" EXACT []
+synonym: "st_turn_iil" EXACT []
+is_a: SO:0001141 ! serine_threonine_turn
+
+[Term]
+id: SO:0001144
+name: st_turn_right_handed_type_one
+alt_id: BS:00235
+def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "st turn right handed type one" EXACT []
+synonym: "st_turn_ir" EXACT []
+is_a: SO:0001141 ! serine_threonine_turn
+
+[Term]
+id: SO:0001145
+name: st_turn_right_handed_type_two
+alt_id: BS:00233
+def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "st turn right handed type two" EXACT []
+synonym: "st_turn_iir" EXACT []
+is_a: SO:0001141 ! serine_threonine_turn
+
+[Term]
+id: SO:0001146
+name: polypeptide_variation_site
+alt_id: BS:00336
+def: "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]
+comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
+subset: biosapiens
+synonym: "sequence_variations" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+
+[Term]
+id: SO:0001147
+name: natural_variant_site
+alt_id: BS:00071
+def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]
+comment: Discrete.
+subset: biosapiens
+synonym: "natural_variant" BROAD []
+synonym: "sequence variation" BROAD []
+synonym: "variant" BROAD [uniprot:feature_type]
+is_a: SO:0001146 ! polypeptide_variation_site
+
+[Term]
+id: SO:0001148
+name: mutated_variant_site
+alt_id: BS:00036
+def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]
+comment: Discrete.
+subset: biosapiens
+synonym: "mutagen" EXACT BS [uniprot:feature_type]
+synonym: "mutagenesis" EXACT []
+synonym: "mutated_site" EXACT []
+is_a: SO:0001146 ! polypeptide_variation_site
+
+[Term]
+id: SO:0001149
+name: alternate_sequence_site
+alt_id: BS:00073
+alt_id: SO:0001065
+def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]
+comment: Discrete.
+subset: biosapiens
+synonym: "alternative_sequence" EXACT []
+synonym: "isoform" NARROW []
+synonym: "sequence variation" NARROW []
+synonym: "var_seq" EXACT [uniprot:feature_type]
+synonym: "varsplic" NARROW []
+is_a: SO:0001146 ! polypeptide_variation_site
+
+[Term]
+id: SO:0001150
+name: beta_turn_type_six
+def: "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]
+subset: biosapiens
+synonym: "beta turn type six" EXACT []
+synonym: "cis-proline loop" EXACT []
+synonym: "type VI beta turn" EXACT []
+synonym: "type VI turn" EXACT []
+is_a: SO:0001133 ! beta_turn
+
+[Term]
+id: SO:0001151
+name: beta_turn_type_six_a
+def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]
+subset: biosapiens
+synonym: "beta turn type six a" EXACT []
+synonym: "type VIa beta turn" EXACT []
+synonym: "type VIa turn" EXACT []
+is_a: SO:0001150 ! beta_turn_type_six
+
+[Term]
+id: SO:0001152
+name: beta_turn_type_six_a_one
+subset: biosapiens
+synonym: "beta turn type six a one" EXACT []
+synonym: "type VIa1 beta turn" EXACT []
+synonym: "type VIa1 turn" EXACT []
+is_a: SO:0001151 ! beta_turn_type_six_a
+
+[Term]
+id: SO:0001153
+name: beta_turn_type_six_a_two
+subset: biosapiens
+synonym: "beta turn type six a two" EXACT []
+synonym: "type VIa2 beta turn" EXACT []
+synonym: "type VIa2 turn" EXACT []
+is_a: SO:0001151 ! beta_turn_type_six_a
+
+[Term]
+id: SO:0001154
+name: beta_turn_type_six_b
+def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]
+subset: biosapiens
+synonym: "beta turn type six b" EXACT []
+synonym: "type VIb beta turn" EXACT []
+synonym: "type VIb turn" EXACT []
+is_a: SO:0001150 ! beta_turn_type_six
+
+[Term]
+id: SO:0001155
+name: beta_turn_type_eight
+def: "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]
+subset: biosapiens
+synonym: "beta turn type eight" EXACT []
+synonym: "type VIII beta turn" EXACT []
+synonym: "type VIII turn" EXACT []
+is_a: SO:0001133 ! beta_turn
+
+[Term]
+id: SO:0001156
+name: DRE_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]
+comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
+synonym: "DRE motif" EXACT []
+synonym: "NDM4" EXACT []
+synonym: "WATCGATW_motif" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001157
+name: DMv4_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]
+synonym: "directional motif v4" EXACT []
+synonym: "DMv4" EXACT []
+synonym: "DMv4 motif" EXACT []
+synonym: "motif 1 element" EXACT []
+synonym: "promoter motif 1" EXACT []
+synonym: "YGGTCACATR" NARROW []
+is_a: SO:0001659 ! promoter_element
+
+[Term]
+id: SO:0001158
+name: E_box_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]
+synonym: "AWCAGCTGWT" NARROW []
+synonym: "E box motif" EXACT []
+synonym: "generic E box motif" EXACT []
+synonym: "NDM5" RELATED []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001159
+name: DMv5_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]
+synonym: "directional motif v5" EXACT []
+synonym: "DMv5" EXACT []
+synonym: "DMv5 motif" EXACT []
+synonym: "KTYRGTATWTTT" NARROW []
+synonym: "promoter motif 6" RELATED []
+is_a: SO:0001659 ! promoter_element
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001160
+name: DMv3_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]
+synonym: "directional motif v3" EXACT []
+synonym: "DMv3" EXACT []
+synonym: "DMv3 motif" EXACT []
+synonym: "KNNCAKCNCTRNY" NARROW []
+synonym: "promoter motif 7" EXACT []
+is_a: SO:0001659 ! promoter_element
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001161
+name: DMv2_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]
+synonym: "directional motif v2" EXACT []
+synonym: "DMv2" EXACT []
+synonym: "DMv2 motif" EXACT []
+synonym: "MKSYGGCARCGSYSS" NARROW []
+synonym: "promoter motif 8" EXACT []
+is_a: SO:0001659 ! promoter_element
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001162
+name: MTE
+def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]
+synonym: "CSARCSSAACGS" NARROW []
+synonym: "motif ten element" EXACT []
+synonym: "motif_ten_element" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0001669 ! RNApol_II_core_promoter
+
+[Term]
+id: SO:0001163
+name: INR1_motif
+def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941]
+synonym: "directional motif p3" EXACT []
+synonym: "directional promoter motif 3" EXACT []
+synonym: "DMp3" EXACT []
+synonym: "INR1 motif" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001164
+name: DPE1_motif
+def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941]
+synonym: "directional motif 5" EXACT []
+synonym: "directional promoter motif 5" RELATED []
+synonym: "DMp5" EXACT []
+synonym: "DPE1 motif" EXACT []
+is_a: SO:0001659 ! promoter_element
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001165
+name: DMv1_motif
+def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941]
+synonym: "directional promoter motif v1" RELATED []
+synonym: "DMv1" RELATED []
+synonym: "DMv1 motif" EXACT []
+is_a: SO:0001659 ! promoter_element
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001166
+name: GAGA_motif
+def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]
+synonym: "GAGA" EXACT []
+synonym: "GAGA motif" EXACT []
+synonym: "NDM1" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001167
+name: NDM2_motif
+def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]
+synonym: "NDM2" EXACT []
+synonym: "NDM2 motif" EXACT []
+synonym: "non directional promoter motif 2" EXACT []
+is_a: SO:0001659 ! promoter_element
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001168
+name: NDM3_motif
+def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]
+synonym: "NDM3" EXACT []
+synonym: "NDM3 motif" EXACT []
+synonym: "non directional motif 3" EXACT []
+is_a: SO:0001659 ! promoter_element
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001169
+name: ds_RNA_viral_sequence
+def: "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]
+synonym: "double stranded RNA virus sequence" EXACT []
+synonym: "ds RNA viral sequence" EXACT []
+is_a: SO:0001041 ! viral_sequence
+
+[Term]
+id: SO:0001170
+name: polinton
+def: "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]
+synonym: "maverick element" RELATED []
+is_a: SO:0000208 ! terminal_inverted_repeat_element
+
+[Term]
+id: SO:0001171
+name: rRNA_21S
+def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]
+synonym: "21S LSU rRNA" EXACT []
+synonym: "21S ribosomal RNA" EXACT []
+synonym: "21S rRNA" EXACT []
+synonym: "rRNA 21S" EXACT []
+is_a: SO:0000651 ! large_subunit_rRNA
+
+[Term]
+id: SO:0001172
+name: tRNA_region
+def: "A region of a tRNA." [RSC:cb]
+synonym: "tRNA region" EXACT []
+is_a: SO:0000834 ! mature_transcript_region
+relationship: part_of SO:0000253 ! tRNA
+
+[Term]
+id: SO:0001173
+name: anticodon_loop
+def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]
+synonym: "anti-codon loop" EXACT []
+synonym: "anticodon loop" EXACT []
+is_a: SO:0001172 ! tRNA_region
+
+[Term]
+id: SO:0001174
+name: anticodon
+def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]
+synonym: "anti-codon" EXACT []
+xref: http://en.wikipedia.org/wiki/Anticodon "wiki"
+is_a: SO:0001172 ! tRNA_region
+relationship: part_of SO:0001173 ! anticodon_loop
+
+[Term]
+id: SO:0001175
+name: CCA_tail
+def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]
+synonym: "CCA sequence" EXACT []
+synonym: "CCA tail" EXACT []
+is_a: SO:0001172 ! tRNA_region
+
+[Term]
+id: SO:0001176
+name: DHU_loop
+def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]
+synonym: "D loop" RELATED []
+synonym: "DHU loop" EXACT []
+is_a: SO:0001172 ! tRNA_region
+
+[Term]
+id: SO:0001177
+name: T_loop
+def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]
+synonym: "T loop" EXACT []
+synonym: "TpsiC loop" EXACT []
+is_a: SO:0001172 ! tRNA_region
+
+[Term]
+id: SO:0001178
+name: pyrrolysine_tRNA_primary_transcript
+def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]
+synonym: "pyrrolysine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0001179
+name: U3_snoRNA
+def: "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]
+comment: The definition is most of the old definition for snoRNA (SO:0000275).
+synonym: "small nucleolar RNA U3" EXACT []
+synonym: "snoRNA U3" EXACT []
+synonym: "U3 small nucleolar RNA" EXACT []
+synonym: "U3 snoRNA" EXACT []
+xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 "wiki"
+is_a: SO:0000593 ! C_D_box_snoRNA
+
+[Term]
+id: SO:0001180
+name: AU_rich_element
+def: "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]
+synonym: "ARE" RELATED []
+synonym: "AU rich element" EXACT []
+synonym: "AU-rich element" EXACT []
+xref: http://en.wikipedia.org/wiki/AU-rich_element "wiki"
+is_a: SO:0000837 ! UTR_region
+relationship: part_of SO:0000205 ! three_prime_UTR
+
+[Term]
+id: SO:0001181
+name: Bruno_response_element
+def: "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]
+comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
+synonym: "BRE" RELATED []
+synonym: "Bruno response element" EXACT []
+is_a: SO:0000837 ! UTR_region
+relationship: part_of SO:0000205 ! three_prime_UTR
+
+[Term]
+id: SO:0001182
+name: iron_responsive_element
+def: "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]
+synonym: "IRE" EXACT []
+synonym: "iron responsive element" EXACT []
+xref: http://en.wikipedia.org/wiki/Iron_responsive_element "wiki"
+is_a: SO:0000837 ! UTR_region
+relationship: part_of SO:0000203 ! UTR
+
+[Term]
+id: SO:0001183
+name: morpholino_backbone
+def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]
+comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
+synonym: "morpholino backbone" EXACT []
+xref: http://en.wikipedia.org/wiki/Morpholino "wiki"
+is_a: SO:0000348 ! nucleic_acid
+
+[Term]
+id: SO:0001184
+name: PNA
+def: "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]
+comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
+synonym: "peptide nucleic acid" RELATED []
+is_a: SO:0000348 ! nucleic_acid
+
+[Term]
+id: SO:0001185
+name: enzymatic
+def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
+comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0001186
+name: ribozymic
+def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]
+comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
+is_a: SO:0001185 ! enzymatic
+
+[Term]
+id: SO:0001187
+name: pseudouridylation_guide_snoRNA
+def: "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
+comment: Has RNA pseudouridylation guide activity (GO:0030558).
+synonym: "pseudouridylation guide snoRNA" EXACT []
+is_a: SO:0000594 ! H_ACA_box_snoRNA
+
+[Term]
+id: SO:0001188
+name: LNA
+def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]
+comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
+is_a: SO:0000348 ! nucleic_acid
+
+[Term]
+id: SO:0001189
+name: LNA_oligo
+def: "An oligo composed of LNA residues." [RSC:cb]
+synonym: "LNA oligo" EXACT []
+synonym: "locked nucleic acid" EXACT []
+xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid "wiki"
+is_a: SO:0001247 ! synthetic_oligo
+relationship: has_quality SO:0001188 ! LNA
+
+[Term]
+id: SO:0001190
+name: TNA
+def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]
+comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
+is_a: SO:0000348 ! nucleic_acid
+
+[Term]
+id: SO:0001191
+name: TNA_oligo
+def: "An oligo composed of TNA residues." [RSC:cb]
+synonym: "threose nucleic acid" EXACT []
+synonym: "TNA oligo" EXACT []
+xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid "wiki"
+is_a: SO:0001247 ! synthetic_oligo
+relationship: has_quality SO:0001190 ! TNA
+
+[Term]
+id: SO:0001192
+name: GNA
+def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]
+comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
+is_a: SO:0000348 ! nucleic_acid
+
+[Term]
+id: SO:0001193
+name: GNA_oligo
+def: "An oligo composed of GNA residues." [RSC:cb]
+synonym: "glycerol nucleic acid" EXACT []
+synonym: "glycol nucleic acid" EXACT []
+synonym: "GNA oligo" EXACT []
+xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid "wiki"
+is_a: SO:0001247 ! synthetic_oligo
+relationship: has_quality SO:0001192 ! GNA
+
+[Term]
+id: SO:0001194
+name: R_GNA
+def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]
+comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
+synonym: "R GNA" EXACT []
+is_a: SO:0001192 ! GNA
+
+[Term]
+id: SO:0001195
+name: R_GNA_oligo
+def: "An oligo composed of (R)-GNA residues." [RSC:cb]
+synonym: "(R)-glycerol nucleic acid" EXACT []
+synonym: "(R)-glycol nucleic acid" EXACT []
+synonym: "R GNA oligo" EXACT []
+is_a: SO:0001193 ! GNA_oligo
+relationship: has_quality SO:0001194 ! R_GNA
+
+[Term]
+id: SO:0001196
+name: S_GNA
+def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]
+comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
+synonym: "S GNA" EXACT []
+is_a: SO:0001192 ! GNA
+
+[Term]
+id: SO:0001197
+name: S_GNA_oligo
+def: "An oligo composed of (S)-GNA residues." [RSC:cb]
+synonym: "(S)-glycerol nucleic acid" EXACT []
+synonym: "(S)-glycol nucleic acid" EXACT []
+synonym: "S GNA oligo" EXACT []
+is_a: SO:0001193 ! GNA_oligo
+relationship: has_quality SO:0001196 ! S_GNA
+
+[Term]
+id: SO:0001198
+name: ds_DNA_viral_sequence
+def: "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]
+synonym: "double stranded DNA virus" EXACT []
+synonym: "ds DNA viral sequence" EXACT []
+is_a: SO:0001041 ! viral_sequence
+
+[Term]
+id: SO:0001199
+name: ss_RNA_viral_sequence
+def: "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]
+synonym: "single strand RNA virus" EXACT []
+synonym: "ss RNA viral sequence" EXACT []
+is_a: SO:0001041 ! viral_sequence
+
+[Term]
+id: SO:0001200
+name: negative_sense_ssRNA_viral_sequence
+def: "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]
+synonym: "negative sense single stranded RNA virus" RELATED []
+synonym: "negative sense ssRNA viral sequence" EXACT []
+is_a: SO:0001199 ! ss_RNA_viral_sequence
+
+[Term]
+id: SO:0001201
+name: positive_sense_ssRNA_viral_sequence
+def: "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]
+synonym: "positive sense single stranded RNA virus" RELATED []
+synonym: "positive sense ssRNA viral sequence" EXACT []
+is_a: SO:0001199 ! ss_RNA_viral_sequence
+
+[Term]
+id: SO:0001202
+name: ambisense_ssRNA_viral_sequence
+def: "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]
+synonym: "ambisense single stranded RNA virus" EXACT []
+synonym: "ambisense ssRNA viral sequence" EXACT []
+is_a: SO:0001199 ! ss_RNA_viral_sequence
+
+[Term]
+id: SO:0001203
+name: RNA_polymerase_promoter
+def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]
+synonym: "RNA polymerase promoter" EXACT []
+is_a: SO:0000167 ! promoter
+
+[Term]
+id: SO:0001204
+name: Phage_RNA_Polymerase_Promoter
+def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]
+synonym: "Phage RNA Polymerase Promoter" EXACT []
+is_a: SO:0001203 ! RNA_polymerase_promoter
+
+[Term]
+id: SO:0001205
+name: SP6_RNA_Polymerase_Promoter
+def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]
+synonym: "SP6 RNA Polymerase Promoter" EXACT []
+is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
+
+[Term]
+id: SO:0001206
+name: T3_RNA_Polymerase_Promoter
+def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]
+synonym: "T3 RNA Polymerase Promoter" EXACT []
+is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
+
+[Term]
+id: SO:0001207
+name: T7_RNA_Polymerase_Promoter
+def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]
+synonym: "T7 RNA Polymerase Promoter" EXACT []
+is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
+
+[Term]
+id: SO:0001208
+name: five_prime_EST
+def: "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]
+synonym: "5' EST" EXACT []
+synonym: "five prime EST" EXACT []
+is_a: SO:0000345 ! EST
+
+[Term]
+id: SO:0001209
+name: three_prime_EST
+def: "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]
+synonym: "3' EST" EXACT []
+synonym: "three prime EST" EXACT []
+is_a: SO:0000345 ! EST
+
+[Term]
+id: SO:0001210
+name: translational_frameshift
+def: "The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
+synonym: "ribosomal frameshift" EXACT []
+synonym: "translational frameshift" EXACT []
+xref: http://en.wikipedia.org/wiki/Translational_frameshift "wiki"
+is_a: SO:0000836 ! mRNA_region
+
+[Term]
+id: SO:0001211
+name: plus_1_translational_frameshift
+def: "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
+synonym: "plus 1 ribosomal frameshift" EXACT []
+synonym: "plus 1 translational frameshift" EXACT []
+is_a: SO:0001210 ! translational_frameshift
+
+[Term]
+id: SO:0001212
+name: plus_2_translational_frameshift
+def: "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
+synonym: "plus 2 ribosomal frameshift" EXACT []
+synonym: "plus 2 translational frameshift" EXACT []
+is_a: SO:0001210 ! translational_frameshift
+
+[Term]
+id: SO:0001213
+name: group_III_intron
+def: "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]
+comment: GO:0000374.
+synonym: "group III intron" EXACT []
+xref: http://en.wikipedia.org/wiki/Group_III_intron "wiki"
+is_a: SO:0000588 ! autocatalytically_spliced_intron
+
+[Term]
+id: SO:0001214
+name: noncoding_region_of_exon
+def: "The maximal intersection of exon and UTR." [SO:ke]
+comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
+subset: SOFA
+synonym: "noncoding region of exon" EXACT []
+is_a: SO:0000852 ! exon_region
+
+[Term]
+id: SO:0001215
+name: coding_region_of_exon
+def: "The region of an exon that encodes for protein sequence." [SO:ke]
+comment: An exon containing either a start or stop codon will be partially coding and partially non coding.
+subset: SOFA
+synonym: "coding region of exon" EXACT []
+is_a: SO:0000852 ! exon_region
+
+[Term]
+id: SO:0001216
+name: endonuclease_spliced_intron
+def: "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]
+synonym: "endonuclease spliced intron" EXACT []
+is_a: SO:0000188 ! intron
+
+[Term]
+id: SO:0001217
+name: protein_coding_gene
+synonym: "protein coding gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000010 ! protein_coding
+
+[Term]
+id: SO:0001218
+name: transgenic_insertion
+def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]
+synonym: "transgenic insertion" EXACT []
+is_a: SO:0000667 ! insertion
+relationship: has_quality SO:0000781 ! transgenic
+
+[Term]
+id: SO:0001219
+name: retrogene
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000569 ! retrotransposed
+
+[Term]
+id: SO:0001220
+name: silenced_by_RNA_interference
+def: "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]
+comment: RNA interference is GO:0016246.
+synonym: "silenced by RNA interference" EXACT []
+is_a: SO:0000893 ! silenced
+
+[Term]
+id: SO:0001221
+name: silenced_by_histone_modification
+def: "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]
+comment: Histone modification is GO:0016570.
+synonym: "silenced by histone modification" EXACT []
+is_a: SO:0000893 ! silenced
+
+[Term]
+id: SO:0001222
+name: silenced_by_histone_methylation
+def: "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]
+comment: Histone methylation is GO:0016571.
+synonym: "silenced by histone methylation" EXACT []
+is_a: SO:0001221 ! silenced_by_histone_modification
+
+[Term]
+id: SO:0001223
+name: silenced_by_histone_deacetylation
+def: "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]
+comment: Histone deacetylation is GO:0016573.
+synonym: "silenced by histone deacetylation" EXACT []
+is_a: SO:0001221 ! silenced_by_histone_modification
+
+[Term]
+id: SO:0001224
+name: gene_silenced_by_RNA_interference
+def: "A gene that is silenced by RNA interference." [SO:xp]
+synonym: "gene silenced by RNA interference" EXACT []
+synonym: "RNA interference silenced gene" EXACT []
+synonym: "RNAi silenced gene" EXACT []
+is_a: SO:0000127 ! silenced_gene
+relationship: has_quality SO:0001220 ! silenced_by_RNA_interference
+
+[Term]
+id: SO:0001225
+name: gene_silenced_by_histone_modification
+def: "A gene that is silenced by histone modification." [SO:xp]
+synonym: "gene silenced by histone modification" EXACT []
+is_a: SO:0000127 ! silenced_gene
+relationship: has_quality SO:0001221 ! silenced_by_histone_modification
+
+[Term]
+id: SO:0001226
+name: gene_silenced_by_histone_methylation
+def: "A gene that is silenced by histone methylation." [SO:xp]
+synonym: "gene silenced by histone methylation" EXACT []
+is_a: SO:0001225 ! gene_silenced_by_histone_modification
+relationship: has_quality SO:0001222 ! silenced_by_histone_methylation
+
+[Term]
+id: SO:0001227
+name: gene_silenced_by_histone_deacetylation
+def: "A gene that is silenced by histone deacetylation." [SO:xp]
+synonym: "gene silenced by histone deacetylation" EXACT []
+is_a: SO:0001225 ! gene_silenced_by_histone_modification
+relationship: has_quality SO:0001223 ! silenced_by_histone_deacetylation
+
+[Term]
+id: SO:0001228
+name: dihydrouridine
+def: "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]
+synonym: " D" EXACT RNAMOD []
+xref: http://en.wikipedia.org/wiki/Dihydrouridine "wiki"
+xref: RNAMOD:051
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001229
+name: pseudouridine
+def: "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]
+comment: The free molecule is CHEBI:17802.
+synonym: " Y" EXACT RNAMOD []
+xref: http://en.wikipedia.org/wiki/Pseudouridine "wiki"
+xref: RNAMOD:050
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001230
+name: inosine
+def: "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]
+comment: The free molecule is CHEBI:17596.
+synonym: "I" RELATED []
+synonym: "RNAMOD:017" RELATED []
+xref: http://en.wikipedia.org/wiki/Inosine "wiki"
+is_a: SO:0000250 ! modified_RNA_base_feature
+
+[Term]
+id: SO:0001231
+name: seven_methylguanine
+def: "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]
+comment: The free molecule is CHEBI:2274.
+synonym: "7-methylguanine" EXACT []
+synonym: "seven methylguanine" EXACT []
+is_a: SO:0000250 ! modified_RNA_base_feature
+
+[Term]
+id: SO:0001232
+name: ribothymidine
+def: "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]
+comment: The free molecule is CHEBI:30832.
+is_a: SO:0000250 ! modified_RNA_base_feature
+
+[Term]
+id: SO:0001233
+name: methylinosine
+def: "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]
+is_a: SO:0001274 ! modified_inosine
+
+[Term]
+id: SO:0001234
+name: mobile
+def: "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb]
+xref: http://en.wikipedia.org/wiki/Mobile "wiki"
+is_a: SO:0000733 ! feature_attribute
+
+[Term]
+id: SO:0001235
+name: replicon
+def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki"
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0001236
+name: base
+def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Nucleobase "wiki"
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0001237
+name: amino_acid
+def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]
+comment: Probably in the future this will cross reference to Chebi.
+synonym: "amino acid" EXACT []
+xref: http://en.wikipedia.org/wiki/Amino_acid "wiki"
+is_a: SO:0001411 ! biological_region
+relationship: part_of SO:0000104 ! polypeptide
+
+[Term]
+id: SO:0001238
+name: major_TSS
+synonym: "major transcription start site" EXACT []
+synonym: "major TSS" EXACT []
+is_a: SO:0000315 ! TSS
+
+[Term]
+id: SO:0001239
+name: minor_TSS
+synonym: "minor TSS" EXACT []
+is_a: SO:0000315 ! TSS
+
+[Term]
+id: SO:0001240
+name: TSS_region
+def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]
+synonym: "TSS region" EXACT []
+is_a: SO:0000842 ! gene_component_region
+relationship: has_part SO:0000315 ! TSS
+
+[Term]
+id: SO:0001241
+name: encodes_alternate_transcription_start_sites
+synonym: "encodes alternate transcription start sites" EXACT []
+is_a: SO:0000401 ! gene_attribute
+
+[Term]
+id: SO:0001243
+name: miRNA_primary_transcript_region
+def: "A part of an miRNA primary_transcript." [SO:ke]
+synonym: "miRNA primary transcript region" EXACT []
+is_a: SO:0000835 ! primary_transcript_region
+
+[Term]
+id: SO:0001244
+name: pre_miRNA
+def: "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]
+synonym: "pre-miRNA" EXACT []
+is_a: SO:0001243 ! miRNA_primary_transcript_region
+
+[Term]
+id: SO:0001245
+name: miRNA_stem
+def: "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]
+synonym: "miRNA stem" EXACT []
+is_a: SO:0001243 ! miRNA_primary_transcript_region
+relationship: part_of SO:0001244 ! pre_miRNA
+
+[Term]
+id: SO:0001246
+name: miRNA_loop
+def: "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]
+synonym: "miRNA loop" EXACT []
+is_a: SO:0001243 ! miRNA_primary_transcript_region
+relationship: part_of SO:0001244 ! pre_miRNA
+
+[Term]
+id: SO:0001247
+name: synthetic_oligo
+def: "An oligo composed of synthetic nucleotides." [SO:ke]
+synonym: "synthetic oligo" EXACT []
+is_a: SO:0000696 ! oligo
+
+[Term]
+id: SO:0001248
+name: assembly
+def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki"
+is_a: SO:0001410 ! experimental_feature
+
+[Term]
+id: SO:0001249
+name: fragment_assembly
+def: "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]
+synonym: "fragment assembly" EXACT []
+synonym: "physical map" EXACT []
+is_a: SO:0001248 ! assembly
+
+[Term]
+id: SO:0001250
+name: fingerprint_map
+def: "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]
+synonym: "BACmap" EXACT []
+synonym: "fingerprint map" EXACT []
+synonym: "FPC" EXACT []
+synonym: "FPCmap" EXACT []
+synonym: "restriction map" EXACT []
+is_a: SO:0001249 ! fragment_assembly
+relationship: has_part SO:0000412 ! restriction_fragment
+
+[Term]
+id: SO:0001251
+name: STS_map
+def: "An STS map is a physical map organized by the unique STS landmarks." [SO:ke]
+synonym: "STS map" EXACT []
+is_a: SO:0001249 ! fragment_assembly
+relationship: has_part SO:0000331 ! STS
+
+[Term]
+id: SO:0001252
+name: RH_map
+def: "A radiation hybrid map is a physical map." [SO:ke]
+synonym: "radiation hybrid map" EXACT []
+synonym: "RH map" EXACT []
+is_a: SO:0001249 ! fragment_assembly
+relationship: has_part SO:0000331 ! STS
+
+[Term]
+id: SO:0001253
+name: sonicate_fragment
+def: "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]
+synonym: "sonicate fragment" EXACT []
+is_a: SO:0000143 ! assembly_component
+
+[Term]
+id: SO:0001254
+name: polyploid
+def: "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Polyploid "wiki"
+is_a: SO:1000182 ! chromosome_number_variation
+
+[Term]
+id: SO:0001255
+name: autopolyploid
+def: "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Autopolyploid "wiki"
+is_a: SO:0001254 ! polyploid
+
+[Term]
+id: SO:0001256
+name: allopolyploid
+def: "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]
+xref: http://en.wikipedia.org/wiki/Allopolyploid "wiki"
+is_a: SO:0001254 ! polyploid
+
+[Term]
+id: SO:0001257
+name: homing_endonuclease_binding_site
+def: "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]
+synonym: "homing endonuclease binding site" EXACT []
+is_a: SO:0000059 ! nuclease_binding_site
+
+[Term]
+id: SO:0001258
+name: octamer_motif
+def: "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]
+comment: Nature. 1986 Oct 16-22;323(6089):640-3.
+synonym: "octamer motif" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000170 ! RNApol_II_promoter
+
+[Term]
+id: SO:0001259
+name: apicoplast_chromosome
+def: "A chromosome originating in an apicoplast." [SO:xp]
+synonym: "apicoplast chromosome" EXACT []
+is_a: SO:0000340 ! chromosome
+relationship: has_origin SO:0000743 ! apicoplast_sequence
+
+[Term]
+id: SO:0001260
+name: sequence_collection
+def: "A collection of discontinuous sequences." [SO:ke]
+synonym: "sequence collection" EXACT []
+
+[Term]
+id: SO:0001261
+name: overlapping_feature_set
+def: "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]
+comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.
+synonym: "overlapping feature set" EXACT []
+is_a: SO:0000703 ! experimental_result_region
+
+[Term]
+id: SO:0001262
+name: overlapping_EST_set
+def: "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]
+synonym: "overlapping EST set" EXACT []
+is_a: SO:0001261 ! overlapping_feature_set
+relationship: has_part SO:0000345 ! EST
+
+[Term]
+id: SO:0001263
+name: ncRNA_gene
+synonym: "ncRNA gen" EXACT []
+synonym: "ncRNA gene" EXACT []
+synonym: "non-coding RNA gene" RELATED []
+is_a: SO:0000704 ! gene
+
+[Term]
+id: SO:0001264
+name: gRNA_gene
+synonym: "gRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+relationship: has_quality SO:0000979 ! gRNA_encoding
+
+[Term]
+id: SO:0001265
+name: miRNA_gene
+alt_id: SO:0001270
+synonym: "miRNA gene" EXACT []
+synonym: "stRNA gene" EXACT []
+synonym: "stRNA_gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+relationship: has_quality SO:0000571 ! miRNA_encoding
+relationship: has_quality SO:0000656 ! stRNA_encoding
+
+[Term]
+id: SO:0001266
+name: scRNA_gene
+synonym: "scRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+relationship: has_quality SO:0000575 ! scRNA_encoding
+
+[Term]
+id: SO:0001267
+name: snoRNA_gene
+synonym: "snoRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+relationship: has_quality SO:0000578 ! snoRNA_encoding
+
+[Term]
+id: SO:0001268
+name: snRNA_gene
+synonym: "snRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+relationship: has_quality SO:0001263 ! ncRNA_gene
+
+[Term]
+id: SO:0001269
+name: SRP_RNA_gene
+synonym: "SRP RNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+relationship: has_quality SO:0000642 ! SRP_RNA_encoding
+
+[Term]
+id: SO:0001271
+name: tmRNA_gene
+synonym: "tmRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+relationship: has_quality SO:0000659 ! tmRNA_encoding
+
+[Term]
+id: SO:0001272
+name: tRNA_gene
+synonym: "tRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+relationship: has_quality SO:0000663 ! tRNA_encoding
+
+[Term]
+id: SO:0001273
+name: modified_adenosine
+def: "A modified adenine is an adenine base feature that has been altered." [SO:ke]
+synonym: "modified adenosine" EXACT []
+is_a: SO:0000250 ! modified_RNA_base_feature
+
+[Term]
+id: SO:0001274
+name: modified_inosine
+def: "A modified inosine is an inosine base feature that has been altered." [SO:ke]
+synonym: "modified inosine" EXACT []
+is_a: SO:0001230 ! inosine
+
+[Term]
+id: SO:0001275
+name: modified_cytidine
+def: "A modified cytidine is a cytidine base feature which has been altered." [SO:ke]
+synonym: "modified cytidine" EXACT []
+is_a: SO:0000250 ! modified_RNA_base_feature
+
+[Term]
+id: SO:0001276
+name: modified_guanosine
+synonym: "modified guanosine" EXACT []
+is_a: SO:0000250 ! modified_RNA_base_feature
+
+[Term]
+id: SO:0001277
+name: modified_uridine
+synonym: "modified uridine" EXACT []
+is_a: SO:0000250 ! modified_RNA_base_feature
+
+[Term]
+id: SO:0001278
+name: one_methylinosine
+def: "1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "1-methylinosine" EXACT []
+synonym: "m1I" EXACT RNAMOD []
+synonym: "one methylinosine" EXACT []
+xref: RNAMOD:018
+is_a: SO:0001274 ! modified_inosine
+
+[Term]
+id: SO:0001279
+name: one_two_prime_O_dimethylinosine
+def: "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "1,2'-O-dimethylinosine" EXACT []
+synonym: "m'Im" EXACT RNAMOD []
+synonym: "one two prime O dimethylinosine" EXACT []
+xref: RNAMOD:019
+is_a: SO:0001274 ! modified_inosine
+
+[Term]
+id: SO:0001280
+name: two_prime_O_methylinosine
+def: "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2'-O-methylinosine" EXACT []
+synonym: "Im" EXACT RNAMOD []
+synonym: "two prime O methylinosine" EXACT []
+xref: RNAMOD:081
+is_a: SO:0001274 ! modified_inosine
+
+[Term]
+id: SO:0001281
+name: three_methylcytidine
+def: "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "3-methylcytidine" EXACT []
+synonym: "m3C" EXACT RNAMOD []
+synonym: "three methylcytidine" EXACT []
+xref: RNAMOD:020
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001282
+name: five_methylcytidine
+def: "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methylcytidine" EXACT []
+synonym: "five methylcytidine" EXACT []
+synonym: "m5C" EXACT RNAMOD []
+xref: RNAMOD:021
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001283
+name: two_prime_O_methylcytidine
+def: "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2'-O-methylcytidine" EXACT []
+synonym: "Cm" EXACT RNAMOD []
+synonym: "two prime O methylcytidine" EXACT []
+xref: RNAMOD:022
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001284
+name: two_thiocytidine
+def: "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-thiocytidine" EXACT []
+synonym: "s2C" EXACT RNAMOD []
+synonym: "two thiocytidine" EXACT []
+xref: RNAMOD:023
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001285
+name: N4_acetylcytidine
+def: "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "ac4C" EXACT RNAMOD []
+synonym: "N4 acetylcytidine" EXACT []
+synonym: "N4-acetylcytidine" EXACT []
+xref: RNAMOD:024
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001286
+name: five_formylcytidine
+def: "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-formylcytidine" EXACT []
+synonym: "f5C" EXACT RNAMOD []
+synonym: "five formylcytidine" EXACT []
+xref: RNAMOD:025
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001287
+name: five_two_prime_O_dimethylcytidine
+def: "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "5,2'-O-dimethylcytidine" EXACT []
+synonym: "five two prime O dimethylcytidine" EXACT []
+synonym: "m5Cm" EXACT RNAMOD []
+xref: RNAMOD:026
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001288
+name: N4_acetyl_2_prime_O_methylcytidine
+def: "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "ac4Cm" EXACT RNAMOD []
+synonym: "N4 acetyl 2 prime O methylcytidine" EXACT []
+synonym: "N4-acetyl-2'-O-methylcytidine" EXACT []
+xref: RNAMOD:027
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001289
+name: lysidine
+def: "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "k2C" EXACT RNAMOD []
+xref: http://en.wikipedia.org/wiki/Lysidine "wiki"
+xref: RNAMOD:028
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001290
+name: N4_methylcytidine
+def: "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "m4C" EXACT RNAMOD []
+synonym: "N4 methylcytidine" EXACT []
+synonym: "N4-methylcytidine" EXACT []
+xref: RNAMOD:082
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001291
+name: N4_2_prime_O_dimethylcytidine
+def: "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "m4Cm" EXACT RNAMOD []
+synonym: "N4 2 prime O dimethylcytidine" EXACT []
+synonym: "N4,2'-O-dimethylcytidine" EXACT []
+xref: RNAMOD:083
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001292
+name: five_hydroxymethylcytidine
+def: "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-hydroxymethylcytidine" EXACT []
+synonym: "five hydroxymethylcytidine" EXACT []
+synonym: "hm5C" EXACT RNAMOD []
+xref: RNAMOD:084
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001293
+name: five_formyl_two_prime_O_methylcytidine
+def: "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-formyl-2'-O-methylcytidine" EXACT []
+synonym: "f5Cm" EXACT RNAMOD []
+synonym: "five formyl two prime O methylcytidine" EXACT []
+xref: RNAMOD:095
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001294
+name: N4_N4_2_prime_O_trimethylcytidine
+def: "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
+synonym: "m42Cm" EXACT RNAMOD []
+synonym: "N4,N4,2'-O-trimethylcytidine" EXACT []
+xref: RNAMOD:107
+is_a: SO:0001275 ! modified_cytidine
+
+[Term]
+id: SO:0001295
+name: one_methyladenosine
+def: "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "1-methyladenosine" EXACT []
+synonym: "m1A" EXACT RNAMOD []
+synonym: "one methyladenosine" EXACT []
+xref: RNAMOD:001
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001296
+name: two_methyladenosine
+def: "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-methyladenosine" EXACT []
+synonym: "m2A" EXACT RNAMOD []
+synonym: "two methyladenosine" EXACT []
+xref: RNAMOD:002
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001297
+name: N6_methyladenosine
+def: "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "m6A" EXACT RNAMOD []
+synonym: "N6 methyladenosine" EXACT []
+synonym: "N6-methyladenosine" EXACT []
+xref: RNAMOD:003
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001298
+name: two_prime_O_methyladenosine
+def: "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2'-O-methyladenosine" EXACT []
+synonym: "Am" EXACT RNAMOD []
+synonym: "two prime O methyladenosine" EXACT []
+xref: RNAMOD:004
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001299
+name: two_methylthio_N6_methyladenosine
+def: "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-methylthio-N6-methyladenosine" EXACT []
+synonym: "ms2m6A" EXACT RNAMOD []
+synonym: "two methylthio N6 methyladenosine" EXACT []
+xref: RNAMOD:005
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001300
+name: N6_isopentenyladenosine
+def: "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "i6A" EXACT RNAMOD []
+synonym: "N6 isopentenyladenosine" EXACT []
+synonym: "N6-isopentenyladenosine" EXACT []
+xref: RNAMOD:006
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001301
+name: two_methylthio_N6_isopentenyladenosine
+def: "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-methylthio-N6-isopentenyladenosine" EXACT []
+synonym: "ms2i6A" EXACT RNAMOD []
+synonym: "two methylthio N6 isopentenyladenosine" EXACT []
+xref: RNAMOD:007
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001302
+name: N6_cis_hydroxyisopentenyl_adenosine
+def: "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "io6A" EXACT RNAMOD []
+synonym: "N6 cis hydroxyisopentenyl adenosine" EXACT []
+synonym: "N6-(cis-hydroxyisopentenyl)adenosine" EXACT []
+xref: RNAMOD:008
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001303
+name: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
+def: "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine" EXACT []
+synonym: "ms2io6A" EXACT RNAMOD []
+synonym: "two methylthio N6 cis hydroxyisopentenyl adenosine" EXACT []
+xref: RNAMOD:009
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001304
+name: N6_glycinylcarbamoyladenosine
+def: "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "g6A" EXACT RNAMOD []
+synonym: "N6 glycinylcarbamoyladenosine" EXACT []
+synonym: "N6-glycinylcarbamoyladenosine" EXACT []
+xref: RNAMOD:010
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001305
+name: N6_threonylcarbamoyladenosine
+def: "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "N6 threonylcarbamoyladenosine" EXACT []
+synonym: "N6-threonylcarbamoyladenosine" EXACT []
+synonym: "t6A" EXACT RNAMOD []
+xref: RNAMOD:011
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001306
+name: two_methylthio_N6_threonyl_carbamoyladenosine
+def: "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-methylthio-N6-threonyl carbamoyladenosine" EXACT []
+synonym: "ms2t6A" EXACT RNAMOD []
+synonym: "two methylthio N6 threonyl carbamoyladenosine" EXACT []
+xref: RNAMOD:012
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001307
+name: N6_methyl_N6_threonylcarbamoyladenosine
+def: "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "m6t6A" EXACT RNAMOD []
+synonym: "N6 methyl N6 threonylcarbamoyladenosine" EXACT []
+synonym: "N6-methyl-N6-threonylcarbamoyladenosine" EXACT []
+xref: RNAMOD:013
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001308
+name: N6_hydroxynorvalylcarbamoyladenosine
+def: "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "hn6A" EXACT RNAMOD []
+synonym: "N6 hydroxynorvalylcarbamoyladenosine" EXACT []
+synonym: "N6-hydroxynorvalylcarbamoyladenosine" EXACT []
+xref: RNAMOD:014
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001309
+name: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
+def: "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine" EXACT []
+synonym: "ms2hn6A" EXACT RNAMOD []
+synonym: "two methylthio N6 hydroxynorvalyl carbamoyladenosine" EXACT []
+xref: RNAMOD:015
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001310
+name: two_prime_O_ribosyladenosine_phosphate
+def: "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "2'-O-ribosyladenosine (phosphate)" EXACT []
+synonym: "Ar(p)" EXACT RNAMOD []
+synonym: "two prime O ribosyladenosine phosphate" EXACT []
+xref: RNAMOD:016
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001311
+name: N6_N6_dimethyladenosine
+def: "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "m62A" EXACT RNAMOD []
+synonym: "N6,N6-dimethyladenosine" EXACT []
+xref: RNAMOD:080
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001312
+name: N6_2_prime_O_dimethyladenosine
+def: "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "m6Am" EXACT RNAMOD []
+synonym: "N6 2 prime O dimethyladenosine" EXACT []
+synonym: "N6,2'-O-dimethyladenosine" EXACT []
+xref: RNAMOD:088
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001313
+name: N6_N6_2_prime_O_trimethyladenosine
+def: "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "m62Am" EXACT RNAMOD []
+synonym: "N6,N6,2'-O-trimethyladenosine" EXACT []
+xref: RNAMOD:089
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001314
+name: one_two_prime_O_dimethyladenosine
+def: "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "1,2'-O-dimethyladenosine" EXACT []
+synonym: "m1Am" EXACT RNAMOD []
+synonym: "one two prime O dimethyladenosine" EXACT []
+xref: RNAMOD:097
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001315
+name: N6_acetyladenosine
+def: "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "ac6A" EXACT RNAMOD []
+synonym: "N6 acetyladenosine" EXACT []
+synonym: "N6-acetyladenosine" EXACT []
+xref: RNAMOD:102
+is_a: SO:0001273 ! modified_adenosine
+
+[Term]
+id: SO:0001316
+name: seven_deazaguanosine
+def: "7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "7-deazaguanosine" RELATED []
+synonym: "seven deazaguanosine" EXACT []
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001317
+name: queuosine
+def: "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
+synonym: " Q" EXACT RNAMOD []
+xref: http://en.wikipedia.org/wiki/Queuosine "wiki"
+xref: RNAMOD:043
+is_a: SO:0001316 ! seven_deazaguanosine
+
+[Term]
+id: SO:0001318
+name: epoxyqueuosine
+def: "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "eQ" EXACT RNAMOD []
+xref: RNAMOD:044
+is_a: SO:0001316 ! seven_deazaguanosine
+
+[Term]
+id: SO:0001319
+name: galactosyl_queuosine
+def: "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "galactosyl queuosine" EXACT []
+synonym: "galactosyl-queuosine" EXACT []
+synonym: "galQ" EXACT RNAMOD []
+xref: RNAMOD:045
+is_a: SO:0001316 ! seven_deazaguanosine
+
+[Term]
+id: SO:0001320
+name: mannosyl_queuosine
+def: "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "mannosyl queuosine" EXACT []
+synonym: "mannosyl-queuosine" EXACT []
+synonym: "manQ" EXACT RNAMOD []
+xref: RNAMOD:046
+is_a: SO:0001316 ! seven_deazaguanosine
+
+[Term]
+id: SO:0001321
+name: seven_cyano_seven_deazaguanosine
+def: "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "7-cyano-7-deazaguanosine" EXACT []
+synonym: "preQ0" EXACT RNAMOD []
+synonym: "seven cyano seven deazaguanosine" EXACT []
+xref: RNAMOD:047
+is_a: SO:0001316 ! seven_deazaguanosine
+
+[Term]
+id: SO:0001322
+name: seven_aminomethyl_seven_deazaguanosine
+def: "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "7-aminomethyl-7-deazaguanosine" EXACT []
+synonym: "preQ1" EXACT RNAMOD []
+synonym: "seven aminomethyl seven deazaguanosine" EXACT []
+xref: RNAMOD:048
+is_a: SO:0001316 ! seven_deazaguanosine
+
+[Term]
+id: SO:0001323
+name: archaeosine
+def: "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
+synonym: "G+" EXACT RNAMOD []
+xref: RNAMOD:049
+is_a: SO:0001316 ! seven_deazaguanosine
+
+[Term]
+id: SO:0001324
+name: one_methylguanosine
+def: "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "1-methylguanosine" EXACT []
+synonym: "m1G" EXACT RNAMOD []
+synonym: "one methylguanosine" EXACT []
+xref: RNAMOD:029
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001325
+name: N2_methylguanosine
+def: "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "m2G" EXACT RNAMOD []
+synonym: "N2 methylguanosine" EXACT []
+synonym: "N2-methylguanosine" EXACT []
+xref: RNAMOD:030
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001326
+name: seven_methylguanosine
+def: "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "7-methylguanosine" EXACT []
+synonym: "m7G" EXACT RNAMOD []
+synonym: "seven methylguanosine" EXACT []
+xref: RNAMOD:031
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001327
+name: two_prime_O_methylguanosine
+def: "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "2'-O-methylguanosine" EXACT []
+synonym: "Gm" EXACT RNAMOD []
+synonym: "two prime O methylguanosine" EXACT []
+xref: RNAMOD:032
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001328
+name: N2_N2_dimethylguanosine
+def: "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "m22G" EXACT RNAMOD []
+synonym: "N2,N2-dimethylguanosine" EXACT []
+xref: RNAMOD:033
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001329
+name: N2_2_prime_O_dimethylguanosine
+def: "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "m2Gm" EXACT RNAMOD []
+synonym: "N2 2 prime O dimethylguanosine" EXACT []
+synonym: "N2,2'-O-dimethylguanosine" EXACT []
+xref: RNAMOD:034
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001330
+name: N2_N2_2_prime_O_trimethylguanosine
+def: "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "m22Gmv" EXACT RNAMOD []
+synonym: "N2,N2,2'-O-trimethylguanosine" EXACT []
+xref: RNAMOD:035
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001331
+name: two_prime_O_ribosylguanosine_phosphate
+def: "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "2'-O-ribosylguanosine (phosphate)" EXACT []
+synonym: "Gr(p)" EXACT RNAMOD []
+synonym: "two prime O ribosylguanosine phosphate" EXACT []
+xref: RNAMOD:036
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001332
+name: wybutosine
+def: "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "yW" EXACT RNAMOD []
+xref: RNAMOD:037
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001333
+name: peroxywybutosine
+def: "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "o2yW" EXACT RNAMOD []
+xref: RNAMOD:038
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001334
+name: hydroxywybutosine
+def: "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "OHyW" EXACT RNAMOD []
+xref: RNAMOD:039
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001335
+name: undermodified_hydroxywybutosine
+def: "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "OHyW*" EXACT RNAMOD []
+synonym: "undermodified hydroxywybutosine" EXACT []
+xref: RNAMOD:040
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001336
+name: wyosine
+def: "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "IMG" EXACT RNAMOD []
+xref: RNAMOD:041
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001337
+name: methylwyosine
+def: "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "mimG" EXACT RNAMOD []
+xref: RNAMOD:042
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001338
+name: N2_7_dimethylguanosine
+def: "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "m2,7G" EXACT RNAMOD []
+synonym: "N2 7 dimethylguanosine" EXACT []
+synonym: "N2,7-dimethylguanosine" EXACT []
+xref: RNAMOD:090
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001339
+name: N2_N2_7_trimethylguanosine
+def: "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "m2,2,7G" EXACT RNAMOD []
+synonym: "N2,N2,7-trimethylguanosine" EXACT []
+xref: RNAMOD:091
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001340
+name: one_two_prime_O_dimethylguanosine
+def: "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "1,2'-O-dimethylguanosine" EXACT []
+synonym: "m1Gm" EXACT RNAMOD []
+synonym: "one two prime O dimethylguanosine" EXACT []
+xref: RNAMOD:096
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001341
+name: four_demethylwyosine
+def: "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "4-demethylwyosine" EXACT []
+synonym: "four demethylwyosine" EXACT []
+synonym: "imG-14" EXACT RNAMOD []
+xref: RNAMOD:100
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001342
+name: isowyosine
+def: "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "imG2" EXACT RNAMOD []
+xref: RNAMOD:101
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001343
+name: N2_7_2prirme_O_trimethylguanosine
+def: "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "m2,7Gm" EXACT RNAMOD []
+synonym: "N2 7 2prirme O trimethylguanosine" EXACT []
+synonym: "N2,7,2'-O-trimethylguanosine" EXACT []
+xref: RNAMOD:106
+is_a: SO:0001276 ! modified_guanosine
+
+[Term]
+id: SO:0001344
+name: five_methyluridine
+def: "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methyluridine" EXACT []
+synonym: "five methyluridine" EXACT []
+synonym: "m5U" EXACT RNAMOD []
+xref: http://en.wikipedia.org/wiki/5-methyluridine "wiki"
+xref: RNAMOD:052
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001345
+name: two_prime_O_methyluridine
+def: "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "2'-O-methyluridine" EXACT []
+synonym: "two prime O methyluridine" EXACT []
+synonym: "Um" EXACT RNAMOD []
+xref: RNAMOD:053
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001346
+name: five_two_prime_O_dimethyluridine
+def: "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5,2'-O-dimethyluridine" EXACT []
+synonym: "five two prime O dimethyluridine" EXACT []
+synonym: "m5Um" EXACT RNAMOD []
+xref: RNAMOD:054
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001347
+name: one_methylpseudouridine
+def: "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "1-methylpseudouridine" EXACT []
+synonym: "m1Y" EXACT RNAMOD []
+synonym: "one methylpseudouridine" EXACT []
+xref: RNAMOD:055
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001348
+name: two_prime_O_methylpseudouridine
+def: "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "2'-O-methylpseudouridine" EXACT []
+synonym: "two prime O methylpseudouridine" EXACT []
+synonym: "Ym" EXACT RNAMOD []
+xref: RNAMOD:056
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001349
+name: two_thiouridine
+def: "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-thiouridine" EXACT []
+synonym: "s2U" EXACT RNAMOD []
+synonym: "two thiouridine" EXACT []
+xref: RNAMOD:057
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001350
+name: four_thiouridine
+def: "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "4-thiouridine" EXACT []
+synonym: "four thiouridine" EXACT []
+synonym: "s4U" EXACT RNAMOD []
+xref: RNAMOD:058
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001351
+name: five_methyl_2_thiouridine
+def: "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methyl-2-thiouridine" EXACT []
+synonym: "five methyl 2 thiouridine" EXACT []
+synonym: "m5s2U" EXACT RNAMOD []
+xref: RNAMOD:059
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001352
+name: two_thio_two_prime_O_methyluridine
+def: "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "2-thio-2'-O-methyluridine" EXACT []
+synonym: "s2Um" EXACT RNAMOD []
+synonym: "two thio two prime O methyluridine" EXACT []
+xref: RNAMOD:060
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001353
+name: three_three_amino_three_carboxypropyl_uridine
+def: "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "3-(3-amino-3-carboxypropyl)uridine" EXACT []
+synonym: "acp3U" EXACT RNAMOD []
+xref: RNAMOD:061
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001354
+name: five_hydroxyuridine
+def: "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-hydroxyuridine" EXACT []
+synonym: "five hydroxyuridine" EXACT []
+synonym: "ho5U" EXACT RNAMOD []
+xref: RNAMOD:060
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001355
+name: five_methoxyuridine
+def: "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methoxyuridine" EXACT []
+synonym: "five methoxyuridine" EXACT []
+synonym: "mo5U" EXACT RNAMOD []
+xref: RNAMOD:063
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001356
+name: uridine_five_oxyacetic_acid
+def: "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "cmo5U" EXACT RNAMOD []
+synonym: "uridine 5-oxyacetic acid" EXACT []
+synonym: "uridine five oxyacetic acid" EXACT []
+xref: RNAMOD:064
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001357
+name: uridine_five_oxyacetic_acid_methyl_ester
+def: "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "mcmo5U" EXACT RNAMOD []
+synonym: "uridine 5-oxyacetic acid methyl ester" EXACT []
+synonym: "uridine five oxyacetic acid methyl ester" EXACT []
+xref: RNAMOD:065
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001358
+name: five_carboxyhydroxymethyl_uridine
+def: "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-(carboxyhydroxymethyl)uridine" EXACT []
+synonym: "chm5U" EXACT RNAMOD []
+synonym: "five carboxyhydroxymethyl uridine" EXACT []
+xref: RNAMOD:066
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001359
+name: five_carboxyhydroxymethyl_uridine_methyl_ester
+def: "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-(carboxyhydroxymethyl)uridine methyl ester" EXACT []
+synonym: "five carboxyhydroxymethyl uridine methyl ester" EXACT []
+synonym: "mchm5U" EXACT RNAMOD []
+xref: RNAMOD:067
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001360
+name: five_methoxycarbonylmethyluridine
+def: "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methoxycarbonylmethyluridine" EXACT []
+synonym: "five methoxycarbonylmethyluridine" EXACT []
+synonym: "mcm5U" EXACT RNAMOD []
+xref: RNAMOD:068
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001361
+name: five_methoxycarbonylmethyl_two_prime_O_methyluridine
+def: "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methoxycarbonylmethyl-2'-O-methyluridine" EXACT []
+synonym: "five methoxycarbonylmethyl two prime O methyluridine" EXACT []
+synonym: "mcm5Um" EXACT RNAMOD []
+xref: RNAMOD:069
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001362
+name: five_methoxycarbonylmethyl_two_thiouridine
+def: "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methoxycarbonylmethyl-2-thiouridine" EXACT []
+synonym: "five methoxycarbonylmethyl two thiouridine" EXACT []
+synonym: "mcm5s2U" EXACT RNAMOD []
+xref: RNAMOD:070
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001363
+name: five_aminomethyl_two_thiouridine
+def: "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-aminomethyl-2-thiouridine" EXACT []
+synonym: "five aminomethyl two thiouridine" EXACT []
+synonym: "nm5s2U" EXACT RNAMOD []
+xref: RNAMOD:071
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001364
+name: five_methylaminomethyluridine
+def: "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methylaminomethyluridine" EXACT []
+synonym: "five methylaminomethyluridine" EXACT []
+synonym: "mnm5U" EXACT RNAMOD []
+xref: RNAMOD:072
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001365
+name: five_methylaminomethyl_two_thiouridine
+def: "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methylaminomethyl-2-thiouridine" EXACT []
+synonym: "five methylaminomethyl two thiouridine" EXACT []
+synonym: "mnm5s2U" EXACT RNAMOD []
+xref: RNAMOD:073
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001366
+name: five_methylaminomethyl_two_selenouridine
+def: "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methylaminomethyl-2-selenouridine" EXACT []
+synonym: "five methylaminomethyl two selenouridine" EXACT []
+synonym: "mnm5se2U" EXACT RNAMOD []
+xref: RNAMOD:074
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001367
+name: five_carbamoylmethyluridine
+def: "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-carbamoylmethyluridine" EXACT []
+synonym: "five carbamoylmethyluridine" EXACT []
+synonym: "ncm5U" EXACT RNAMOD []
+xref: RNAMOD:075
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001368
+name: five_carbamoylmethyl_two_prime_O_methyluridine
+def: "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-carbamoylmethyl-2'-O-methyluridine" EXACT []
+synonym: "five carbamoylmethyl two prime O methyluridine" EXACT []
+synonym: "ncm5Um" EXACT RNAMOD []
+xref: RNAMOD:076
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001369
+name: five_carboxymethylaminomethyluridine
+def: "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-carboxymethylaminomethyluridine" EXACT []
+synonym: "cmnm5U" EXACT RNAMOD []
+synonym: "five carboxymethylaminomethyluridine" EXACT []
+xref: RNAMOD:077
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001370
+name: five_carboxymethylaminomethyl_two_prime_O_methyluridine
+def: "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-carboxymethylaminomethyl- 2'-O-methyluridine" EXACT []
+synonym: "cmnm5Um" EXACT RNAMOD []
+synonym: "five carboxymethylaminomethyl two prime O methyluridine" EXACT []
+xref: RNAMOD:078
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001371
+name: five_carboxymethylaminomethyl_two_thiouridine
+def: "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-carboxymethylaminomethyl-2-thiouridine" EXACT []
+synonym: "cmnm5s2U" EXACT RNAMOD []
+synonym: "five carboxymethylaminomethyl two thiouridine" EXACT []
+xref: RNAMOD:079
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001372
+name: three_methyluridine
+def: "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "3-methyluridine" EXACT []
+synonym: "m3U" EXACT RNAMOD []
+synonym: "three methyluridine" EXACT []
+xref: RNAMOD:085
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001373
+name: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
+def: "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine" EXACT []
+synonym: "m1acp3Y" EXACT RNAMOD []
+xref: RNAMOD:086
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001374
+name: five_carboxymethyluridine
+def: "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-carboxymethyluridine" EXACT []
+synonym: "cm5U" EXACT RNAMOD []
+synonym: "five carboxymethyluridine" EXACT []
+xref: RNAMOD:087
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001375
+name: three_two_prime_O_dimethyluridine
+def: "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "3,2'-O-dimethyluridine" EXACT []
+synonym: "m3Um" EXACT RNAMOD []
+synonym: "three two prime O dimethyluridine" EXACT []
+xref: RNAMOD:092
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001376
+name: five_methyldihydrouridine
+def: "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-methyldihydrouridine" EXACT []
+synonym: "five methyldihydrouridine" EXACT []
+synonym: "m5D" EXACT RNAMOD []
+xref: RNAMOD:093
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001377
+name: three_methylpseudouridine
+def: "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "3-methylpseudouridine" EXACT []
+synonym: "m3Y" EXACT RNAMOD []
+synonym: "three methylpseudouridine" EXACT []
+xref: RNAMOD:094
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001378
+name: five_taurinomethyluridine
+def: "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-taurinomethyluridine" EXACT []
+synonym: "five taurinomethyluridine" EXACT []
+synonym: "tm5U" EXACT RNAMOD []
+xref: RNAMOD:098
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001379
+name: five_taurinomethyl_two_thiouridine
+def: "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-taurinomethyl-2-thiouridine" EXACT []
+synonym: "five taurinomethyl two thiouridine" EXACT []
+synonym: "tm5s2U" EXACT RNAMOD []
+xref: RNAMOD:099
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001380
+name: five_isopentenylaminomethyl_uridine
+def: "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-(isopentenylaminomethyl)uridine" EXACT []
+synonym: "five isopentenylaminomethyl uridine" EXACT []
+synonym: "inm5U" EXACT RNAMOD []
+xref: RNAMOD:103
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001381
+name: five_isopentenylaminomethyl_two_thiouridine
+def: "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-(isopentenylaminomethyl)- 2-thiouridine" EXACT []
+synonym: "five isopentenylaminomethyl two thiouridine" EXACT []
+synonym: "inm5s2U" EXACT RNAMOD []
+xref: RNAMOD:104
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001382
+name: five_isopentenylaminomethyl_two_prime_O_methyluridine
+def: "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
+synonym: "5-(isopentenylaminomethyl)- 2'-O-methyluridine" EXACT []
+synonym: "five isopentenylaminomethyl two prime O methyluridine" EXACT []
+synonym: "inm5Um" EXACT RNAMOD []
+xref: RNAMOD:105
+is_a: SO:0001277 ! modified_uridine
+
+[Term]
+id: SO:0001383
+name: histone_binding_site
+def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]
+synonym: "histone binding site" EXACT []
+is_a: SO:0001654 ! nucleotide_to_protein_binding_site
+
+[Term]
+id: SO:0001384
+name: CDS_fragment
+synonym: "CDS fragment" EXACT []
+synonym: "incomplete CDS" EXACT []
+is_a: SO:0000316 ! CDS
+relationship: has_quality SO:0000731 ! fragmentary
+
+[Term]
+id: SO:0001385
+name: modified_amino_acid_feature
+def: "A post translationally modified amino acid feature." [SO:ke]
+synonym: "modified amino acid feature" EXACT []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001386
+name: modified_glycine
+def: "A post translationally modified glycine amino acid feature." [SO:ke]
+synonym: "ModGly" EXACT AAMOD []
+synonym: "modified glycine" EXACT []
+xref: MOD:00908
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001387
+name: modified_L_alanine
+def: "A post translationally modified alanine amino acid feature." [SO:ke]
+synonym: "ModAla" EXACT AAMOD []
+synonym: "modified L alanine" EXACT []
+synonym: "modified L-alanine" EXACT []
+xref: MOD:00901
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001388
+name: modified_L_asparagine
+def: "A post translationally modified asparagine amino acid feature." [SO:ke]
+synonym: "ModAsn" EXACT AAMOD []
+synonym: "modified L asparagine" EXACT []
+synonym: "modified L-asparagine" EXACT []
+xref: MOD:00903
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001389
+name: modified_L_aspartic_acid
+def: "A post translationally modified aspartic acid amino acid feature." [SO:ke]
+synonym: "ModAsp" EXACT AAMOD []
+synonym: "modified L aspartic acid" EXACT []
+synonym: "modified L-aspartic acid" EXACT []
+xref: MOD:00904
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001390
+name: modified_L_cysteine
+def: "A post translationally modified cysteine amino acid feature." [SO:ke]
+synonym: "ModCys" EXACT AAMOD []
+synonym: "modified L cysteine" EXACT []
+synonym: "modified L-cysteine" EXACT []
+xref: MOD:00905
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001391
+name: modified_L_glutamic_acid
+synonym: "ModGlu" EXACT AAMOD []
+synonym: "modified L glutamic acid" EXACT []
+synonym: "modified L-glutamic acid" EXACT []
+xref: MOD:00906
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001392
+name: modified_L_threonine
+def: "A post translationally modified threonine amino acid feature." [SO:ke]
+synonym: "modified L threonine" EXACT []
+synonym: "modified L-threonine" EXACT []
+synonym: "ModThr" EXACT AAMOD []
+xref: MOD:00917
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001393
+name: modified_L_tryptophan
+def: "A post translationally modified tryptophan amino acid feature." [SO:ke]
+synonym: "modified L tryptophan" EXACT []
+synonym: "modified L-tryptophan" EXACT []
+synonym: "ModTrp" EXACT AAMOD []
+xref: MOD:00918
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001394
+name: modified_L_glutamine
+def: "A post translationally modified glutamine amino acid feature." [SO:ke]
+synonym: "ModGln" EXACT []
+synonym: "modified L glutamine" EXACT []
+synonym: "modified L-glutamine" EXACT []
+xref: MOD:00907
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001395
+name: modified_L_methionine
+def: "A post translationally modified methionine amino acid feature." [SO:ke]
+synonym: "modified L methionine" EXACT []
+synonym: "modified L-methionine" EXACT []
+synonym: "ModMet" EXACT AAMOD []
+xref: MOD:00913
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001396
+name: modified_L_isoleucine
+def: "A post translationally modified isoleucine amino acid feature." [SO:ke]
+synonym: "modified L isoleucine" EXACT []
+synonym: "modified L-isoleucine" EXACT []
+synonym: "ModIle" EXACT AAMOD []
+xref: MOD:00910
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001397
+name: modified_L_phenylalanine
+def: "A post translationally modified phenylalanine amino acid feature." [SO:ke]
+synonym: "modified L phenylalanine" EXACT []
+synonym: "modified L-phenylalanine" EXACT []
+synonym: "ModPhe" EXACT AAMOD []
+xref: MOD:00914
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001398
+name: modified_L_histidine
+def: "A post translationally modified histidine amino acid feature." [SO:ke]
+synonym: "ModHis" EXACT []
+synonym: "modified L histidine" EXACT []
+synonym: "modified L-histidine" EXACT []
+xref: MOD:00909
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001399
+name: modified_L_serine
+def: "A post translationally modified serine amino acid feature." [SO:ke]
+synonym: "modified L serine" EXACT []
+synonym: "modified L-serine" EXACT []
+synonym: "MosSer" EXACT AAMOD []
+xref: MOD:00916 "http://www.psidev.info/index.php?q=node/104"
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001400
+name: modified_L_lysine
+def: "A post translationally modified lysine amino acid feature." [SO:ke]
+synonym: "modified L lysine" EXACT []
+synonym: "modified L-lysine" EXACT []
+synonym: "ModLys" EXACT AAMOD []
+xref: MOD:00912
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001401
+name: modified_L_leucine
+def: "A post translationally modified leucine amino acid feature." [SO:ke]
+synonym: "modified L leucine" EXACT []
+synonym: "modified L-leucine " EXACT []
+synonym: "ModLeu" EXACT AAMOD []
+xref: MOD:00911
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001402
+name: modified_L_selenocysteine
+def: "A post translationally modified selenocysteine amino acid feature." [SO:ke]
+synonym: "modified L selenocysteine" EXACT []
+synonym: "modified L-selenocysteine" EXACT []
+xref: MOD:01158
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001403
+name: modified_L_valine
+def: "A post translationally modified valine amino acid feature." [SO:ke]
+synonym: "modified L valine" EXACT []
+synonym: "modified L-valine" EXACT []
+synonym: "ModVal" EXACT AAMOD []
+xref: MOD:00920
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001404
+name: modified_L_proline
+def: "A post translationally modified proline amino acid feature." [SO:ke]
+synonym: "modified L proline" EXACT []
+synonym: "modified L-proline " EXACT []
+synonym: "ModPro" EXACT AAMOD []
+xref: MOD:00915
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001405
+name: modified_L_tyrosine
+def: "A post translationally modified tyrosine amino acid feature." [SO:ke]
+synonym: "modified L tyrosine" EXACT []
+synonym: "modified L-tyrosine" EXACT []
+synonym: "ModTry" EXACT AAMOD []
+xref: MOD:00919
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001406
+name: modified_L_arginine
+def: "A post translationally modified arginine amino acid feature." [SO:ke]
+synonym: "ModArg" EXACT AAMOD []
+synonym: "modified L arginine" EXACT []
+synonym: "modified L-arginine" EXACT []
+xref: MOD:00902
+is_a: SO:0001385 ! modified_amino_acid_feature
+
+[Term]
+id: SO:0001407
+name: peptidyl
+def: "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke]
+is_a: SO:0000443 ! polymer_attribute
+
+[Term]
+id: SO:0001408
+name: cleaved_for_gpi_anchor_region
+def: "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]
+synonym: "cleaved for gpi anchor region" EXACT []
+is_a: SO:0100011 ! cleaved_peptide_region
+
+[Term]
+id: SO:0001409
+name: biomaterial_region
+def: "A region which is intended for use in an experiment." [SO:cb]
+subset: SOFA
+synonym: "biomaterial region" EXACT []
+is_a: SO:0000001 ! region
+
+[Term]
+id: SO:0001410
+name: experimental_feature
+def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]
+subset: SOFA
+synonym: "analysis feature" RELATED []
+synonym: "experimental output artefact" EXACT []
+synonym: "experimental_output_artefact" EXACT []
+is_a: SO:0000001 ! region
+
+[Term]
+id: SO:0001411
+name: biological_region
+def: "A region defined by its disposition to be involved in a biological process." [SO:cb]
+subset: SOFA
+synonym: "biological region" EXACT []
+is_a: SO:0000001 ! region
+
+[Term]
+id: SO:0001412
+name: topologically_defined_region
+def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb]
+subset: SOFA
+synonym: "topologically defined region" EXACT []
+is_a: SO:0000001 ! region
+
+[Term]
+id: SO:0001413
+name: translocation_breakpoint
+def: "The point within a chromosome where a translocation begins or ends." [SO:cb]
+synonym: "translocation breakpoint" EXACT []
+is_a: SO:0001021 ! chromosome_breakpoint
+
+[Term]
+id: SO:0001414
+name: insertion_breakpoint
+def: "The point within a chromosome where a insertion begins or ends." [SO:cb]
+synonym: "insertion breakpoint" EXACT []
+is_a: SO:0001021 ! chromosome_breakpoint
+
+[Term]
+id: SO:0001415
+name: deletion_breakpoint
+def: "The point within a chromosome where a deletion begins or ends." [SO:cb]
+synonym: "deletion breakpoint" EXACT []
+is_a: SO:0001021 ! chromosome_breakpoint
+
+[Term]
+id: SO:0001416
+name: five_prime_flanking_region
+def: "A flanking region located five prime of a specific region." [SO:chado]
+synonym: "5' flanking region" RELATED []
+synonym: "five prime flanking region" EXACT []
+is_a: SO:0000239 ! flanking_region
+
+[Term]
+id: SO:0001417
+name: three_prime_flanking_region
+def: "A flanking region located three prime of a specific region." [SO:chado]
+synonym: "3' flanking region" RELATED []
+synonym: "three prime flanking region" EXACT []
+is_a: SO:0000239 ! flanking_region
+
+[Term]
+id: SO:0001418
+name: transcribed_fragment
+def: "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]
+comment: Term requested by the MODencode group.
+synonym: "transcribed fragment" EXACT []
+synonym: "transfrag" RELATED []
+is_a: SO:0001410 ! experimental_feature
+
+[Term]
+id: SO:0001419
+name: cis_splice_site
+def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]
+subset: SOFA
+synonym: "cis splice site" EXACT []
+is_a: SO:0000162 ! splice_site
+
+[Term]
+id: SO:0001420
+name: trans_splice_site
+def: "Primary transcript region bordering trans-splice junction." [SO:ke]
+subset: SOFA
+synonym: "trans splice site" EXACT []
+is_a: SO:0000162 ! splice_site
+
+[Term]
+id: SO:0001421
+name: splice_junction
+def: "The boundary between an intron and an exon." [SO:ke]
+synonym: "splice boundary" EXACT []
+synonym: "splice junction" EXACT []
+is_a: SO:0000699 ! junction
+
+[Term]
+id: SO:0001422
+name: conformational_switch
+def: "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]
+comment: MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.
+synonym: "polypeptide conformational switch" EXACT []
+is_a: SO:0100001 ! biochemical_region_of_peptide
+
+[Term]
+id: SO:0001423
+name: dye_terminator_read
+def: "A read produced by the dye terminator method of sequencing." [SO:ke]
+synonym: "dye terminator read" RELATED []
+is_a: SO:0000150 ! read
+
+[Term]
+id: SO:0001424
+name: pyrosequenced_read
+def: "A read produced by pyrosequencing technology." [SO:ke]
+comment: An example is a read produced by Roche 454 technology.
+synonym: "pyorsequenced read" RELATED []
+is_a: SO:0000150 ! read
+
+[Term]
+id: SO:0001425
+name: ligation_based_read
+def: "A read produced by ligation based sequencing technologies." [SO:ke]
+comment: An example of this kind of read is one produced by ABI SOLiD.
+synonym: "ligation based read" RELATED []
+is_a: SO:0000150 ! read
+
+[Term]
+id: SO:0001426
+name: polymerase_synthesis_read
+def: "A read produced by the polymerase based sequence by synthesis method." [SO:ke]
+comment: An example is a read produced by Illumina technology.
+synonym: "polymerase synthesis read" RELATED []
+is_a: SO:0000150 ! read
+
+[Term]
+id: SO:0001427
+name: cis_regulatory_frameshift_element
+def: "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]
+synonym: "cis regulatory frameshift element" EXACT []
+is_a: SO:0001679 ! transcription_regulatory_region
+
+[Term]
+id: SO:0001428
+name: expressed_sequence_assembly
+def: "A sequence assembly derived from expressed sequences." [SO:ke]
+comment: From tracker [ 2372385 ] expressed_sequence_assembly.
+synonym: "expressed sequence assembly" EXACT []
+is_a: SO:0000353 ! sequence_assembly
+
+[Term]
+id: SO:0001429
+name: DNA_binding_site
+def: "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]
+synonym: "DNA binding site" EXACT []
+is_a: SO:0001655 ! nucleotide_binding_site
+
+[Term]
+id: SO:0001431
+name: cryptic_gene
+def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]
+synonym: "cryptic gene" EXACT []
+is_a: SO:0000704 ! gene
+relationship: has_quality SO:0000976 ! cryptic
+
+[Term]
+id: SO:0001432
+name: sequence_variant_affecting_polyadenylation
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting polyadenylation" RELATED []
+synonym: "sequence variant affecting polyadenylation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001545
+
+[Term]
+id: SO:0001433
+name: three_prime_RACE_clone
+def: "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]
+synonym: "3' RACE clone" RELATED []
+is_a: SO:0000317 ! cDNA_clone
+
+[Term]
+id: SO:0001434
+name: cassette_pseudogene
+def: "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]
+comment: Requested by the Trypanosome community.
+synonym: "cassette pseudogene" EXACT []
+synonym: "cassette type psedogene" RELATED []
+is_a: SO:0001760 ! non_processed_pseudogene
+
+[Term]
+id: SO:0001435
+name: alanine
+comment: A place holder for a cross product with chebi.
+synonym: "A" EXACT aa1 []
+synonym: "Ala" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001436
+name: valine
+comment: A place holder for a cross product with chebi.
+synonym: "V" EXACT aa1 []
+synonym: "Val" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001437
+name: leucine
+comment: A place holder for a cross product with chebi.
+synonym: "L" EXACT aa1 []
+synonym: "Leu" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001438
+name: isoleucine
+comment: A place holder for a cross product with chebi.
+synonym: "I" EXACT aa1 []
+synonym: "Ile" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001439
+name: proline
+comment: A place holder for a cross product with chebi.
+synonym: "P" EXACT aa1 []
+synonym: "Pro" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001440
+name: tryptophan
+comment: A place holder for a cross product with chebi.
+synonym: "Trp" EXACT aa3 []
+synonym: "W" EXACT aa1 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001441
+name: phenylalanine
+comment: A place holder for a cross product with chebi.
+synonym: "F" EXACT aa1 []
+synonym: "Phe" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001442
+name: methionine
+comment: A place holder for a cross product with chebi.
+synonym: "M" EXACT aa1 []
+synonym: "Met" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001443
+name: glycine
+comment: A place holder for a cross product with chebi.
+synonym: "G" EXACT aa1 []
+synonym: "Gly" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001444
+name: serine
+comment: A place holder for a cross product with chebi.
+synonym: "S" EXACT aa1 []
+synonym: "Ser" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001445
+name: threonine
+comment: A place holder for a cross product with chebi.
+synonym: "T" EXACT aa1 []
+synonym: "Thr" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001446
+name: tyrosine
+comment: A place holder for a cross product with chebi.
+synonym: "Tyr" EXACT aa3 []
+synonym: "Y" EXACT aa1 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001447
+name: cysteine
+comment: A place holder for a cross product with chebi.
+synonym: "C" EXACT aa1 []
+synonym: "Cys" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001448
+name: glutamine
+comment: A place holder for a cross product with chebi.
+synonym: "Gln" EXACT aa3 []
+synonym: "Q" EXACT aa1 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001449
+name: asparagine
+comment: A place holder for a cross product with chebi.
+synonym: "Asn" EXACT aa3 []
+synonym: "N" EXACT aa1 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001450
+name: lysine
+comment: A place holder for a cross product with chebi.
+synonym: "K" EXACT aa1 []
+synonym: "Lys" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001451
+name: arginine
+comment: A place holder for a cross product with chebi.
+synonym: "Arg" EXACT aa3 []
+synonym: "R" EXACT aa1 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001452
+name: histidine
+comment: A place holder for a cross product with chebi.
+synonym: "H" EXACT aa1 []
+synonym: "His" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001453
+name: aspartic_acid
+comment: A place holder for a cross product with chebi.
+synonym: "Asp" EXACT aa3 []
+synonym: "aspartic acid" EXACT []
+synonym: "D" EXACT aa1 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001454
+name: glutamic_acid
+comment: A place holder for a cross product with chebi.
+synonym: "E" EXACT aa1 []
+synonym: "Glu" EXACT aa3 []
+synonym: "glutamic acid" EXACT []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001455
+name: selenocysteine
+comment: A place holder for a cross product with chebi.
+synonym: "Sec" EXACT aa3 []
+synonym: "U" EXACT aa1 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001456
+name: pyrrolysine
+comment: A place holder for a cross product with chebi.
+synonym: "O" EXACT aa1 []
+synonym: "Pyl" EXACT aa3 []
+is_a: SO:0001237 ! amino_acid
+
+[Term]
+id: SO:0001457
+name: transcribed_cluster
+def: "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]
+comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
+synonym: "transcribed cluster" EXACT []
+synonym: "unigene cluster" RELATED []
+is_a: SO:0001410 ! experimental_feature
+relationship: has_part SO:0000695 ! reagent
+
+[Term]
+id: SO:0001458
+name: unigene_cluster
+def: "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]
+comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
+synonym: "unigene cluster" RELATED []
+is_a: SO:0001457 ! transcribed_cluster
+
+[Term]
+id: SO:0001459
+name: CRISPR
+def: "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]
+synonym: "Clustered_Regularly_Interspaced_Short_Palindromic_Repeat" EXACT []
+synonym: "CRISPR element" EXACT []
+xref: http:en.wikipedia.org/wiki/CRISPR
+is_a: SO:0000314 ! direct_repeat
+
+[Term]
+id: SO:0001460
+name: insulator_binding_site
+def: "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
+comment: See tracker ID 2060908.
+synonym: "insulator binding site" RELATED []
+is_a: SO:0001654 ! nucleotide_to_protein_binding_site
+relationship: part_of SO:0000627 ! insulator
+
+[Term]
+id: SO:0001461
+name: enhancer_binding_site
+def: "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
+synonym: "enhancer binding site" RELATED []
+is_a: SO:0001654 ! nucleotide_to_protein_binding_site
+relationship: part_of SO:0000165 ! enhancer
+
+[Term]
+id: SO:0001462
+name: contig_collection
+def: "A collection of contigs." [SO:ke]
+comment: See tracker ID: 2138359.
+synonym: "contig collection" EXACT []
+is_a: SO:0001085 ! sequence_conflict
+is_a: SO:0001260 ! sequence_collection
+relationship: has_part SO:0000149 ! contig
+
+[Term]
+id: SO:0001463
+name: lincRNA
+def: "A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]
+synonym: "large intervening non-coding RNA" EXACT []
+synonym: "long intergenic non-coding RNA" EXACT []
+is_a: SO:0001877 ! lnc_RNA
+
+[Term]
+id: SO:0001464
+name: UST
+def: "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]
+synonym: "UTR sequence tag" EXACT []
+is_a: SO:0000345 ! EST
+
+[Term]
+id: SO:0001465
+name: three_prime_UST
+def: "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]
+synonym: "3' UST" RELATED []
+is_a: SO:0001464 ! UST
+
+[Term]
+id: SO:0001466
+name: five_prime_UST
+def: "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]
+synonym: "5' UST" RELATED []
+is_a: SO:0001464 ! UST
+
+[Term]
+id: SO:0001467
+name: RST
+def: "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]
+synonym: "RACE sequence tag" EXACT []
+is_a: SO:0000345 ! EST
+
+[Term]
+id: SO:0001468
+name: three_prime_RST
+def: "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]
+synonym: "3' RST" EXACT []
+is_a: SO:0001467 ! RST
+
+[Term]
+id: SO:0001469
+name: five_prime_RST
+def: "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]
+synonym: "5' RST" RELATED []
+is_a: SO:0001467 ! RST
+
+[Term]
+id: SO:0001470
+name: UST_match
+def: "A match against an UST sequence." [SO:nlw]
+synonym: "UST match" EXACT []
+is_a: SO:0000102 ! expressed_sequence_match
+
+[Term]
+id: SO:0001471
+name: RST_match
+def: "A match against an RST sequence." [SO:nlw]
+synonym: "RST match" EXACT []
+is_a: SO:0000102 ! expressed_sequence_match
+
+[Term]
+id: SO:0001472
+name: primer_match
+def: "A nucleotide match to a primer sequence." [SO:nlw]
+synonym: "primer match" EXACT []
+is_a: SO:0000347 ! nucleotide_match
+
+[Term]
+id: SO:0001473
+name: miRNA_antiguide
+def: "A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]
+synonym: "miRNA antiguide " EXACT []
+synonym: "miRNA passenger strand" EXACT []
+synonym: "miRNA star" EXACT []
+is_a: SO:0001243 ! miRNA_primary_transcript_region
+created_by: kareneilbeck
+creation_date: 2009-05-27T03:35:43Z
+
+[Term]
+id: SO:0001474
+name: trans_splice_junction
+def: "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke]
+synonym: "trans-splice junction" EXACT []
+is_a: SO:0000699 ! junction
+created_by: kareneilbeck
+creation_date: 2009-07-13T04:50:49Z
+
+[Term]
+id: SO:0001475
+name: outron
+def: "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]
+is_a: SO:0000835 ! primary_transcript_region
+created_by: kareneilbeck
+creation_date: 2009-07-14T11:36:08Z
+
+[Term]
+id: SO:0001476
+name: natural_plasmid
+def: "A plasmid that occurs naturally." [SO:xp]
+synonym: "natural plasmid" EXACT []
+is_a: SO:0000155 ! plasmid
+is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
+relationship: has_quality SO:0000782 ! natural
+created_by: kareneilbeck
+creation_date: 2009-09-01T03:43:06Z
+
+[Term]
+id: SO:0001477
+name: gene_trap_construct
+def: "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]
+synonym: "gene trap construct" EXACT []
+is_a: SO:0000637 ! engineered_plasmid
+created_by: kareneilbeck
+creation_date: 2009-09-01T03:49:09Z
+
+[Term]
+id: SO:0001478
+name: promoter_trap_construct
+def: "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]
+synonym: "promoter trap construct" EXACT []
+is_a: SO:0000637 ! engineered_plasmid
+created_by: kareneilbeck
+creation_date: 2009-09-01T03:52:01Z
+
+[Term]
+id: SO:0001479
+name: enhancer_trap_construct
+def: "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]
+synonym: "enhancer trap construct" EXACT []
+is_a: SO:0000637 ! engineered_plasmid
+created_by: kareneilbeck
+creation_date: 2009-09-01T03:53:26Z
+
+[Term]
+id: SO:0001480
+name: PAC_end
+def: "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]
+synonym: "PAC end" EXACT []
+is_a: SO:0000150 ! read
+relationship: part_of SO:0000154 ! PAC
+created_by: kareneilbeck
+creation_date: 2009-09-09T05:18:12Z
+
+[Term]
+id: SO:0001481
+name: RAPD
+def: "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]
+synonym: "Random Amplification Polymorphic DNA" EXACT []
+is_a: SO:0000006 ! PCR_product
+created_by: kareneilbeck
+creation_date: 2009-09-09T05:26:10Z
+
+[Term]
+id: SO:0001482
+name: shadow_enhancer
+synonym: "shadow enhancer" EXACT []
+is_a: SO:0000165 ! enhancer
+created_by: kareneilbeck
+creation_date: 2009-09-09T05:29:29Z
+
+[Term]
+id: SO:0001483
+name: SNV
+def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]
+subset: SOFA
+synonym: "single nucleotide variant" EXACT []
+is_a: SO:1000002 ! substitution
+created_by: kareneilbeck
+creation_date: 2009-10-08T11:37:49Z
+
+[Term]
+id: SO:0001484
+name: X_element_combinatorial_repeat
+def: "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]
+comment: X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
+synonym: "X element combinatorial repeat" EXACT []
+is_a: SO:0000657 ! repeat_region
+relationship: part_of SO:0000624 ! telomere
+created_by: kareneilbeck
+creation_date: 2009-11-10T11:03:37Z
+
+[Term]
+id: SO:0001485
+name: Y_prime_element
+def: "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]
+comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
+synonym: "Y' element" EXACT []
+is_a: SO:0000657 ! repeat_region
+relationship: part_of SO:0000624 ! telomere
+created_by: kareneilbeck
+creation_date: 2009-11-10T12:08:57Z
+
+[Term]
+id: SO:0001486
+name: standard_draft
+def: "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]
+synonym: "standard draft" EXACT []
+is_a: SO:0001499 ! whole_genome_sequence_status
+created_by: kareneilbeck
+creation_date: 2009-10-23T12:48:32Z
+
+[Term]
+id: SO:0001487
+name: high_quality_draft
+def: "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]
+synonym: "high quality draft" EXACT []
+is_a: SO:0001499 ! whole_genome_sequence_status
+created_by: kareneilbeck
+creation_date: 2009-10-23T12:52:36Z
+
+[Term]
+id: SO:0001488
+name: improved_high_quality_draft
+def: "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]
+synonym: "improved high quality draft" EXACT []
+is_a: SO:0001499 ! whole_genome_sequence_status
+created_by: kareneilbeck
+creation_date: 2009-10-23T12:54:35Z
+
+[Term]
+id: SO:0001489
+name: annotation_directed_improved_draft
+def: "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]
+synonym: "annotation directed improvement" EXACT []
+is_a: SO:0001499 ! whole_genome_sequence_status
+created_by: kareneilbeck
+creation_date: 2009-10-23T12:57:10Z
+
+[Term]
+id: SO:0001490
+name: noncontiguous_finished
+def: "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]
+synonym: "non contiguous finished" EXACT []
+is_a: SO:0001499 ! whole_genome_sequence_status
+created_by: kareneilbeck
+creation_date: 2009-10-23T01:01:07Z
+
+[Term]
+id: SO:0001491
+name: finished_genome
+def: "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]
+synonym: "finished" EXACT []
+synonym: "finished genome" EXACT []
+is_a: SO:0001499 ! whole_genome_sequence_status
+created_by: kareneilbeck
+creation_date: 2009-10-23T01:04:43Z
+
+[Term]
+id: SO:0001492
+name: intronic_regulatory_region
+def: "A regulatory region that is part of an intron." [SO:ke]
+synonym: "intronic regulatory region" EXACT []
+is_a: SO:0001679 ! transcription_regulatory_region
+relationship: part_of SO:0000188 ! intron
+created_by: kareneilbeck
+creation_date: 2009-11-08T02:48:02Z
+
+[Term]
+id: SO:0001493
+name: centromere_DNA_Element_I
+def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]
+comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
+synonym: "CDEI" EXACT []
+synonym: "Centromere DNA Element I" EXACT []
+is_a: SO:0000330 ! conserved_region
+relationship: part_of SO:0001794 ! point_centromere
+created_by: kareneilbeck
+creation_date: 2009-11-09T05:47:23Z
+
+[Term]
+id: SO:0001494
+name: centromere_DNA_Element_II
+def: "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]
+comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
+synonym: "CDEII" EXACT []
+synonym: "centromere DNA Element II" EXACT []
+is_a: SO:0000330 ! conserved_region
+relationship: part_of SO:0001794 ! point_centromere
+created_by: kareneilbeck
+creation_date: 2009-11-09T05:51:26Z
+
+[Term]
+id: SO:0001495
+name: centromere_DNA_Element_III
+def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]
+comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
+synonym: "CDEIII" EXACT []
+synonym: "centromere DNA Element III" EXACT []
+is_a: SO:0000330 ! conserved_region
+relationship: part_of SO:0001794 ! point_centromere
+created_by: kareneilbeck
+creation_date: 2009-11-09T05:54:47Z
+
+[Term]
+id: SO:0001496
+name: telomeric_repeat
+def: "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]
+comment: The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739.
+synonym: "telomeric repeat" EXACT []
+is_a: SO:0000657 ! repeat_region
+relationship: part_of SO:0000624 ! telomere
+created_by: kareneilbeck
+creation_date: 2009-11-09T06:00:42Z
+
+[Term]
+id: SO:0001497
+name: X_element
+def: "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]
+comment: Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. \n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1.
+synonym: "X element" RELATED []
+synonym: "X element core sequence" EXACT []
+is_a: SO:0000330 ! conserved_region
+relationship: part_of SO:0000624 ! telomere
+created_by: kareneilbeck
+creation_date: 2009-11-10T10:56:54Z
+
+[Term]
+id: SO:0001498
+name: YAC_end
+def: "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]
+synonym: "YAC end" EXACT []
+is_a: SO:0000150 ! read
+relationship: part_of SO:0000152 ! YAC
+created_by: kareneilbeck
+creation_date: 2009-11-19T11:07:18Z
+
+[Term]
+id: SO:0001499
+name: whole_genome_sequence_status
+def: "The status of whole genome sequence." [DOI:10.1126]
+comment: This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.
+synonym: "whole genome sequence status" EXACT []
+is_a: SO:0000905 ! status
+created_by: kareneilbeck
+creation_date: 2009-10-23T12:47:47Z
+
+[Term]
+id: SO:0001500
+name: heritable_phenotypic_marker
+def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]
+synonym: "heritable phenotypic marker" EXACT []
+synonym: "phenotypic marker" EXACT []
+is_a: SO:0001645 ! genetic_marker
+created_by: kareneilbeck
+creation_date: 2009-12-07T01:50:55Z
+
+[Term]
+id: SO:0001501
+name: peptide_collection
+def: "A collection of peptide sequences." [BBOP:nlw]
+comment: Term requested via tracker ID: 2910829.
+synonym: "peptide collection" EXACT []
+synonym: "peptide set" EXACT []
+is_a: SO:0001260 ! sequence_collection
+relationship: has_part SO:0000104 ! polypeptide
+created_by: kareneilbeck
+creation_date: 2009-12-11T10:58:58Z
+
+[Term]
+id: SO:0001502
+name: high_identity_region
+def: "An experimental feature with high sequence identity to another sequence." [SO:ke]
+comment: Requested by tracker ID: 2902685.
+synonym: "high identity region" EXACT []
+is_a: SO:0001410 ! experimental_feature
+created_by: kareneilbeck
+creation_date: 2009-12-11T11:06:05Z
+
+[Term]
+id: SO:0001503
+name: processed_transcript
+def: "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]
+comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.
+synonym: "processed transcript" EXACT []
+is_a: SO:0000673 ! transcript
+created_by: kareneilbeck
+creation_date: 2009-12-21T05:37:14Z
+
+[Term]
+id: SO:0001504
+name: assortment_derived_variation
+def: "A chromosome variation derived from an event during meiosis." [SO:ke]
+synonym: "assortment derived variation" RELATED []
+is_a: SO:0000240 ! chromosome_variation
+created_by: kareneilbeck
+creation_date: 2010-03-02T05:03:18Z
+
+[Term]
+id: SO:0001505
+name: reference_genome
+def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke]
+synonym: "reference genome" RELATED []
+is_a: SO:0001026 ! genome
+created_by: kareneilbeck
+creation_date: 2010-03-03T02:10:03Z
+
+[Term]
+id: SO:0001506
+name: variant_genome
+def: "A collection of sequences (often chromosomes) of an individual." [SO:ke]
+synonym: "variant genome" RELATED []
+is_a: SO:0001026 ! genome
+created_by: kareneilbeck
+creation_date: 2010-03-03T02:11:25Z
+
+[Term]
+id: SO:0001507
+name: variant_collection
+def: "A collection of one or more sequences of an individual." [SO:ke]
+synonym: "variant collection" RELATED []
+is_a: SO:0001260 ! sequence_collection
+relationship: has_part SO:0001059 ! sequence_alteration
+created_by: kareneilbeck
+creation_date: 2010-03-03T02:13:28Z
+
+[Term]
+id: SO:0001508
+name: alteration_attribute
+synonym: "alteration attribute" EXACT []
+is_a: SO:0000733 ! feature_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:53:23Z
+
+[Term]
+id: SO:0001509
+name: chromosomal_variation_attribute
+synonym: "chromosomal variation attribute" EXACT []
+is_a: SO:0001508 ! alteration_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:54:30Z
+
+[Term]
+id: SO:0001510
+name: intrachromosomal
+is_a: SO:0001509 ! chromosomal_variation_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:55:25Z
+
+[Term]
+id: SO:0001511
+name: interchromosomal
+is_a: SO:0001509 ! chromosomal_variation_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:55:43Z
+
+[Term]
+id: SO:0001512
+name: insertion_attribute
+def: "A quality of a chromosomal insertion,." [SO:ke]
+synonym: "insertion attribute" EXACT []
+is_a: SO:0001508 ! alteration_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:55:56Z
+
+[Term]
+id: SO:0001513
+name: tandem
+is_a: SO:0001512 ! insertion_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:56:37Z
+
+[Term]
+id: SO:0001514
+name: direct
+def: "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]
+is_a: SO:0001512 ! insertion_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:56:49Z
+
+[Term]
+id: SO:0001515
+name: inverted
+def: "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]
+is_a: SO:0001512 ! insertion_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:57:40Z
+
+[Term]
+id: SO:0001516
+name: free
+def: "The quality of a duplication where the new region exists independently of the original." [SO:ke]
+is_a: SO:0001523 ! duplication_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:57:51Z
+
+[Term]
+id: SO:0001517
+name: inversion_attribute
+synonym: "inversion attribute" EXACT []
+is_a: SO:0001508 ! alteration_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:58:10Z
+
+[Term]
+id: SO:0001518
+name: pericentric
+is_a: SO:0001517 ! inversion_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:58:24Z
+
+[Term]
+id: SO:0001519
+name: paracentric
+is_a: SO:0001517 ! inversion_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:58:35Z
+
+[Term]
+id: SO:0001520
+name: translocaton_attribute
+synonym: "translocation attribute" EXACT []
+is_a: SO:0001508 ! alteration_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:58:47Z
+
+[Term]
+id: SO:0001521
+name: reciprocal
+is_a: SO:0001520 ! translocaton_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:59:34Z
+
+[Term]
+id: SO:0001522
+name: insertional
+is_a: SO:0001520 ! translocaton_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-04T02:59:51Z
+
+[Term]
+id: SO:0001523
+name: duplication_attribute
+synonym: "duplication attribute" RELATED []
+is_a: SO:0001508 ! alteration_attribute
+created_by: kareneilbeck
+creation_date: 2010-03-05T01:56:33Z
+
+[Term]
+id: SO:0001524
+name: chromosomally_aberrant_genome
+synonym: "chromosomally aberrant genome" RELATED []
+is_a: SO:0001506 ! variant_genome
+created_by: kareneilbeck
+creation_date: 2010-03-05T02:21:00Z
+
+[Term]
+id: SO:0001525
+name: assembly_error_correction
+def: "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]
+synonym: "assembly error correction" RELATED []
+is_a: SO:0000413 ! sequence_difference
+created_by: kareneilbeck
+creation_date: 2010-03-09T02:16:31Z
+
+[Term]
+id: SO:0001526
+name: base_call_error_correction
+def: "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]
+synonym: "base call error correction" RELATED []
+is_a: SO:0000413 ! sequence_difference
+created_by: kareneilbeck
+creation_date: 2010-03-09T02:18:07Z
+
+[Term]
+id: SO:0001527
+name: peptide_localization_signal
+def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]
+subset: SOFA
+synonym: "localization signal" RELATED []
+synonym: "peptide localization signal" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+created_by: kareneilbeck
+creation_date: 2010-03-11T02:15:05Z
+
+[Term]
+id: SO:0001528
+name: nuclear_localization_signal
+def: "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]
+synonym: "NLS" EXACT []
+xref: http://en.wikipedia.org/wiki/Nuclear_localization_signal "wikipedia"
+is_a: SO:0001527 ! peptide_localization_signal
+created_by: kareneilbeck
+creation_date: 2010-03-11T02:16:38Z
+
+[Term]
+id: SO:0001529
+name: endosomal_localization_signal
+def: "A polypeptide region that targets a polypeptide to the endosome." [SO:ke]
+synonym: "endosomal localization signal" EXACT []
+is_a: SO:0001527 ! peptide_localization_signal
+created_by: kareneilbeck
+creation_date: 2010-03-11T02:20:58Z
+
+[Term]
+id: SO:0001530
+name: lysosomal_localization_signal
+def: "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]
+synonym: "lysosomal localization signal" EXACT []
+is_a: SO:0001527 ! peptide_localization_signal
+created_by: kareneilbeck
+creation_date: 2010-03-11T02:24:10Z
+
+[Term]
+id: SO:0001531
+name: nuclear_export_signal
+def: "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]
+synonym: "NES" EXACT []
+synonym: "nuclear export signal" EXACT []
+xref: http://en.wikipedia.org/wiki/Nuclear_export_signal
+is_a: SO:0001527 ! peptide_localization_signal
+created_by: kareneilbeck
+creation_date: 2010-03-11T02:25:25Z
+
+[Term]
+id: SO:0001532
+name: recombination_signal_sequence
+def: "A region recognized by a recombinase." [SO:ke]
+synonym: "recombination signal sequence" RELATED []
+xref: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences "wikipedia"
+is_a: SO:0000299 ! specific_recombination_site
+created_by: kareneilbeck
+creation_date: 2010-03-11T03:16:47Z
+
+[Term]
+id: SO:0001533
+name: cryptic_splice_site
+def: "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]
+synonym: "cryptic splice signal" RELATED []
+synonym: "cryptic splice site" EXACT []
+is_a: SO:0000162 ! splice_site
+created_by: kareneilbeck
+creation_date: 2010-03-11T03:25:06Z
+
+[Term]
+id: SO:0001534
+name: nuclear_rim_localization_signal
+def: "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]
+synonym: "nuclear rim localization signal" RELATED []
+xref: PMID:16027110
+is_a: SO:0001527 ! peptide_localization_signal
+created_by: kareneilbeck
+creation_date: 2010-03-11T03:31:30Z
+
+[Term]
+id: SO:0001535
+name: p_element
+def: "A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]
+synonym: "P element" RELATED []
+is_a: SO:0000182 ! DNA_transposon
+created_by: kareneilbeck
+creation_date: 2010-03-12T03:40:33Z
+
+[Term]
+id: SO:0001536
+name: functional_variant
+def: "A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]
+synonym: "functional variant" EXACT []
+is_a: SO:0001060 ! sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:30:25Z
+
+[Term]
+id: SO:0001537
+name: structural_variant
+def: "A sequence variant that changes one or more sequence features." [SO:ke]
+synonym: "structural variant" RELATED []
+is_a: SO:0001060 ! sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:31:01Z
+
+[Term]
+id: SO:0001538
+name: transcript_function_variant
+def: "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]
+synonym: "transcript function variant" EXACT []
+is_a: SO:0001536 ! functional_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:32:58Z
+
+[Term]
+id: SO:0001539
+name: translational_product_function_variant
+def: "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]
+synonym: "translational product variant" EXACT []
+is_a: SO:0001536 ! functional_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:46:15Z
+
+[Term]
+id: SO:0001540
+name: level_of_transcript_variant
+def: "A sequence variant which alters the level of a transcript." [SO:ke]
+synonym: "level of transcript variant" EXACT []
+is_a: SO:0001538 ! transcript_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:47:07Z
+
+[Term]
+id: SO:0001541
+name: decreased_transcript_level_variant
+def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]
+synonym: "decreased transcript level" EXACT []
+is_a: SO:0001540 ! level_of_transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:47:47Z
+
+[Term]
+id: SO:0001542
+name: increased_transcript_level_variant
+def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]
+synonym: "increased transcript level variant" EXACT []
+is_a: SO:0001540 ! level_of_transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:48:17Z
+
+[Term]
+id: SO:0001543
+name: transcript_processing_variant
+def: "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]
+synonym: "transcript processing variant" EXACT []
+is_a: SO:0001538 ! transcript_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:48:48Z
+
+[Term]
+id: SO:0001544
+name: editing_variant
+def: "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]
+synonym: "editing variant" EXACT []
+is_a: SO:0001543 ! transcript_processing_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:49:25Z
+
+[Term]
+id: SO:0001545
+name: polyadenylation_variant
+def: "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]
+synonym: "polyadenylation variant" EXACT []
+is_a: SO:0001543 ! transcript_processing_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:49:40Z
+
+[Term]
+id: SO:0001546
+name: transcript_stability_variant
+def: "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]
+synonym: "transcript stability variant" EXACT []
+is_a: SO:0001538 ! transcript_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:50:01Z
+
+[Term]
+id: SO:0001547
+name: decreased_transcript_stability_variant
+def: "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]
+synonym: "decrease transcript stability variant" EXACT []
+is_a: SO:0001546 ! transcript_stability_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:50:23Z
+
+[Term]
+id: SO:0001548
+name: increased_transcript_stability_variant
+def: "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]
+synonym: "increased transcript stability variant" EXACT []
+is_a: SO:0001546 ! transcript_stability_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:50:39Z
+
+[Term]
+id: SO:0001549
+name: transcription_variant
+def: "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]
+synonym: "transcription variant" EXACT []
+is_a: SO:0001538 ! transcript_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:51:26Z
+
+[Term]
+id: SO:0001550
+name: rate_of_transcription_variant
+def: "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]
+synonym: "rate of transcription variant" EXACT []
+is_a: SO:0001549 ! transcription_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:51:50Z
+
+[Term]
+id: SO:0001551
+name: increased_transcription_rate_variant
+def: "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]
+synonym: "increased transcription rate variant" EXACT []
+is_a: SO:0001550 ! rate_of_transcription_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:52:17Z
+
+[Term]
+id: SO:0001552
+name: decreased_transcription_rate_variant
+def: "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]
+synonym: "decreased transcription rate variant" EXACT []
+is_a: SO:0001550 ! rate_of_transcription_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:52:43Z
+
+[Term]
+id: SO:0001553
+name: translational_product_level_variant
+def: "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]
+synonym: "translational product level variant" EXACT []
+is_a: SO:0001539 ! translational_product_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:53:32Z
+
+[Term]
+id: SO:0001554
+name: polypeptide_function_variant
+def: "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]
+synonym: "polypeptide function variant" EXACT []
+is_a: SO:0001539 ! translational_product_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:53:54Z
+
+[Term]
+id: SO:0001555
+name: decreased_translational_product_level
+def: "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]
+synonym: "decrease translational product level" EXACT []
+is_a: SO:0001553 ! translational_product_level_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:54:25Z
+
+[Term]
+id: SO:0001556
+name: increased_translational_product_level
+def: "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]
+synonym: "increase translational product level" EXACT []
+is_a: SO:0001553 ! translational_product_level_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:55:25Z
+
+[Term]
+id: SO:0001557
+name: polypeptide_gain_of_function_variant
+def: "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]
+synonym: "polypeptide gain of function variant" EXACT []
+is_a: SO:0001554 ! polypeptide_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:56:12Z
+
+[Term]
+id: SO:0001558
+name: polypeptide_localization_variant
+def: "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]
+synonym: "polypeptide localization variant" EXACT []
+is_a: SO:0001554 ! polypeptide_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:56:37Z
+
+[Term]
+id: SO:0001559
+name: polypeptide_loss_of_function_variant
+def: "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]
+synonym: "polypeptide loss of function variant" EXACT []
+is_a: SO:0001554 ! polypeptide_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:56:58Z
+
+[Term]
+id: SO:0001560
+name: inactive_ligand_binding_site
+def: "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]
+synonym: "inactive ligand binding site" EXACT []
+is_a: SO:0001559 ! polypeptide_loss_of_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:58:00Z
+
+[Term]
+id: SO:0001561
+name: polypeptide_partial_loss_of_function
+def: "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]
+synonym: "polypeptide partial loss of function" EXACT []
+is_a: SO:0001559 ! polypeptide_loss_of_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:58:32Z
+
+[Term]
+id: SO:0001562
+name: polypeptide_post_translational_processing_variant
+def: "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]
+synonym: "polypeptide post translational processing variant" EXACT []
+is_a: SO:0001554 ! polypeptide_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T11:59:06Z
+
+[Term]
+id: SO:0001563
+name: copy_number_change
+def: "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]
+synonym: "copy number change" EXACT []
+is_a: SO:0001537 ! structural_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:27:33Z
+
+[Term]
+id: SO:0001564
+name: gene_variant
+def: "A sequence variant where the structure of the gene is changed." [SO:ke]
+synonym: "gene structure variant" EXACT []
+synonym: "snpEff:GENE" EXACT VAR []
+synonym: "VAAST:gene_variant" EXACT VAR []
+is_a: SO:0001878 ! feature_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:28:01Z
+
+[Term]
+id: SO:0001565
+name: gene_fusion
+def: "A sequence variant whereby a two genes have become joined." [SO:ke]
+synonym: "gene fusion" EXACT []
+is_a: SO:0001564 ! gene_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:28:28Z
+
+[Term]
+id: SO:0001566
+name: regulatory_region_variant
+def: "A sequence variant located within a regulatory region." [SO:ke]
+comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
+synonym: "regulatory region variant" EXACT []
+synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+is_a: SO:0001878 ! feature_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:28:48Z
+
+[Term]
+id: SO:0001567
+name: stop_retained_variant
+def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]
+synonym: "snpEff:SYNONYMOUS_STOP" EXACT VAR []
+synonym: "stop retained variant" EXACT []
+synonym: "VAAST:stop_retained" EXACT VAR []
+is_a: SO:0001590 ! terminator_codon_variant
+is_a: SO:0001819 ! synonymous_variant
+created_by: kareneilbeck
+creation_date: 2010-04-19T05:02:30Z
+
+[Term]
+id: SO:0001568
+name: splicing_variant
+def: "A sequence variant that changes the process of splicing." [SO:ke]
+synonym: "splicing variant" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:29:22Z
+
+[Term]
+id: SO:0001569
+name: cryptic_splice_site_variant
+def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+synonym: "cryptic splice site activation" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001568 ! splicing_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:29:41Z
+
+[Term]
+id: SO:0001570
+name: cryptic_splice_acceptor
+def: "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]
+synonym: "cryptic splice acceptor" EXACT []
+is_a: SO:0001569 ! cryptic_splice_site_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:30:11Z
+
+[Term]
+id: SO:0001571
+name: cryptic_splice_donor
+def: "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]
+synonym: "cryptic splice donor" EXACT []
+is_a: SO:0001569 ! cryptic_splice_site_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:30:35Z
+
+[Term]
+id: SO:0001572
+name: exon_loss_variant
+def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke]
+synonym: "exon loss" EXACT []
+synonym: "snpEff:EXON_DELETED" EXACT VAR []
+is_a: SO:0001568 ! splicing_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:31:09Z
+
+[Term]
+id: SO:0001573
+name: intron_gain_variant
+def: "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+synonym: "intron gain" EXACT []
+synonym: "intron gain variant" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001568 ! splicing_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:31:25Z
+
+[Term]
+id: SO:0001574
+name: splice_acceptor_variant
+def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]
+synonym: "snpEff:SPLICE_SITE_ACCEPTOR" EXACT VAR []
+synonym: "splice acceptor variant" EXACT []
+synonym: "VAAST:splice_acceptor_variant" EXACT VAR []
+is_a: SO:0001629 ! splice_site_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:31:52Z
+
+[Term]
+id: SO:0001575
+name: splice_donor_variant
+def: "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]
+synonym: "snpEff:SPLICE_SITE_DONOR" EXACT VAR []
+synonym: "splice donor variant" EXACT []
+synonym: "VAAST:splice_donor_variant" EXACT VAR []
+is_a: SO:0001629 ! splice_site_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:32:10Z
+
+[Term]
+id: SO:0001576
+name: transcript_variant
+def: "A sequence variant that changes the structure of the transcript." [SO:ke]
+synonym: "snpEff:TRANSCRIPT" EXACT VAR []
+synonym: "transcript variant" EXACT []
+synonym: "VAAST:transcript_variant" EXACT VAR []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001564 ! gene_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:32:41Z
+
+[Term]
+id: SO:0001577
+name: complex_transcript_variant
+def: "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]
+comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
+synonym: "complex transcript variant" EXACT []
+synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "complext change in transcript" EXACT []
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:33:03Z
+
+[Term]
+id: SO:0001578
+name: stop_lost
+def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]
+comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
+synonym: "ANNOVAR:stoploss" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "snpEff:STOP_LOST" EXACT VAR []
+synonym: "stop codon lost" EXACT []
+synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "VAAST:stop_lost" EXACT VAR []
+is_a: SO:0001590 ! terminator_codon_variant
+is_a: SO:0001907 ! feature_elongation
+is_a: SO:0001992 ! nonsynonymous_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T03:46:42Z
+
+[Term]
+id: SO:0001579
+name: transcript_sequence_variant
+synonym: "transcript sequence variant" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:0001580
+name: coding_sequence_variant
+alt_id: SO:0001581
+def: "A sequence variant that changes the coding sequence." [SO:ke]
+synonym: "coding sequence variant" EXACT []
+synonym: "coding variant" EXACT []
+synonym: "codon variant" EXACT []
+synonym: "codon_variant" EXACT []
+synonym: "snpEff:CDS" EXACT VAR []
+synonym: "snpEff:CODON_CHANGE" RELATED VAR []
+synonym: "VAAST:coding_sequence_variant" EXACT VAR []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001791 ! exon_variant
+is_a: SO:0001968 ! coding_transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:34:36Z
+
+[Term]
+id: SO:0001582
+name: initiator_codon_variant
+def: "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]
+comment: This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called.
+synonym: "initiatior codon variant" EXACT []
+synonym: "initiator codon change" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+xref: loinc:LA6695-6 "Initiating Methionine"
+is_a: SO:0001580 ! coding_sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:35:18Z
+
+[Term]
+id: SO:0001583
+name: missense_variant
+alt_id: SO:0001584
+alt_id: SO:0001783
+def: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]
+comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.
+synonym: "ANNOVAR:nonsynonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+synonym: "missense codon" EXACT []
+synonym: "snpEff:NON_SYSNONYMOUS_CODING" EXACT VAR []
+synonym: "VAAST:non_synonymous_codon" RELATED VAR []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+xref: http://en.wikipedia.org/wiki/Missense_mutation
+xref: loinc:LA6698-0 "Missense"
+is_a: SO:0001992 ! nonsynonymous_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:35:49Z
+
+[Term]
+id: SO:0001585
+name: conservative_missense_variant
+def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]
+synonym: "conservative missense codon" EXACT []
+synonym: "conservative missense variant" EXACT []
+synonym: "neutral missense codon" RELATED []
+synonym: "quiet missense codon" RELATED []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001583 ! missense_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:36:40Z
+
+[Term]
+id: SO:0001586
+name: non_conservative_missense_variant
+def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]
+synonym: "non conservative missense codon" EXACT []
+synonym: "non conservative missense variant" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001583 ! missense_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:37:16Z
+
+[Term]
+id: SO:0001587
+name: stop_gained
+def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]
+comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
+synonym: "ANNOVAR:stopgain" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+synonym: "nonsense codon" EXACT []
+synonym: "snpEFF:STOP_GAINED" EXACT VAR []
+synonym: "stop codon gained" RELATED []
+synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "VAAST:stop_gained" EXACT VAR []
+xref: loinc:LA6699-8 "Nonsense"
+is_a: SO:0001906 ! feature_truncation
+is_a: SO:0001992 ! nonsynonymous_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:37:52Z
+
+[Term]
+id: SO:0001589
+name: frameshift_variant
+def: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]
+comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
+synonym: "ANNOVAR:frameshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "frameshift variant" EXACT []
+synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "snpEff:FRAME_SHIFT" EXACT VAR []
+synonym: "VAAST:frameshift_variant" EXACT VAR []
+xref: loinc:LA6694-9 "Frameshift"
+is_a: SO:0001818 ! protein_altering_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:40:19Z
+
+[Term]
+id: SO:0001590
+name: terminator_codon_variant
+alt_id: SO:0001625
+def: "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]
+comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon.
+synonym: "terminal codon variant" EXACT []
+synonym: "terminal_codon_variant" EXACT []
+synonym: "terminator codon variant" EXACT []
+xref: loinc:LA6700-2 "Stop Codon Mutation"
+is_a: SO:0001580 ! coding_sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:40:37Z
+
+[Term]
+id: SO:0001591
+name: frame_restoring_variant
+def: "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
+synonym: "frame restoring variant" EXACT []
+is_a: SO:0001589 ! frameshift_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:41:09Z
+
+[Term]
+id: SO:0001592
+name: minus_1_frameshift_variant
+def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]
+synonym: "-1 frameshift variant" EXACT []
+synonym: "minus 1 frameshift variant" EXACT []
+is_a: SO:0001589 ! frameshift_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:41:30Z
+
+[Term]
+id: SO:0001593
+name: minus_2_frameshift_variant
+synonym: "-2 frameshift variant" EXACT []
+synonym: "minus 2 frameshift variant" EXACT []
+is_a: SO:0001589 ! frameshift_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:41:52Z
+
+[Term]
+id: SO:0001594
+name: plus_1_frameshift_variant
+def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]
+synonym: "+1 frameshift variant" EXACT []
+synonym: "plus 1 frameshift variant" EXACT []
+is_a: SO:0001589 ! frameshift_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:42:06Z
+
+[Term]
+id: SO:0001595
+name: plus_2_frameshift_variant
+synonym: "+2 frameshift variant" EXACT []
+synonym: "plus 2 frameshift variant" EXACT []
+is_a: SO:0001589 ! frameshift_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:42:23Z
+
+[Term]
+id: SO:0001596
+name: transcript_secondary_structure_variant
+def: "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]
+synonym: "transcript secondary structure variant" EXACT []
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:43:18Z
+
+[Term]
+id: SO:0001597
+name: compensatory_transcript_secondary_structure_variant
+def: "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]
+synonym: "compensatory transcript secondary structure variant" EXACT []
+is_a: SO:0001596 ! transcript_secondary_structure_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:43:54Z
+
+[Term]
+id: SO:0001598
+name: translational_product_structure_variant
+def: "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]
+synonym: "translational product structure variant" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001564 ! gene_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:44:17Z
+
+[Term]
+id: SO:0001599
+name: 3D_polypeptide_structure_variant
+def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke]
+synonym: "3D polypeptide structure variant" EXACT []
+is_a: SO:0001539 ! translational_product_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:44:46Z
+
+[Term]
+id: SO:0001600
+name: complex_3D_structural_variant
+def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke]
+synonym: "complex 3D structural variant" EXACT []
+is_a: SO:0001599 ! 3D_polypeptide_structure_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:45:13Z
+
+[Term]
+id: SO:0001601
+name: conformational_change_variant
+def: "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]
+synonym: "conformational change variant" EXACT []
+is_a: SO:0001599 ! 3D_polypeptide_structure_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:45:48Z
+
+[Term]
+id: SO:0001602
+name: complex_change_of_translational_product_variant
+synonym: "complex change of translational product variant" EXACT []
+is_a: SO:0001539 ! translational_product_function_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:46:54Z
+
+[Term]
+id: SO:0001603
+name: polypeptide_sequence_variant
+def: "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]
+synonym: "polypeptide sequence variant" EXACT []
+is_a: SO:0001598 ! translational_product_structure_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:47:13Z
+
+[Term]
+id: SO:0001604
+name: amino_acid_deletion
+def: "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]
+synonym: "amino acid deletion" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001603 ! polypeptide_sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:47:36Z
+
+[Term]
+id: SO:0001605
+name: amino_acid_insertion
+def: "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]
+synonym: "amino acid insertion" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001603 ! polypeptide_sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:47:56Z
+
+[Term]
+id: SO:0001606
+name: amino_acid_substitution
+def: "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]
+synonym: "amino acid substitution" EXACT []
+synonym: "VAAST:amino_acid_substitution" EXACT VAR []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001603 ! polypeptide_sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:48:17Z
+
+[Term]
+id: SO:0001607
+name: conservative_amino_acid_substitution
+def: "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]
+synonym: "conservative amino acid substitution" EXACT []
+is_a: SO:0001606 ! amino_acid_substitution
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:48:57Z
+
+[Term]
+id: SO:0001608
+name: non_conservative_amino_acid_substitution
+def: "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]
+synonym: "non conservative amino acid substitution" EXACT []
+is_a: SO:0001606 ! amino_acid_substitution
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:49:23Z
+
+[Term]
+id: SO:0001609
+name: elongated_polypeptide
+def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]
+synonym: "elongated polypeptide" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001603 ! polypeptide_sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:49:52Z
+
+[Term]
+id: SO:0001610
+name: elongated_polypeptide_C_terminal
+def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
+synonym: "elongated polypeptide C terminal" EXACT []
+is_a: SO:0001609 ! elongated_polypeptide
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:50:20Z
+
+[Term]
+id: SO:0001611
+name: elongated_polypeptide_N_terminal
+def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
+synonym: "elongated polypeptide N terminal" EXACT []
+is_a: SO:0001609 ! elongated_polypeptide
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:50:31Z
+
+[Term]
+id: SO:0001612
+name: elongated_in_frame_polypeptide_C_terminal
+def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
+synonym: "elongated in frame polypeptide C terminal" EXACT []
+is_a: SO:0001610 ! elongated_polypeptide_C_terminal
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:51:05Z
+
+[Term]
+id: SO:0001613
+name: elongated_out_of_frame_polypeptide_C_terminal
+def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
+synonym: "elongated polypeptide out of frame C terminal" EXACT []
+is_a: SO:0001610 ! elongated_polypeptide_C_terminal
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:51:20Z
+
+[Term]
+id: SO:0001614
+name: elongated_in_frame_polypeptide_N_terminal_elongation
+def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
+synonym: "elongated in frame polypeptide N terminal" EXACT []
+is_a: SO:0001611 ! elongated_polypeptide_N_terminal
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:51:49Z
+
+[Term]
+id: SO:0001615
+name: elongated_out_of_frame_polypeptide_N_terminal
+def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
+synonym: "elongated out of frame N terminal" EXACT []
+is_a: SO:0001611 ! elongated_polypeptide_N_terminal
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:52:05Z
+
+[Term]
+id: SO:0001616
+name: polypeptide_fusion
+def: "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]
+synonym: "polypeptide fusion" EXACT []
+is_a: SO:0001603 ! polypeptide_sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:52:43Z
+
+[Term]
+id: SO:0001617
+name: polypeptide_truncation
+def: "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]
+synonym: "polypeptide truncation" EXACT []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+is_a: SO:0001603 ! polypeptide_sequence_variant
+created_by: kareneilbeck
+creation_date: 2010-03-22T02:53:07Z
+
+[Term]
+id: SO:0001618
+name: inactive_catalytic_site
+def: "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]
+synonym: "inactive catalytic site" EXACT []
+is_a: SO:0001560 ! inactive_ligand_binding_site
+created_by: kareneilbeck
+creation_date: 2010-03-22T03:06:14Z
+
+[Term]
+id: SO:0001619
+name: non_coding_transcript_variant
+def: "A transcript variant of a non coding RNA gene." [SO:ke]
+comment: Within non-coding gene - Located within a gene that does not code for a protein.
+synonym: "ANNOVAR:ncRNA" RELATED VAR [http:http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "nc transcript variant" EXACT []
+synonym: "non coding transcript variant" EXACT []
+synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html]
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T11:16:23Z
+
+[Term]
+id: SO:0001620
+name: mature_miRNA_variant
+def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke]
+comment: EBI term: Within mature miRNA - Located within a microRNA.
+synonym: "mature miRNA variant" EXACT []
+synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+is_a: SO:0001619 ! non_coding_transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T11:16:58Z
+
+[Term]
+id: SO:0001621
+name: NMD_transcript_variant
+def: "A variant in a transcript that is the target of NMD." [SO:ke]
+synonym: "NMD transcript variant" EXACT []
+synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T11:20:40Z
+
+[Term]
+id: SO:0001622
+name: UTR_variant
+def: "A transcript variant that is located within the UTR." [SO:ke]
+synonym: "UTR variant" EXACT []
+synonym: "UTR_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+is_a: SO:0001791 ! exon_variant
+is_a: SO:0001968 ! coding_transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T11:22:58Z
+
+[Term]
+id: SO:0001623
+name: 5_prime_UTR_variant
+def: "A UTR variant of the 5' UTR." [SO:ke]
+comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).
+synonym: "5'UTR variant" EXACT []
+synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "ANNOVAR:UTR5" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "five prime UTR variant" EXACT []
+synonym: "snpEff:UTR_5_PRIME" EXACT VAR []
+synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+synonym: "VAAST:five_prime_UTR_variant" EXACT VAR []
+is_a: SO:0001622 ! UTR_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T11:23:29Z
+
+[Term]
+id: SO:0001624
+name: 3_prime_UTR_variant
+def: "A UTR variant of the 3' UTR." [SO:ke]
+comment: EBI term 3prime UTR variations - In 3prime UTR.
+synonym: "3'UTR variant" EXACT []
+synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "ANNOVAR:UTR3" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "snpEff:UTR_3_PRIME" EXACT VAR []
+synonym: "three prime UTR variant" EXACT []
+synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+synonym: "VAAST:three_prime_UTR_variant" EXACT VAR []
+is_a: SO:0001622 ! UTR_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T11:23:54Z
+
+[Term]
+id: SO:0001626
+name: incomplete_terminal_codon_variant
+def: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]
+comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
+synonym: "incomplete terminal codon variant" EXACT []
+synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+is_a: SO:0001590 ! terminator_codon_variant
+is_a: SO:0001650 ! inframe_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T03:51:15Z
+
+[Term]
+id: SO:0001627
+name: intron_variant
+def: "A transcript variant occurring within an intron." [SO:ke]
+comment: EBI term: Intronic variations - In intron.
+synonym: "ANNOVAR:intronic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "intron variant" EXACT []
+synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "snpEff:INTRON" EXACT VAR []
+synonym: "VAAST:intron_variant" EXACT VAR []
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T03:52:38Z
+
+[Term]
+id: SO:0001628
+name: intergenic_variant
+def: "A sequence variant located in the intergenic region, between genes." [SO:ke]
+comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
+synonym: "ANNOVAR:intergenic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "intergenic variant" EXACT []
+synonym: "snpEff:INTERGENIC" EXACT VAR []
+is_a: SO:0001878 ! feature_variant
+created_by: kareneilbeck
+creation_date: 2010-03-23T05:07:37Z
+
+[Term]
+id: SO:0001629
+name: splice_site_variant
+def: "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]
+comment: EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.
+synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "splice site variant" EXACT []
+is_a: SO:0001568 ! splicing_variant
+is_a: SO:0001627 ! intron_variant
+created_by: kareneilbeck
+creation_date: 2010-03-24T09:42:00Z
+
+[Term]
+id: SO:0001630
+name: splice_region_variant
+def: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]
+comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
+synonym: "ANNOVAR:splicing" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "splice region variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "VAAST:splice_region_variant" EXACT VAR []
+is_a: SO:0001568 ! splicing_variant
+created_by: kareneilbeck
+creation_date: 2010-03-24T09:46:02Z
+
+[Term]
+id: SO:0001631
+name: upstream_gene_variant
+def: "A sequence variant located 5' of a gene." [SO:ke]
+comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
+synonym: "ANNOVAR:upstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "snpEff:UPSTREAM" EXACT VAR []
+synonym: "upstream gene variant" EXACT []
+is_a: SO:0001628 ! intergenic_variant
+created_by: kareneilbeck
+creation_date: 2010-03-24T09:49:13Z
+
+[Term]
+id: SO:0001632
+name: downstream_gene_variant
+def: "A sequence variant located 3' of a gene." [SO:ke]
+comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
+synonym: "ANNOVAR:downstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "downstream gene variant" EXACT []
+synonym: "snpEff:DOWNSTREAM" EXACT VAR []
+is_a: SO:0001628 ! intergenic_variant
+created_by: kareneilbeck
+creation_date: 2010-03-24T09:49:38Z
+
+[Term]
+id: SO:0001633
+name: 5KB_downstream_variant
+def: "A sequence variant located within 5 KB of the end of a gene." [SO:ke]
+comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
+synonym: "5KB downstream variant" EXACT []
+synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+synonym: "within 5KB downstream" RELATED []
+is_a: SO:0001632 ! downstream_gene_variant
+created_by: kareneilbeck
+creation_date: 2010-03-24T09:50:16Z
+
+[Term]
+id: SO:0001634
+name: 500B_downstream_variant
+def: "A sequence variant located within a half KB of the end of a gene." [SO:ke]
+synonym: "500B downstream variant" EXACT []
+synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+is_a: SO:0001633 ! 5KB_downstream_variant
+created_by: kareneilbeck
+creation_date: 2010-03-24T09:50:42Z
+
+[Term]
+id: SO:0001635
+name: 5KB_upstream_variant
+def: "A sequence variant located within 5KB 5' of a gene." [SO:ke]
+comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
+synonym: "5kb upstream variant" EXACT []
+synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
+is_a: SO:0001631 ! upstream_gene_variant
+created_by: kareneilbeck
+creation_date: 2010-03-24T09:51:06Z
+
+[Term]
+id: SO:0001636
+name: 2KB_upstream_variant
+def: "A sequence variant located within 2KB 5' of a gene." [SO:ke]
+synonym: "2KB upstream variant" EXACT []
+synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+is_a: SO:0001635 ! 5KB_upstream_variant
+created_by: kareneilbeck
+creation_date: 2010-03-24T09:51:22Z
+
+[Term]
+id: SO:0001637
+name: rRNA_gene
+def: "A gene that encodes for ribosomal RNA." [SO:ke]
+synonym: "rDNA" EXACT []
+synonym: "rRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+created_by: kareneilbeck
+creation_date: 2010-04-21T10:10:32Z
+
+[Term]
+id: SO:0001638
+name: piRNA_gene
+def: "A gene that encodes for an piwi associated RNA." [SO:ke]
+synonym: "piRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+created_by: kareneilbeck
+creation_date: 2010-04-21T10:11:36Z
+
+[Term]
+id: SO:0001639
+name: RNase_P_RNA_gene
+def: "A gene that encodes an RNase P RNA." [SO:ke]
+synonym: "RNase P RNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+created_by: kareneilbeck
+creation_date: 2010-04-21T10:13:23Z
+
+[Term]
+id: SO:0001640
+name: RNase_MRP_RNA_gene
+def: "A gene that encodes a RNase_MRP_RNA." [SO:ke]
+synonym: "RNase MRP RNA gene" RELATED []
+is_a: SO:0001263 ! ncRNA_gene
+created_by: kareneilbeck
+creation_date: 2010-04-21T10:13:58Z
+
+[Term]
+id: SO:0001641
+name: lincRNA_gene
+def: "A gene that encodes large intervening non-coding RNA." [SO:ke]
+synonym: "lincRNA gene" EXACT []
+is_a: SO:0001263 ! ncRNA_gene
+created_by: kareneilbeck
+creation_date: 2010-04-21T10:14:24Z
+
+[Term]
+id: SO:0001642
+name: mathematically_defined_repeat
+def: "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill]
+comment: Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).
+synonym: "mathematically defined repeat" EXACT []
+is_a: SO:0001410 ! experimental_feature
+created_by: kareneilbeck
+creation_date: 2010-05-03T11:50:14Z
+
+[Term]
+id: SO:0001643
+name: telomerase_RNA_gene
+def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]
+synonym: "Telomerase RNA component" EXACT []
+synonym: "telomerase RNA gene" EXACT []
+synonym: "TERC" EXACT []
+xref: http:http://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia"
+is_a: SO:0001263 ! ncRNA_gene
+created_by: kareneilbeck
+creation_date: 2010-05-18T05:26:38Z
+
+[Term]
+id: SO:0001644
+name: targeting_vector
+def: "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]
+synonym: "targeting vector" RELATED []
+is_a: SO:0000440 ! vector_replicon
+is_a: SO:0000804 ! engineered_region
+relationship: has_part SO:0000853 ! homologous_region
+relationship: has_quality SO:0000783 ! engineered
+created_by: kareneilbeck
+creation_date: 2010-05-28T02:05:25Z
+
+[Term]
+id: SO:0001645
+name: genetic_marker
+def: "A measurable sequence feature that varies within a population." [SO:db]
+synonym: "genetic marker" RELATED []
+is_a: SO:0001411 ! biological_region
+created_by: kareneilbeck
+creation_date: 2010-05-28T02:33:07Z
+
+[Term]
+id: SO:0001646
+name: DArT_marker
+def: "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]
+synonym: "DArT marker" EXACT []
+is_a: SO:0001645 ! genetic_marker
+created_by: kareneilbeck
+creation_date: 2010-05-28T02:34:43Z
+
+[Term]
+id: SO:0001647
+name: kozak_sequence
+def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]
+subset: SOFA
+synonym: "kozak consensus" EXACT []
+synonym: "kozak consensus sequence" EXACT []
+synonym: "kozak sequence" EXACT []
+xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia"
+is_a: SO:0000139 ! ribosome_entry_site
+created_by: kareneilbeck
+creation_date: 2010-06-07T03:12:20Z
+
+[Term]
+id: SO:0001648
+name: nested_transposon
+def: "A transposon that is disrupted by the insertion of another element." [SO:ke]
+synonym: "nested transposon" EXACT []
+is_a: SO:0000101 ! transposable_element
+created_by: kareneilbeck
+creation_date: 2010-06-23T03:22:57Z
+
+[Term]
+id: SO:0001649
+name: nested_repeat
+def: "A repeat that is disrupted by the insertion of another element." [SO:ke]
+synonym: "nested repeat" RELATED []
+is_a: SO:0000657 ! repeat_region
+created_by: kareneilbeck
+creation_date: 2010-06-23T03:24:55Z
+
+[Term]
+id: SO:0001650
+name: inframe_variant
+def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]
+synonym: "ANNOVAR:nonframeshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "cds-indel" EXACT dbsnp []
+synonym: "inframe variant" EXACT []
+synonym: "VAAST:inframe_variant" EXACT VAR []
+is_a: SO:0001818 ! protein_altering_variant
+created_by: kareneilbeck
+creation_date: 2010-07-19T01:24:44Z
+
+[Term]
+id: SO:0001653
+name: retinoic_acid_responsive_element
+def: "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]
+synonym: "RARE" EXACT []
+synonym: "retinoic acid responsive element" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000167 ! promoter
+created_by: kareneilbeck
+creation_date: 2010-08-03T10:46:12Z
+
+[Term]
+id: SO:0001654
+name: nucleotide_to_protein_binding_site
+def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
+subset: SOFA
+synonym: "nucleotide to protein binding site" RELATED []
+is_a: SO:0000410 ! protein_binding_site
+created_by: kareneilbeck
+creation_date: 2010-08-03T12:26:05Z
+
+[Term]
+id: SO:0001655
+name: nucleotide_binding_site
+def: "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]
+comment: See GO:0000166 : nucleotide binding.
+synonym: "np_bind" EXACT BS [uniprot:feature]
+synonym: "nucleotide binding site" EXACT []
+is_a: SO:0000409 ! binding_site
+created_by: kareneilbeck
+creation_date: 2010-08-03T12:30:04Z
+
+[Term]
+id: SO:0001656
+name: metal_binding_site
+def: "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]
+comment: See GO:0046872 : metal ion binding.
+synonym: "metal binding site" RELATED []
+is_a: SO:0000409 ! binding_site
+created_by: kareneilbeck
+creation_date: 2010-08-03T12:31:42Z
+
+[Term]
+id: SO:0001657
+name: ligand_binding_site
+def: "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]
+synonym: "ligand binding site" EXACT []
+is_a: SO:0000409 ! binding_site
+created_by: kareneilbeck
+creation_date: 2010-08-03T12:32:58Z
+
+[Term]
+id: SO:0001658
+name: nested_tandem_repeat
+def: "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]
+comment: Tracker ID: 3052459.
+synonym: "nested tandem repeat" EXACT []
+synonym: "NTR" EXACT []
+is_a: SO:0001649 ! nested_repeat
+created_by: kareneilbeck
+creation_date: 2010-08-26T09:36:16Z
+
+[Term]
+id: SO:0001659
+name: promoter_element
+synonym: "promoter element" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: overlaps SO:0000235 ! TF_binding_site
+created_by: kareneilbeck
+creation_date: 2010-10-01T11:48:32Z
+
+[Term]
+id: SO:0001660
+name: core_promoter_element
+synonym: "core promoter element" EXACT []
+synonym: "general transcription factor binding site" RELATED []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2010-10-01T11:49:03Z
+
+[Term]
+id: SO:0001661
+name: RNA_polymerase_II_TATA_box
+def: "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]
+synonym: "RNA polymerase II TATA box" EXACT []
+is_a: SO:0000174 ! TATA_box
+relationship: part_of SO:0001669 ! RNApol_II_core_promoter
+created_by: kareneilbeck
+creation_date: 2010-10-01T02:42:12Z
+
+[Term]
+id: SO:0001662
+name: RNA_polymerase_III_TATA_box
+def: "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]
+synonym: "RNA polymerase III TATA box" EXACT []
+is_a: SO:0000174 ! TATA_box
+relationship: part_of SO:0000171 ! RNApol_III_promoter
+created_by: kareneilbeck
+creation_date: 2010-10-01T02:43:16Z
+
+[Term]
+id: SO:0001663
+name: BREd_motif
+def: "A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]
+synonym: "BREd" EXACT []
+synonym: "BREd motif" RELATED []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0001669 ! RNApol_II_core_promoter
+created_by: kareneilbeck
+creation_date: 2010-10-01T02:49:55Z
+
+[Term]
+id: SO:0001664
+name: DCE
+def: "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]
+synonym: "downstream core element" RELATED []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0001669 ! RNApol_II_core_promoter
+created_by: kareneilbeck
+creation_date: 2010-10-01T02:56:41Z
+
+[Term]
+id: SO:0001665
+name: DCE_SI
+def: "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]
+synonym: "DCE SI" RELATED []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0001664 ! DCE
+created_by: kareneilbeck
+creation_date: 2010-10-01T03:00:10Z
+
+[Term]
+id: SO:0001666
+name: DCE_SII
+def: "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]
+synonym: "DCE SII" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0001664 ! DCE
+created_by: kareneilbeck
+creation_date: 2010-10-01T03:00:30Z
+
+[Term]
+id: SO:0001667
+name: DCE_SIII
+def: "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]
+synonym: "DCE SIII" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0001664 ! DCE
+created_by: kareneilbeck
+creation_date: 2010-10-01T03:00:44Z
+
+[Term]
+id: SO:0001668
+name: proximal_promoter_element
+def: "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]
+synonym: "proximal promoter element" RELATED []
+synonym: "specific transcription factor binding site" RELATED []
+is_a: SO:0001678 ! regulatory_promoter_element
+created_by: kareneilbeck
+creation_date: 2010-10-01T03:10:23Z
+
+[Term]
+id: SO:0001669
+name: RNApol_II_core_promoter
+def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]
+synonym: "RNApol II core promoter" EXACT []
+is_a: SO:0000170 ! RNApol_II_promoter
+created_by: kareneilbeck
+creation_date: 2010-10-01T03:13:41Z
+
+[Term]
+id: SO:0001670
+name: distal_promoter_element
+synonym: "distal promoter element" RELATED []
+is_a: SO:0001678 ! regulatory_promoter_element
+created_by: kareneilbeck
+creation_date: 2010-10-01T03:21:08Z
+
+[Term]
+id: SO:0001671
+name: bacterial_RNApol_promoter_sigma_70
+synonym: "bacterial RNA polymerase promoter sigma 70" EXACT []
+is_a: SO:0000613 ! bacterial_RNApol_promoter
+created_by: kareneilbeck
+creation_date: 2010-10-06T01:41:34Z
+
+[Term]
+id: SO:0001672
+name: bacterial_RNApol_promoter_sigma54
+synonym: "bacterial RNA polymerase promoter sigma54" EXACT []
+is_a: SO:0000613 ! bacterial_RNApol_promoter
+created_by: kareneilbeck
+creation_date: 2010-10-06T01:42:37Z
+
+[Term]
+id: SO:0001673
+name: minus_12_signal
+def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]
+synonym: "minus 12 signal" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54
+created_by: kareneilbeck
+creation_date: 2010-10-06T01:44:57Z
+
+[Term]
+id: SO:0001674
+name: minus_24_signal
+def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]
+synonym: "minus 24 signal" RELATED []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54
+created_by: kareneilbeck
+creation_date: 2010-10-06T01:45:24Z
+
+[Term]
+id: SO:0001675
+name: A_box_type_1
+def: "An A box within an RNA polymerase III type 1 promoter." [SO:ke]
+comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
+synonym: "A box type 1" RELATED []
+is_a: SO:0000619 ! A_box
+relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
+created_by: kareneilbeck
+creation_date: 2010-10-06T05:43:43Z
+
+[Term]
+id: SO:0001676
+name: A_box_type_2
+def: "An A box within an RNA polymerase III type 2 promoter." [SO:ke]
+comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
+synonym: "A box type 2" RELATED []
+is_a: SO:0000619 ! A_box
+relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2
+created_by: kareneilbeck
+creation_date: 2010-10-06T05:44:18Z
+
+[Term]
+id: SO:0001677
+name: intermediate_element
+def: "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]
+synonym: "IE" EXACT []
+synonym: "intermediate element" RELATED []
+is_a: SO:0001660 ! core_promoter_element
+relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
+created_by: kareneilbeck
+creation_date: 2010-10-06T05:52:03Z
+
+[Term]
+id: SO:0001678
+name: regulatory_promoter_element
+def: "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]
+synonym: "regulatory promoter element" RELATED []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2010-10-07T04:39:48Z
+
+[Term]
+id: SO:0001679
+name: transcription_regulatory_region
+def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke]
+subset: SOFA
+synonym: "transcription regulatory region" EXACT []
+is_a: SO:0005836 ! regulatory_region
+created_by: kareneilbeck
+creation_date: 2010-10-12T03:49:35Z
+
+[Term]
+id: SO:0001680
+name: translation_regulatory_region
+def: "A regulatory region that is involved in the control of the process of translation." [SO:ke]
+synonym: "translation regulatory region" EXACT []
+is_a: SO:0005836 ! regulatory_region
+created_by: kareneilbeck
+creation_date: 2010-10-12T03:52:45Z
+
+[Term]
+id: SO:0001681
+name: recombination_regulatory_region
+def: "A regulatory region that is involved in the control of the process of recombination." [SO:ke]
+synonym: "recombination regulatory region" EXACT []
+is_a: SO:0005836 ! regulatory_region
+created_by: kareneilbeck
+creation_date: 2010-10-12T03:53:35Z
+
+[Term]
+id: SO:0001682
+name: replication_regulatory_region
+def: "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]
+synonym: "replication regulatory region" RELATED []
+is_a: SO:0005836 ! regulatory_region
+created_by: kareneilbeck
+creation_date: 2010-10-12T03:54:09Z
+
+[Term]
+id: SO:0001683
+name: sequence_motif
+def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]
+subset: SOFA
+synonym: "sequence motif" RELATED []
+xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia"
+is_a: SO:0001411 ! biological_region
+created_by: kareneilbeck
+creation_date: 2010-10-14T04:13:22Z
+
+[Term]
+id: SO:0001684
+name: experimental_feature_attribute
+def: "An attribute of an experimentally derived feature." [SO:ke]
+synonym: "experimental feature attribute" RELATED []
+is_a: SO:0000733 ! feature_attribute
+created_by: kareneilbeck
+creation_date: 2010-10-28T02:22:23Z
+
+[Term]
+id: SO:0001685
+name: score
+def: "The score of an experimentally derived feature such as a p-value." [SO:ke]
+is_a: SO:0001684 ! experimental_feature_attribute
+created_by: kareneilbeck
+creation_date: 2010-10-28T02:23:16Z
+
+[Term]
+id: SO:0001686
+name: quality_value
+def: "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]
+synonym: "quality value" RELATED []
+is_a: SO:0001684 ! experimental_feature_attribute
+created_by: kareneilbeck
+creation_date: 2010-10-28T02:24:11Z
+
+[Term]
+id: SO:0001687
+name: restriction_enzyme_recognition_site
+def: "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]
+synonym: "restriction endonuclease recognition site" EXACT []
+synonym: "restriction enzyme recognition site" EXACT []
+is_a: SO:0001954 ! restriction_enzyme_region
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:29:57Z
+
+[Term]
+id: SO:0001688
+name: restriction_enzyme_cleavage_junction
+def: "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]
+synonym: "restriction enzyme cleavage junction" EXACT []
+is_a: SO:0000699 ! junction
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:35:02Z
+
+[Term]
+id: SO:0001689
+name: five_prime_restriction_enzyme_junction
+def: "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]
+synonym: "5' restriction enzyme junction" EXACT []
+is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site
+relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:36:24Z
+
+[Term]
+id: SO:0001690
+name: three_prime_restriction_enzyme_junction
+synonym: "3' restriction enzyme junction" EXACT []
+is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site
+relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:37:52Z
+
+[Term]
+id: SO:0001691
+name: blunt_end_restriction_enzyme_cleavage_site
+synonym: "blunt end restriction enzyme cleavage site" EXACT []
+is_a: SO:0001687 ! restriction_enzyme_recognition_site
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:39:53Z
+
+[Term]
+id: SO:0001692
+name: sticky_end_restriction_enzyme_cleavage_site
+synonym: "sticky end restriction enzyme cleavage site" RELATED []
+is_a: SO:0001687 ! restriction_enzyme_recognition_site
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:40:50Z
+
+[Term]
+id: SO:0001693
+name: blunt_end_restriction_enzyme_cleavage_junction
+def: "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]
+synonym: "blunt end restriction enzyme cleavage site" RELATED []
+is_a: SO:0001688 ! restriction_enzyme_cleavage_junction
+relationship: part_of SO:0001691 ! blunt_end_restriction_enzyme_cleavage_site
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:43:14Z
+
+[Term]
+id: SO:0001694
+name: single_strand_restriction_enzyme_cleavage_site
+def: "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]
+synonym: "single strand restriction enzyme cleavage site" RELATED []
+is_a: SO:0001688 ! restriction_enzyme_cleavage_junction
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:44:48Z
+
+[Term]
+id: SO:0001695
+name: restriction_enzyme_single_strand_overhang
+def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]
+synonym: "single strand overhang" EXACT []
+synonym: "sticky end" RELATED []
+is_a: SO:0001954 ! restriction_enzyme_region
+relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
+created_by: kareneilbeck
+creation_date: 2010-10-29T12:48:35Z
+
+[Term]
+id: SO:0001696
+name: experimentally_defined_binding_region
+def: "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]
+synonym: "experimentally defined binding region" RELATED []
+is_a: SO:0001410 ! experimental_feature
+created_by: kareneilbeck
+creation_date: 2010-11-02T11:39:59Z
+
+[Term]
+id: SO:0001697
+name: ChIP_seq_region
+def: "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]
+synonym: "ChIP seq region" RELATED []
+is_a: SO:0001696 ! experimentally_defined_binding_region
+relationship: contains SO:0000410 ! protein_binding_site
+created_by: kareneilbeck
+creation_date: 2010-11-02T11:43:07Z
+
+[Term]
+id: SO:0001698
+name: ASPE_primer
+def: "\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]
+synonym: "allele specific primer extension primer" EXACT []
+synonym: "ASPE primer" EXACT []
+is_a: SO:0000112 ! primer
+created_by: kareneilbeck
+creation_date: 2010-11-11T03:25:21Z
+
+[Term]
+id: SO:0001699
+name: dCAPS_primer
+def: "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]
+synonym: "dCAPS primer" EXACT []
+synonym: "derived cleaved amplified polymorphic primer" EXACT []
+is_a: SO:0000112 ! primer
+created_by: kareneilbeck
+creation_date: 2010-11-11T03:27:09Z
+
+[Term]
+id: SO:0001700
+name: histone_modification
+def: "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]
+synonym: "histone modification" EXACT []
+synonym: "histone modification site" RELATED []
+is_a: SO:0001089 ! post_translationally_modified_region
+is_a: SO:0001720 ! epigenetically_modified_region
+relationship: has_quality SO:0000133 ! epigenetically_modified
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:22:08Z
+
+[Term]
+id: SO:0001701
+name: histone_methylation_site
+def: "A histone modification site where the modification is the methylation of the residue." [SO:ke]
+synonym: "histone methylation" EXACT []
+synonym: "histone methylation site" EXACT []
+is_a: SO:0001700 ! histone_modification
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:23:02Z
+
+[Term]
+id: SO:0001702
+name: histone_acetylation_site
+def: "A histone modification where the modification is the acylation of the residue." [SO:ke]
+synonym: "histone acetylation" EXACT []
+synonym: "histone acetylation site" EXACT []
+is_a: SO:0001700 ! histone_modification
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:23:27Z
+
+[Term]
+id: SO:0001703
+name: H3K9_acetylation_site
+def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K9 acetylation site" EXACT []
+synonym: "H3K9Ac" RELATED []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:25:05Z
+
+[Term]
+id: SO:0001704
+name: H3K14_acetylation_site
+def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K14 acetylation site" EXACT []
+synonym: "H3K14Ac" RELATED []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:25:53Z
+
+[Term]
+id: SO:0001705
+name: H3K4_monomethylation_site
+def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K4 mono-methylation site" EXACT []
+synonym: "H3K4me1" RELATED []
+is_a: SO:0001734 ! H3K4_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:28:14Z
+
+[Term]
+id: SO:0001706
+name: H3K4_trimethylation
+def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K4 tri-methylation" EXACT []
+synonym: "H3K4me3" RELATED []
+is_a: SO:0001734 ! H3K4_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:29:12Z
+
+[Term]
+id: SO:0001707
+name: H3K9_trimethylation_site
+def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K9 tri-methylation site" EXACT []
+synonym: "H3K9Me3" RELATED []
+is_a: SO:0001736 ! H3K9_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:30:34Z
+
+[Term]
+id: SO:0001708
+name: H3K27_monomethylation_site
+def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H2K27 mono-methylation site" EXACT []
+synonym: "H2K27Me1" RELATED []
+is_a: SO:0001732 ! H3K27_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:31:54Z
+
+[Term]
+id: SO:0001709
+name: H3K27_trimethylation_site
+def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K27 tri-methylation site" EXACT []
+synonym: "H3K27Me3" RELATED []
+is_a: SO:0001732 ! H3K27_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:32:41Z
+
+[Term]
+id: SO:0001710
+name: H3K79_monomethylation_site
+def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K79 mono-methylation site" EXACT []
+synonym: "H3K79me1" RELATED []
+is_a: SO:0001735 ! H3K79_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:33:42Z
+
+[Term]
+id: SO:0001711
+name: H3K79_dimethylation_site
+def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K79 di-methylation site" EXACT []
+synonym: "H3K79Me2" RELATED []
+is_a: SO:0001735 ! H3K79_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:34:39Z
+
+[Term]
+id: SO:0001712
+name: H3K79_trimethylation_site
+def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H3K79 tri-methylation site" EXACT []
+synonym: "H3K79Me3" RELATED []
+is_a: SO:0001735 ! H3K79_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:35:30Z
+
+[Term]
+id: SO:0001713
+name: H4K20_monomethylation_site
+def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H4K20 mono-methylation site" EXACT []
+synonym: "H4K20Me1" RELATED []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:36:43Z
+
+[Term]
+id: SO:0001714
+name: H2BK5_monomethylation_site
+def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]
+synonym: "H2BK5 mono-methylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-03-31T10:38:12Z
+
+[Term]
+id: SO:0001715
+name: ISRE
+def: "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]
+comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term.
+synonym: "interferon stimulated response element" EXACT []
+is_a: SO:0001055 ! transcriptional_cis_regulatory_region
+created_by: kareneilbeck
+creation_date: 2010-04-05T11:15:08Z
+
+[Term]
+id: SO:0001716
+name: histone_ubiqitination_site
+def: "A histone modification site where ubiquitin may be added." [SO:ke]
+synonym: "histone ubiquitination site" RELATED []
+is_a: SO:0001700 ! histone_modification
+created_by: kareneilbeck
+creation_date: 2010-04-13T10:12:18Z
+
+[Term]
+id: SO:0001717
+name: H2B_ubiquitination_site
+def: "A histone modification site on H2B where ubiquitin may be added." [SO:ke]
+synonym: "H2BUbiq" RELATED []
+is_a: SO:0001716 ! histone_ubiqitination_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T10:13:28Z
+
+[Term]
+id: SO:0001718
+name: H3K18_acetylation_site
+def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
+synonym: "H3K18 acetylation site" EXACT []
+synonym: "H3K18Ac" RELATED []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T10:39:35Z
+
+[Term]
+id: SO:0001719
+name: H3K23_acylation_site
+def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
+synonym: "H3K23 acylation site" RELATED []
+synonym: "H3K23Ac" RELATED []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T10:42:45Z
+
+[Term]
+id: SO:0001720
+name: epigenetically_modified_region
+def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]
+subset: SOFA
+synonym: "epigenetically modified region" RELATED []
+is_a: SO:0001411 ! biological_region
+relationship: has_quality SO:0000133 ! epigenetically_modified
+created_by: kareneilbeck
+creation_date: 2010-03-27T12:02:29Z
+
+[Term]
+id: SO:0001721
+name: H3K27_acylation_site
+def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
+synonym: "H3K27 acylation site" EXACT []
+synonym: "H3K27Ac" RELATED []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T10:44:09Z
+
+[Term]
+id: SO:0001722
+name: H3K36_monomethylation_site
+def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]
+synonym: "H3K36 mono-methylation site" EXACT []
+synonym: "H3K36<Me1" RELATED []
+is_a: SO:0001733 ! H3K36_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T10:46:32Z
+
+[Term]
+id: SO:0001723
+name: H3K36_dimethylation_site
+def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]
+synonym: "H3K36 di-methylation site" EXACT []
+synonym: "H3K36Me2" RELATED []
+is_a: SO:0001733 ! H3K36_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T10:59:35Z
+
+[Term]
+id: SO:0001724
+name: H3K36_trimethylation_site
+def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]
+synonym: "H3K36 tri-methylation site" EXACT []
+synonym: "H3K36Me3" RELATED []
+is_a: SO:0001733 ! H3K36_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:01:58Z
+
+[Term]
+id: SO:0001725
+name: H3K4_dimethylation_site
+def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]
+synonym: "H3K4 di-methylation site" EXACT []
+synonym: "H3K4Me2" RELATED []
+is_a: SO:0001734 ! H3K4_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:03:15Z
+
+[Term]
+id: SO:0001726
+name: H3K27_dimethylation_site
+def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]
+synonym: "H3K27 di-methylation site" EXACT []
+synonym: "H3K27Me2" RELATED []
+is_a: SO:0001732 ! H3K27_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T01:45:41Z
+
+[Term]
+id: SO:0001727
+name: H3K9_monomethylation_site
+def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]
+synonym: "H3K9 mono-methylation site" EXACT []
+synonym: "H3K9Me1" RELATED []
+is_a: SO:0001736 ! H3K9_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:06:17Z
+
+[Term]
+id: SO:0001728
+name: H3K9_dimethylation_site
+def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]
+synonym: "H3K9 di-methylation site" EXACT []
+synonym: "H3K9Me2" RELATED []
+is_a: SO:0001736 ! H3K9_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:08:19Z
+
+[Term]
+id: SO:0001729
+name: H4K16_acylation_site
+def: "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
+synonym: "H4K16 acylation_site" RELATED []
+synonym: "H4K16Ac" RELATED []
+is_a: SO:0001972 ! histone_4_acylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:09:41Z
+
+[Term]
+id: SO:0001730
+name: H4K5_acylation_site
+def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
+synonym: "H4K5 acylation site" RELATED []
+synonym: "H4K5Ac" RELATED []
+is_a: SO:0001972 ! histone_4_acylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:13:00Z
+
+[Term]
+id: SO:0001731
+name: H4K8_acylation_site
+def: "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]
+synonym: "H4K8 acylation site" RELATED []
+synonym: "H4K8Ac" RELATED []
+is_a: SO:0001972 ! histone_4_acylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:14:24Z
+
+[Term]
+id: SO:0001732
+name: H3K27_methylation_site
+def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
+synonym: "H3K27 methylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:26:22Z
+
+[Term]
+id: SO:0001733
+name: H3K36_methylation_site
+def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
+synonym: "H3K36 methylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:27:28Z
+
+[Term]
+id: SO:0001734
+name: H3K4_methylation_site
+def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]
+synonym: "H3K4 methylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:28:14Z
+
+[Term]
+id: SO:0001735
+name: H3K79_methylation_site
+def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
+synonym: "H3K79 methylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:29:16Z
+
+[Term]
+id: SO:0001736
+name: H3K9_methylation_site
+def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
+synonym: "H3K9 methylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2010-04-13T11:31:37Z
+
+[Term]
+id: SO:0001737
+name: histone_acylation_region
+def: "A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]
+synonym: "histone acylation region" RELATED []
+is_a: SO:0001700 ! histone_modification
+created_by: kareneilbeck
+creation_date: 2010-04-13T01:58:21Z
+
+[Term]
+id: SO:0001738
+name: H4K_acylation_region
+def: "A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]
+synonym: "H4K acylation region" EXACT []
+synonym: "H4KAc" RELATED []
+is_a: SO:0001737 ! histone_acylation_region
+created_by: kareneilbeck
+creation_date: 2010-04-13T02:00:06Z
+
+[Term]
+id: SO:0001739
+name: gene_with_non_canonical_start_codon
+def: "A gene with a start codon other than AUG." [SO:xp]
+comment: Requested by flybase, Dec 2010.
+synonym: "gene with non canonical start codon" EXACT []
+is_a: SO:0000704 ! gene
+relationship: contains SO:0000680 ! non_canonical_start_codon
+created_by: kareneilbeck
+creation_date: 2011-01-10T01:30:31Z
+
+[Term]
+id: SO:0001740
+name: gene_with_start_codon_CUG
+def: "A gene with a translational start codon of CUG." [SO:mc]
+comment: Requested by flybase, Dec 2010.
+synonym: "gene with start codon CUG" EXACT []
+is_a: SO:0001739 ! gene_with_non_canonical_start_codon
+created_by: kareneilbeck
+creation_date: 2011-01-10T01:32:35Z
+
+[Term]
+id: SO:0001741
+name: pseudogenic_gene_segment
+def: "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]
+synonym: "pseudogenic gene segment" EXACT []
+is_a: SO:3000000 ! gene_segment
+created_by: batchelorc
+creation_date: 2011-02-15T05:07:52Z
+
+[Term]
+id: SO:0001742
+name: copy_number_gain
+def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]
+subset: DBVAR
+synonym: "copy number gain" EXACT []
+synonym: "gain" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
+is_a: SO:0001019 ! copy_number_variation
+created_by: kareneilbeck
+creation_date: 2011-02-28T01:54:09Z
+
+[Term]
+id: SO:0001743
+name: copy_number_loss
+def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]
+subset: DBVAR
+synonym: "copy number loss" EXACT []
+synonym: "loss" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
+is_a: SO:0001019 ! copy_number_variation
+created_by: kareneilbeck
+creation_date: 2011-02-28T01:55:02Z
+
+[Term]
+id: SO:0001744
+name: UPD
+def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]
+subset: DBVAR
+synonym: "uniparental disomy" EXACT []
+synonym: "UPD" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
+xref: http:http://en.wikipedia.org/wiki/Uniparental_disomy "wikipedia"
+is_a: SO:0001059 ! sequence_alteration
+created_by: kareneilbeck
+creation_date: 2011-02-28T02:01:05Z
+
+[Term]
+id: SO:0001745
+name: maternal_uniparental_disomy
+def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm]
+synonym: "maternal uniparental disomy" EXACT []
+is_a: SO:0001744 ! UPD
+created_by: kareneilbeck
+creation_date: 2011-02-28T02:03:01Z
+
+[Term]
+id: SO:0001746
+name: paternal_uniparental_disomy
+def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm]
+synonym: "paternal uniparental disomy" EXACT []
+is_a: SO:0001744 ! UPD
+created_by: kareneilbeck
+creation_date: 2011-02-28T02:03:30Z
+
+[Term]
+id: SO:0001747
+name: open_chromatin_region
+def: "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb]
+comment: Requested by John Calley 3125900.
+synonym: "open chromatin region" EXACT []
+is_a: SO:0001411 ! biological_region
+created_by: kareneilbeck
+creation_date: 2011-02-28T02:21:52Z
+
+[Term]
+id: SO:0001748
+name: SL3_acceptor_site
+def: "A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL3 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T02:58:40Z
+
+[Term]
+id: SO:0001749
+name: SL4_acceptor_site
+def: "A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL4 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:08:47Z
+
+[Term]
+id: SO:0001750
+name: SL5_acceptor_site
+def: "A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL5 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:09:36Z
+
+[Term]
+id: SO:0001751
+name: SL6_acceptor_site
+def: "A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL6 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:10:14Z
+
+[Term]
+id: SO:0001752
+name: SL7_acceptor_site
+def: "A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL37 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:13:20Z
+
+[Term]
+id: SO:0001753
+name: SL8_acceptor_site
+def: "A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL8 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:15:26Z
+
+[Term]
+id: SO:0001754
+name: SL9_acceptor_site
+def: "A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL9 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:15:57Z
+
+[Term]
+id: SO:0001755
+name: SL10_acceptor_site
+def: "A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL10 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:16:31Z
+
+[Term]
+id: SO:0001756
+name: SL11_acceptor_site
+def: "A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL11 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:16:54Z
+
+[Term]
+id: SO:0001757
+name: SL12_acceptor_site
+def: "A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
+synonym: "SL12 acceptor site" EXACT []
+is_a: SO:0000709 ! SL2_acceptor_site
+created_by: kareneilbeck
+creation_date: 2011-02-28T03:17:23Z
+
+[Term]
+id: SO:0001758
+name: duplicated_pseudogene
+def: "A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]
+synonym: "duplicated pseudogene" RELATED []
+is_a: SO:0001760 ! non_processed_pseudogene
+created_by: kareneilbeck
+creation_date: 2011-03-09T09:58:04Z
+
+[Term]
+id: SO:0001759
+name: unitary_pseudogene
+def: "A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]
+comment: This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
+synonym: "disabled gene" RELATED []
+synonym: "unitary pseudogene" RELATED []
+is_a: SO:0001760 ! non_processed_pseudogene
+created_by: kareneilbeck
+creation_date: 2011-03-09T10:04:04Z
+
+[Term]
+id: SO:0001760
+name: non_processed_pseudogene
+def: "A pseudogene that arose from a means other than retrotransposition." [SO:ke]
+synonym: "non processed pseudogene" RELATED []
+is_a: SO:0000336 ! pseudogene
+created_by: kareneilbeck
+creation_date: 2011-03-09T10:54:47Z
+
+[Term]
+id: SO:0001761
+name: variant_quality
+def: "A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]
+synonym: "variant quality" EXACT []
+is_a: SO:0000400 ! sequence_attribute
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:40:35Z
+
+[Term]
+id: SO:0001762
+name: variant_origin
+def: "A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]
+synonym: "variant origin" EXACT []
+is_a: SO:0001761 ! variant_quality
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:42:13Z
+
+[Term]
+id: SO:0001763
+name: variant_frequency
+def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]
+synonym: "variant frequency" EXACT []
+is_a: SO:0001761 ! variant_quality
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:44:39Z
+
+[Term]
+id: SO:0001764
+name: unique_variant
+def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]
+synonym: "unique variant" EXACT []
+is_a: SO:0001763 ! variant_frequency
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:47:20Z
+
+[Term]
+id: SO:0001765
+name: rare_variant
+synonym: "rare variant" EXACT []
+is_a: SO:0001763 ! variant_frequency
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:48:29Z
+
+[Term]
+id: SO:0001766
+name: polymorphic_variant
+synonym: "polymorphic variant" EXACT []
+is_a: SO:0001763 ! variant_frequency
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:48:51Z
+
+[Term]
+id: SO:0001767
+name: common_variant
+synonym: "common variant" EXACT []
+is_a: SO:0001763 ! variant_frequency
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:50:36Z
+
+[Term]
+id: SO:0001768
+name: fixed_variant
+synonym: "fixed variant" EXACT []
+is_a: SO:0001763 ! variant_frequency
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:50:53Z
+
+[Term]
+id: SO:0001769
+name: variant_phenotype
+def: "A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]
+synonym: "variant phenotype" EXACT []
+is_a: SO:0001761 ! variant_quality
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:53:15Z
+
+[Term]
+id: SO:0001770
+name: benign_variant
+synonym: "benign variant" EXACT []
+is_a: SO:0001769 ! variant_phenotype
+created_by: kareneilbeck
+creation_date: 2011-03-15T03:55:40Z
+
+[Term]
+id: SO:0001771
+name: disease_associated_variant
+synonym: "disease associated variant" EXACT []
+is_a: SO:0001769 ! variant_phenotype
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:05:16Z
+
+[Term]
+id: SO:0001772
+name: disease_causing_variant
+synonym: "disease causing variant" EXACT []
+is_a: SO:0001769 ! variant_phenotype
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:05:46Z
+
+[Term]
+id: SO:0001773
+name: lethal_variant
+synonym: "lethal variant" EXACT []
+is_a: SO:0001536 ! functional_variant
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:06:22Z
+
+[Term]
+id: SO:0001774
+name: quantitative_variant
+synonym: "quantitative variant" EXACT []
+is_a: SO:0001769 ! variant_phenotype
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:28:13Z
+
+[Term]
+id: SO:0001775
+name: maternal_variant
+synonym: "maternal variant" EXACT []
+is_a: SO:0001762 ! variant_origin
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:30:23Z
+
+[Term]
+id: SO:0001776
+name: paternal_variant
+synonym: "paternal variant" EXACT []
+is_a: SO:0001762 ! variant_origin
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:30:47Z
+
+[Term]
+id: SO:0001777
+name: somatic_variant
+synonym: "somatic variant" EXACT []
+is_a: SO:0001762 ! variant_origin
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:31:12Z
+
+[Term]
+id: SO:0001778
+name: germline_variant
+synonym: "germline variant" EXACT []
+is_a: SO:0001762 ! variant_origin
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:31:46Z
+
+[Term]
+id: SO:0001779
+name: pedigree_specific_variant
+synonym: "pedigree specific variant" EXACT []
+is_a: SO:0001762 ! variant_origin
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:32:18Z
+
+[Term]
+id: SO:0001780
+name: population_specific_variant
+synonym: "population specific variant" EXACT []
+is_a: SO:0001762 ! variant_origin
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:33:05Z
+
+[Term]
+id: SO:0001781
+name: de_novo_variant
+synonym: "de novo variant" EXACT []
+is_a: SO:0001762 ! variant_origin
+created_by: kareneilbeck
+creation_date: 2011-03-15T04:33:34Z
+
+[Term]
+id: SO:0001782
+name: TF_binding_site_variant
+def: "A sequence variant located within a transcription factor binding site." [EBI:fc]
+synonym: "TF binding site variant" EXACT []
+is_a: SO:0001566 ! regulatory_region_variant
+created_by: kareneilbeck
+creation_date: 2011-03-17T10:59:20Z
+
+[Term]
+id: SO:0001784
+name: complex_structural_alteration
+alt_id: SO:1000146
+def: "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints." [FB:reference_manual, NCBI:th, SO:ke]
+subset: DBVAR
+synonym: "complex" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
+synonym: "complex chromosomal mutation" EXACT []
+synonym: "complex_chromosomal_mutation" EXACT []
+is_a: SO:0001785 ! structural_alteration
+is_a: SO:1000183 ! chromosome_structure_variation
+created_by: kareneilbeck
+creation_date: 2011-03-23T03:21:19Z
+
+[Term]
+id: SO:0001785
+name: structural_alteration
+subset: DBVAR
+synonym: "structural alteration" EXACT []
+is_a: SO:0001059 ! sequence_alteration
+created_by: kareneilbeck
+creation_date: 2011-03-25T02:27:41Z
+
+[Term]
+id: SO:0001786
+name: loss_of_heterozygosity
+def: "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke]
+subset: DBVAR
+synonym: "LOH" EXACT []
+synonym: "loss of heterozygosity" EXACT []
+is_a: SO:0001536 ! functional_variant
+created_by: kareneilbeck
+creation_date: 2011-03-25T02:32:58Z
+
+[Term]
+id: SO:0001787
+name: splice_donor_5th_base_variant
+def: "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]
+synonym: "splice donor 5th base variant" EXACT []
+is_a: SO:0001629 ! splice_site_variant
+created_by: kareneilbeck
+creation_date: 2011-04-05T04:16:28Z
+
+[Term]
+id: SO:0001788
+name: U_box
+def: "An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]
+synonym: "U-box" EXACT []
+is_a: SO:0000330 ! conserved_region
+relationship: part_of SO:0000186 ! LTR_retrotransposon
+created_by: kareneilbeck
+creation_date: 2011-04-08T10:39:14Z
+
+[Term]
+id: SO:0001789
+name: mating_type_region
+def: "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]
+synonym: "mating type region" EXACT []
+xref: http://en.wikipedia.org/wiki/Mating-type_region
+is_a: SO:0005855 ! gene_group
+created_by: kareneilbeck
+creation_date: 2011-04-08T11:14:07Z
+
+[Term]
+id: SO:0001790
+name: paired_end_fragment
+def: "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]
+subset: SOFA
+synonym: "paired end fragment" EXACT []
+is_a: SO:0000143 ! assembly_component
+created_by: kareneilbeck
+creation_date: 2011-04-14T01:48:20Z
+
+[Term]
+id: SO:0001791
+name: exon_variant
+def: "A sequence variant that changes exon sequence." [SO:ke]
+synonym: "ANNOVAR:exonic" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "exon variant" EXACT []
+synonym: "snpEff:EXON" EXACT VAR []
+synonym: "VAAST:exon_variant" EXACT VAR []
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2011-05-06T01:51:17Z
+
+[Term]
+id: SO:0001792
+name: non_coding_transcript_exon_variant
+def: "A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]
+synonym: "non coding transcript exon variant" EXACT []
+is_a: SO:0001619 ! non_coding_transcript_variant
+is_a: SO:0001791 ! exon_variant
+created_by: kareneilbeck
+creation_date: 2011-05-06T01:51:59Z
+
+[Term]
+id: SO:0001793
+name: clone_end
+def: "A read from an end of the clone sequence." [SO:ke]
+synonym: "clone end" EXACT []
+is_a: SO:0000150 ! read
+relationship: part_of SO:0000151 ! clone
+created_by: kareneilbeck
+creation_date: 2011-05-13T11:32:27Z
+
+[Term]
+id: SO:0001794
+name: point_centromere
+def: "A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]
+synonym: "point centromere" EXACT []
+is_a: SO:0000577 ! centromere
+created_by: kareneilbeck
+creation_date: 2011-05-31T12:42:35Z
+
+[Term]
+id: SO:0001795
+name: regional_centromere
+def: "A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]
+synonym: "regional centromere" EXACT []
+is_a: SO:0000577 ! centromere
+created_by: kareneilbeck
+creation_date: 2011-05-31T12:43:07Z
+
+[Term]
+id: SO:0001796
+name: regional_centromere_central_core
+def: "A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]
+synonym: "regional centromere central core" EXACT []
+is_a: SO:0000330 ! conserved_region
+relationship: part_of SO:0001795 ! regional_centromere
+created_by: kareneilbeck
+creation_date: 2011-05-31T12:56:30Z
+
+[Term]
+id: SO:0001797
+name: centromeric_repeat
+def: "A repeat region found within the modular centromere." [SO:ke]
+synonym: "centromeric repeat" EXACT []
+is_a: SO:0000657 ! repeat_region
+created_by: kareneilbeck
+creation_date: 2011-05-31T12:59:27Z
+
+[Term]
+id: SO:0001798
+name: regional_centromere_inner_repeat_region
+def: "The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]
+synonym: "lmr repeat" EXACT []
+synonym: "lmr1L" EXACT []
+synonym: "lmr1R" EXACT []
+synonym: "regional centromere inner repeat region" EXACT []
+is_a: SO:0001797 ! centromeric_repeat
+relationship: part_of SO:0001796 ! regional_centromere_central_core
+created_by: kareneilbeck
+creation_date: 2011-05-31T01:01:08Z
+
+[Term]
+id: SO:0001799
+name: regional_centromere_outer_repeat_region
+def: "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]
+synonym: "regional centromere outer repeat region" EXACT []
+is_a: SO:0001797 ! centromeric_repeat
+relationship: part_of SO:0001795 ! regional_centromere
+created_by: kareneilbeck
+creation_date: 2011-05-31T01:03:23Z
+
+[Term]
+id: SO:0001800
+name: tasiRNA
+def: "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]
+synonym: "trans acting small interfering RNA" RELATED []
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0001801 ! tasiRNA_primary_transcript
+created_by: kareneilbeck
+creation_date: 2011-05-31T03:24:06Z
+
+[Term]
+id: SO:0001801
+name: tasiRNA_primary_transcript
+def: "A primary transcript encoding a tasiRNA." [PMID:16145017]
+synonym: "tasiRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+created_by: kareneilbeck
+creation_date: 2011-05-31T03:27:35Z
+
+[Term]
+id: SO:0001802
+name: increased_polyadenylation_variant
+def: "A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]
+comment: Term requested by M. Dumontier, June 1 2011.
+synonym: "increased polyadenylation variant" EXACT []
+is_a: SO:0001545 ! polyadenylation_variant
+created_by: kareneilbeck
+creation_date: 2011-06-01T10:53:12Z
+
+[Term]
+id: SO:0001803
+name: decreased_polyadenylation_variant
+def: "A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]
+comment: Term requested by M. Dumontier, June 1 2011.
+synonym: "decreased polyadenylation variant" EXACT []
+is_a: SO:0001545 ! polyadenylation_variant
+created_by: kareneilbeck
+creation_date: 2011-06-01T10:53:40Z
+
+[Term]
+id: SO:0001804
+name: DDB_box
+def: "A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]
+comment: Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence.
+synonym: "DDB box" EXACT []
+synonym: "DDB-box" EXACT []
+is_a: SO:0001093 ! protein_protein_contact
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:10:44Z
+
+[Term]
+id: SO:0001805
+name: destruction_box
+def: "A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]
+synonym: "D-box" EXACT []
+synonym: "destruction box" EXACT []
+is_a: SO:0100017 ! polypeptide_conserved_motif
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:16:02Z
+
+[Term]
+id: SO:0001806
+name: ER_retention_signal
+def: "A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]
+synonym: "endoplasmic reticulum retention signal" EXACT []
+synonym: "ER retention signal" EXACT []
+is_a: SO:0001527 ! peptide_localization_signal
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:19:49Z
+
+[Term]
+id: SO:0001807
+name: KEN_box
+def: "A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]
+synonym: "KEN box" EXACT []
+is_a: SO:0100017 ! polypeptide_conserved_motif
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:24:14Z
+
+[Term]
+id: SO:0001808
+name: mitochondrial_targeting_signal
+def: "A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]
+synonym: "mitochondrial signal sequence" EXACT []
+synonym: "mitochondrial targeting signal" EXACT []
+synonym: "MTS" EXACT []
+is_a: SO:0001527 ! peptide_localization_signal
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:26:35Z
+
+[Term]
+id: SO:0001809
+name: signal_anchor
+def: "A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]
+synonym: "signal anchor" EXACT []
+synonym: "uncleaved signal peptide" EXACT []
+is_a: SO:0000418 ! signal_peptide
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:28:53Z
+
+[Term]
+id: SO:0001810
+name: PIP_box
+def: "A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]
+synonym: "PIP box" EXACT []
+is_a: SO:0001093 ! protein_protein_contact
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:33:25Z
+
+[Term]
+id: SO:0001811
+name: phosphorylation_site
+def: "A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]
+synonym: "phosphorylation site" EXACT []
+is_a: SO:0001089 ! post_translationally_modified_region
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:36:20Z
+
+[Term]
+id: SO:0001812
+name: transmembrane_helix
+def: "A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]
+synonym: "transmembrane helix" EXACT []
+is_a: SO:0001114 ! peptide_helix
+relationship: part_of SO:0001077 ! transmembrane_polypeptide_region
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:39:46Z
+
+[Term]
+id: SO:0001813
+name: vacuolar_sorting_signal
+def: "A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]
+synonym: "vacuolar sorting signal" EXACT []
+is_a: SO:0001527 ! peptide_localization_signal
+created_by: kareneilbeck
+creation_date: 2011-06-17T12:42:48Z
+
+[Term]
+id: SO:0001814
+name: coding_variant_quality
+synonym: "coding variant quality" EXACT []
+is_a: SO:0001761 ! variant_quality
+created_by: kareneilbeck
+creation_date: 2011-06-24T03:32:25Z
+
+[Term]
+id: SO:0001815
+name: synonymous
+is_a: SO:0001814 ! coding_variant_quality
+created_by: kareneilbeck
+creation_date: 2011-06-24T03:33:16Z
+
+[Term]
+id: SO:0001816
+name: non_synonymous
+synonym: "non synonymous" RELATED []
+is_a: SO:0001814 ! coding_variant_quality
+created_by: kareneilbeck
+creation_date: 2011-06-24T03:33:36Z
+
+[Term]
+id: SO:0001817
+name: inframe
+def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]
+is_a: SO:0000863 ! mRNA_attribute
+created_by: kareneilbeck
+creation_date: 2011-06-24T03:34:03Z
+
+[Term]
+id: SO:0001818
+name: protein_altering_variant
+def: "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]
+synonym: "protein altering variant" EXACT []
+is_a: SO:0001580 ! coding_sequence_variant
+created_by: kareneilbeck
+creation_date: 2011-06-24T03:38:02Z
+
+[Term]
+id: SO:0001819
+name: synonymous_variant
+alt_id: SO:0001588
+def: "A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]
+comment: EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).\nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
+synonym: "ANNOVAR:synonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "coding-synon" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
+synonym: "silent mutation" RELATED []
+synonym: "silent substitution" RELATED []
+synonym: "silent_mutation" RELATED []
+synonym: "snpEff:SYNONYMOUS_CODING" EXACT VAR []
+synonym: "synonymous codon" EXACT []
+synonym: "synonymous_coding" EXACT []
+synonym: "synonymous_codon" EXACT []
+synonym: "VAAST:synonymous_codon" EXACT VAR []
+xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
+xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
+xref: http://en.wikipedia.org/wiki/Synonymous_mutation
+is_a: SO:0001580 ! coding_sequence_variant
+created_by: kareneilbeck
+creation_date: 2011-06-24T03:38:30Z
+
+[Term]
+id: SO:0001820
+name: inframe_indel
+def: "A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]
+synonym: "inframe change in CDS length" EXACT []
+synonym: "inframe indel" EXACT []
+is_a: SO:0001650 ! inframe_variant
+created_by: kareneilbeck
+creation_date: 2011-06-27T11:25:33Z
+
+[Term]
+id: SO:0001821
+name: inframe_insertion
+alt_id: SO:0001651
+def: "An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]
+synonym: "ANNOVAR:nonframeshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "inframe codon gain" RELATED []
+synonym: "inframe increase in CDS length" EXACT []
+synonym: "inframe insertion" EXACT []
+synonym: "inframe_codon_gain" EXACT []
+synonym: "snpEFF:CODON_INSERTION" EXACT VAR []
+is_a: SO:0001820 ! inframe_indel
+is_a: SO:0001908 ! internal_feature_elongation
+created_by: kareneilbeck
+creation_date: 2011-06-27T11:26:22Z
+
+[Term]
+id: SO:0001822
+name: inframe_deletion
+alt_id: SO:0001652
+def: "An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]
+synonym: "ANNOVAR:nonframeshift deletion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "inframe codon loss" RELATED []
+synonym: "inframe decrease in CDS length" EXACT []
+synonym: "inframe deletion" RELATED []
+synonym: "inframe_codon_loss" EXACT []
+synonym: "snpEff:CODON_DELETION" RELATED VAR []
+is_a: SO:0001820 ! inframe_indel
+is_a: SO:0001906 ! feature_truncation
+created_by: kareneilbeck
+creation_date: 2011-06-27T11:27:10Z
+
+[Term]
+id: SO:0001823
+name: conservative_inframe_insertion
+def: "An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]
+synonym: "conservative increase in CDS length" EXACT []
+synonym: "conservative inframe insertion" EXACT []
+is_a: SO:0001821 ! inframe_insertion
+created_by: kareneilbeck
+creation_date: 2011-06-27T11:28:02Z
+
+[Term]
+id: SO:0001824
+name: disruptive_inframe_insertion
+def: "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]
+synonym: "disruptive increase in CDS length" EXACT []
+synonym: "disruptive inframe insertion" EXACT []
+synonym: "snpEff:CODON_CHANGE_PLUS_CODON_INSERTION" EXACT VAR []
+is_a: SO:0001821 ! inframe_insertion
+created_by: kareneilbeck
+creation_date: 2011-06-27T11:28:37Z
+
+[Term]
+id: SO:0001825
+name: conservative_inframe_deletion
+def: "An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]
+synonym: "conservative decrease in CDS length" RELATED []
+synonym: "conservative inframe deletion" EXACT []
+is_a: SO:0001822 ! inframe_deletion
+created_by: kareneilbeck
+creation_date: 2011-06-27T11:30:43Z
+
+[Term]
+id: SO:0001826
+name: disruptive_inframe_deletion
+def: "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]
+synonym: "disruptive decrease in CDS length" EXACT []
+synonym: "disruptive inframe deletion" EXACT []
+synonym: "snpEff:CODON_CHANGE_PLUS_CODON_DELETION" EXACT VAR []
+is_a: SO:0001822 ! inframe_deletion
+created_by: kareneilbeck
+creation_date: 2011-06-27T11:31:31Z
+
+[Term]
+id: SO:0001827
+name: mRNA_read
+def: "A sequencer read of an mRNA substrate." [SO:ke]
+comment: Requested by Bayer Cropscience June, 2011.
+synonym: "mRNA read" EXACT []
+is_a: SO:0000150 ! read
+created_by: kareneilbeck
+creation_date: 2011-06-28T04:04:32Z
+
+[Term]
+id: SO:0001828
+name: genomic_DNA_read
+def: "A sequencer read of a genomic DNA substrate." [SO:ke]
+synonym: "genomic DNA read" EXACT []
+is_a: SO:0000150 ! read
+created_by: kareneilbeck
+creation_date: 2011-06-28T04:06:10Z
+
+[Term]
+id: SO:0001829
+name: mRNA_contig
+def: "A contig composed of mRNA_reads." [SO:ke]
+comment: Requested by Bayer Cropscience June, 2011.
+synonym: "mRNA contig" RELATED []
+is_a: SO:0000149 ! contig
+created_by: kareneilbeck
+creation_date: 2011-06-28T04:07:09Z
+
+[Term]
+id: SO:0001830
+name: AFLP_fragment
+def: "A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]
+comment: Requested by Bayer Cropscience June, 2011.
+synonym: "AFLP" EXACT []
+synonym: "AFLP fragment" EXACT []
+synonym: "AFLP-PCR" EXACT []
+synonym: "amplified fragment length polymorphism" EXACT []
+synonym: "amplified fragment length polymorphism PCR" EXACT []
+xref: http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism "wiki"
+is_a: SO:0000006 ! PCR_product
+created_by: kareneilbeck
+creation_date: 2011-07-14T12:12:35Z
+
+[Term]
+id: SO:0001831
+name: protein_hmm_match
+def: "A match to a protein HMM such as pfam." [SO:ke]
+synonym: "protein hmm match" EXACT []
+is_a: SO:0000349 ! protein_match
+created_by: kareneilbeck
+creation_date: 2011-08-11T03:20:27Z
+
+[Term]
+id: SO:0001832
+name: immunoglobulin_region
+def: "A region of immunoglobulin sequence, either constant or variable." [SO:ke]
+synonym: "immunoglobulin region" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+created_by: kareneilbeck
+creation_date: 2011-09-01T03:27:20Z
+
+[Term]
+id: SO:0001833
+name: V_region
+def: "The variable region of an immunoglobulin polypeptide sequence." [SO:ke]
+synonym: "V region" EXACT []
+is_a: SO:0001832 ! immunoglobulin_region
+created_by: kareneilbeck
+creation_date: 2011-09-01T03:28:40Z
+
+[Term]
+id: SO:0001834
+name: C_region
+def: "The constant region of an immunoglobulin polypeptide sequence." [SO:ke]
+synonym: "C region" EXACT []
+is_a: SO:0001832 ! immunoglobulin_region
+created_by: kareneilbeck
+creation_date: 2011-09-01T03:29:41Z
+
+[Term]
+id: SO:0001835
+name: N_region
+def: "Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]
+synonym: "N-region" EXACT []
+is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
+created_by: kareneilbeck
+creation_date: 2011-09-01T03:50:16Z
+
+[Term]
+id: SO:0001836
+name: S_region
+def: "The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]
+synonym: "S region" EXACT []
+is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
+created_by: kareneilbeck
+creation_date: 2011-09-01T03:52:05Z
+
+[Term]
+id: SO:0001837
+name: mobile_element_insertion
+def: "A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]
+comment: Requested by the EBI.
+synonym: "mobile element insertion" EXACT []
+is_a: SO:0000667 ! insertion
+relationship: contains SO:0001037 ! mobile_genetic_element
+created_by: kareneilbeck
+creation_date: 2011-10-04T12:36:52Z
+
+[Term]
+id: SO:0001838
+name: novel_sequence_insertion
+def: "An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]
+comment: Requested by the NCBI.
+synonym: "novel sequence insertion" EXACT []
+is_a: SO:0000667 ! insertion
+created_by: kareneilbeck
+creation_date: 2011-10-04T01:14:50Z
+
+[Term]
+id: SO:0001839
+name: CSL_response_element
+def: "A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]
+synonym: "CSL response element" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T03:37:43Z
+
+[Term]
+id: SO:0001840
+name: GATA_box
+def: "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]
+synonym: "GATA box" EXACT []
+synonym: "GATA element" RELATED []
+is_a: SO:0001660 ! core_promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T03:42:05Z
+
+[Term]
+id: SO:0001841
+name: polymorphic_pseudogene
+def: "Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]
+comment: This terms is used by Ensembl and Vega.
+synonym: "polymorphic psuedogene" EXACT []
+is_a: SO:0000336 ! pseudogene
+created_by: kareneilbeck
+creation_date: 2011-10-07T03:46:57Z
+
+[Term]
+id: SO:0001842
+name: AP_1_binding_site
+def: "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]
+synonym: "AP-1 binding site" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T03:54:52Z
+
+[Term]
+id: SO:0001843
+name: CRE
+def: "A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]
+synonym: "ATF/CRE site" EXACT [PMID:11483993]
+synonym: "cyclic AMP response element" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T03:58:48Z
+
+[Term]
+id: SO:0001844
+name: CuRE
+def: "A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]
+synonym: "copper-response element" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:02:51Z
+
+[Term]
+id: SO:0001845
+name: DRE
+def: "A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]
+synonym: "DNA damage response element" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:17:25Z
+
+[Term]
+id: SO:0001846
+name: FLEX_element
+def: "A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]
+synonym: "FLEX element" RELATED []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:20:01Z
+
+[Term]
+id: SO:0001847
+name: forkhead_motif
+def: "A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]
+synonym: "forkhead motif" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:22:06Z
+
+[Term]
+id: SO:0001848
+name: homol_D_box
+def: "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]
+synonym: "homol D box" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:24:14Z
+
+[Term]
+id: SO:0001849
+name: homol_E_box
+def: "A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]
+synonym: "homol E box" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:26:09Z
+
+[Term]
+id: SO:0001850
+name: HSE
+def: "A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]
+synonym: "heat shock element" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:29:10Z
+
+[Term]
+id: SO:0001851
+name: iron_repressed_GATA_element
+def: "A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]
+comment: The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes.
+synonym: "IDP (GATA)" EXACT []
+synonym: "iron repressed GATA element" EXACT []
+is_a: SO:0001840 ! GATA_box
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:32:42Z
+
+[Term]
+id: SO:0001852
+name: mating_type_M_box
+def: "A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]
+comment: Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF.
+synonym: "mating type M-box" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-07T04:39:43Z
+
+[Term]
+id: SO:0001853
+name: androgen_response_element
+def: "A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]
+synonym: "androgen response element" EXACT []
+synonym: "ARE" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2011-10-10T04:52:44Z
+
+[Term]
+id: SO:0001854
+name: smFISH_probe
+def: "A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]
+synonym: "single molecule fish probe" EXACT []
+synonym: "smFISH probe" RELATED []
+is_a: SO:0000051 ! probe
+created_by: kareneilbeck
+creation_date: 2011-10-10T05:00:30Z
+
+[Term]
+id: SO:0001855
+name: MCB
+def: "A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]
+synonym: "MluI cell cycle box" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-10T05:09:45Z
+
+[Term]
+id: SO:0001856
+name: CCAAT_motif
+def: "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]
+synonym: "CCAAT motif" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-10T05:13:54Z
+
+[Term]
+id: SO:0001857
+name: Ace2_UAS
+def: "A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]
+synonym: "Ace2 upstream activating sequence" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-10T05:19:10Z
+
+[Term]
+id: SO:0001858
+name: TR_box
+def: "A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]
+synonym: "TR box" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-10T05:22:13Z
+
+[Term]
+id: SO:0001859
+name: STREP_motif
+def: "A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]
+synonym: "STREP motif" RELATED []
+synonym: "stress-starvation response element of Schizosaccharomyces pombe" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-14T10:25:02Z
+
+[Term]
+id: SO:0001860
+name: rDNA_intergenic_spacer_element
+def: "A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]
+synonym: "rDIS" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2011-10-19T11:23:09Z
+
+[Term]
+id: SO:0001861
+name: sterol_regulatory_element
+def: "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]
+synonym: "SRE" BROAD [GO:mah]
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-19T03:02:05Z
+
+[Term]
+id: SO:0001862
+name: GT_dinucleotide_repeat
+def: "A dinucleotide repeat region composed of GT repeating elements." [SO:ke]
+comment: paper:PMID:16043634.
+synonym: "d(GT)n" EXACT []
+is_a: SO:0000290 ! dinucleotide_repeat_microsatellite_feature
+created_by: kareneilbeck
+creation_date: 2011-10-19T03:54:37Z
+
+[Term]
+id: SO:0001863
+name: GTT_trinucleotide_repeat
+def: "A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]
+synonym: "d(GTT)" EXACT []
+is_a: SO:0000291 ! trinucleotide_repeat_microsatellite_feature
+created_by: kareneilbeck
+creation_date: 2011-10-19T03:56:54Z
+
+[Term]
+id: SO:0001864
+name: Sap1_recognition_motif
+def: "A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]
+synonym: "Sap1 recognitions site" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2011-10-19T04:24:16Z
+
+[Term]
+id: SO:0001865
+name: CDRE_motif
+def: "An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]
+synonym: "calcineurin-dependent response element" EXACT [PMID:16928959]
+synonym: "CDRE motif" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2011-10-20T10:12:19Z
+
+[Term]
+id: SO:0001866
+name: BAC_read_contig
+def: "A contig of BAC reads." [GMOD:ea]
+comment: Requested by Bayer Cropscience December, 2011.
+synonym: "BAC read contig" EXACT []
+is_a: SO:0000149 ! contig
+relationship: has_origin SO:0000153 ! BAC
+relationship: part_of SO:0000153 ! BAC
+created_by: kareneilbeck
+creation_date: 2012-01-17T02:45:04Z
+
+[Term]
+id: SO:0001867
+name: candidate_gene
+def: "A gene suspected of being involved in the expression of a trait." [GMOD:ea]
+comment: Requested by Bayer Cropscience December, 2011.
+synonym: "candidate gene" EXACT []
+synonym: "target gene" EXACT []
+is_a: SO:0000704 ! gene
+created_by: kareneilbeck
+creation_date: 2012-01-17T02:53:03Z
+
+[Term]
+id: SO:0001868
+name: positional_candidate_gene
+def: "A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]
+comment: Requested by Bayer Cropscience December, 2011.
+synonym: "positional candidate gene" EXACT []
+synonym: "positional target gene" RELATED []
+is_a: SO:0001867 ! candidate_gene
+created_by: kareneilbeck
+creation_date: 2012-01-17T02:54:42Z
+
+[Term]
+id: SO:0001869
+name: functional_candidate_gene
+def: "A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]
+comment: Requested by Bayer Cropscience December, 2011.
+synonym: "functional candidate gene" EXACT []
+synonym: "functional target gene" EXACT []
+is_a: SO:0001867 ! candidate_gene
+created_by: kareneilbeck
+creation_date: 2012-01-17T02:57:30Z
+
+[Term]
+id: SO:0001870
+name: enhancerRNA
+def: "A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]
+synonym: "eRNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+relationship: transcribed_from SO:0000165 ! enhancer
+created_by: kareneilbeck
+creation_date: 2012-01-17T03:09:35Z
+
+[Term]
+id: SO:0001871
+name: PCB
+def: "A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2012-01-17T03:14:02Z
+
+[Term]
+id: SO:0001872
+name: rearrangement_region
+def: "A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]
+comment: NCBI definition: An orphan rearrangement between chromosomal location observed in isolation.
+synonym: "rearrangement region" EXACT []
+is_a: SO:0001411 ! biological_region
+is_a: SO:0001785 ! structural_alteration
+created_by: kareneilbeck
+creation_date: 2012-02-03T04:38:35Z
+
+[Term]
+id: SO:0001873
+name: interchromosomal_breakpoint
+def: "A rearrangement breakpoint between two different chromosomes." [NCBI:th]
+synonym: "interchromosomal breakpoint" EXACT []
+is_a: SO:0001021 ! chromosome_breakpoint
+created_by: kareneilbeck
+creation_date: 2012-02-03T04:43:45Z
+
+[Term]
+id: SO:0001874
+name: intrachromosomal_breakpoint
+def: "A rearrangement breakpoint within the same chromosome." [NCBI:th]
+synonym: "intrachromosomal breakpoint" EXACT []
+is_a: SO:0001021 ! chromosome_breakpoint
+created_by: kareneilbeck
+creation_date: 2012-02-03T04:44:53Z
+
+[Term]
+id: SO:0001875
+name: unassigned_supercontig
+def: "A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]
+comment: Requested by Bayer Cropscience January, 2012.
+synonym: "unassigned scaffold" RELATED []
+synonym: "unassigned supercontig" EXACT []
+is_a: SO:0000148 ! supercontig
+created_by: kareneilbeck
+creation_date: 2012-02-14T05:02:20Z
+
+[Term]
+id: SO:0001876
+name: partial_genomic_sequence_assembly
+def: "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]
+comment: Requested by Bayer Cropscience January, 2012.
+synonym: "partial genomic sequence assembly" EXACT []
+synonym: "pseudomolecule" BROAD []
+synonym: "sequence assembly with N-gaps" EXACT []
+is_a: SO:0000353 ! sequence_assembly
+created_by: kareneilbeck
+creation_date: 2012-02-14T05:05:32Z
+
+[Term]
+id: SO:0001877
+name: lnc_RNA
+def: "A non-coding RNA over 200nucleotides in length." [HGNC:mw]
+synonym: "long non-coding RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+created_by: kareneilbeck
+creation_date: 2012-02-14T05:18:01Z
+
+[Term]
+id: SO:0001878
+name: feature_variant
+def: "A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "feature alteration" EXACT []
+is_a: SO:0001537 ! structural_variant
+created_by: kareneilbeck
+creation_date: 2012-04-03T11:27:27Z
+
+[Term]
+id: SO:0001879
+name: feature_ablation
+def: "A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "feature ablation" EXACT []
+is_a: SO:0001537 ! structural_variant
+created_by: kareneilbeck
+creation_date: 2012-04-03T11:36:48Z
+
+[Term]
+id: SO:0001880
+name: feature_amplification
+def: "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "feature amplification" EXACT []
+is_a: SO:0001537 ! structural_variant
+created_by: kareneilbeck
+creation_date: 2012-04-03T11:37:48Z
+
+[Term]
+id: SO:0001881
+name: feature_translocation
+def: "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "feature translocation" EXACT []
+is_a: SO:0001537 ! structural_variant
+created_by: kareneilbeck
+creation_date: 2012-04-03T11:38:52Z
+
+[Term]
+id: SO:0001882
+name: feature_fusion
+def: "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "feature fusion" EXACT []
+is_a: SO:0001537 ! structural_variant
+created_by: kareneilbeck
+creation_date: 2012-04-03T11:39:20Z
+
+[Term]
+id: SO:0001883
+name: transcript_translocation
+def: "A feature translocation where the region contains a transcript." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "transcript translocation" EXACT []
+is_a: SO:0001881 ! feature_translocation
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:29:52Z
+
+[Term]
+id: SO:0001884
+name: regulatory_region_translocation
+def: "A feature translocation where the region contains a regulatory region." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "regulatory region translocation" EXACT []
+is_a: SO:0001881 ! feature_translocation
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:31:04Z
+
+[Term]
+id: SO:0001885
+name: TFBS_translocation
+def: "A feature translocation where the region contains a transcription factor binding site." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "TFBS binding site translocation" EXACT []
+synonym: "transcription factor binding site translocation" EXACT []
+is_a: SO:0001884 ! regulatory_region_translocation
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:31:15Z
+
+[Term]
+id: SO:0001886
+name: transcript_fusion
+def: "A feature fusion where the deletion brings together transcript regions." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "transcript fusion" EXACT []
+is_a: SO:0001882 ! feature_fusion
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:34:56Z
+
+[Term]
+id: SO:0001887
+name: regulatory_region_fusion
+def: "A feature fusion where the deletion brings together regulatory regions." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "regulatory region fusion" EXACT []
+is_a: SO:0001882 ! feature_fusion
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:35:58Z
+
+[Term]
+id: SO:0001888
+name: TFBS_fusion
+def: "A fusion where the deletion brings together transcription factor binding sites." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "TFBS fusion " EXACT []
+synonym: "transcription factor binding site fusion" EXACT []
+is_a: SO:0001887 ! regulatory_region_fusion
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:36:42Z
+
+[Term]
+id: SO:0001889
+name: transcript_amplification
+def: "A feature amplification of a region containing a transcript." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "transcript amplification" EXACT []
+is_a: SO:0001880 ! feature_amplification
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:39:23Z
+
+[Term]
+id: SO:0001890
+name: transcript_regulatory_region_fusion
+def: "A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "transcript regulatory region fusion" EXACT []
+is_a: SO:0001882 ! feature_fusion
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:40:17Z
+
+[Term]
+id: SO:0001891
+name: regulatory_region_amplification
+def: "A feature amplification of a region containing a regulatory region." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "regulatory region amplification" EXACT []
+is_a: SO:0001880 ! feature_amplification
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:41:28Z
+
+[Term]
+id: SO:0001892
+name: TFBS_amplification
+def: "A feature amplification of a region containing a transcription factor binding site." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "TFBS amplification " EXACT []
+synonym: "transcription factor binding site amplification" EXACT []
+is_a: SO:0001891 ! regulatory_region_amplification
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:42:48Z
+
+[Term]
+id: SO:0001893
+name: transcript_ablation
+def: "A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "transcript ablation" EXACT []
+is_a: SO:0001879 ! feature_ablation
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:44:19Z
+
+[Term]
+id: SO:0001894
+name: regulatory_region_ablation
+def: "A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "regulatory region ablation" EXACT []
+is_a: SO:0001879 ! feature_ablation
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:45:13Z
+
+[Term]
+id: SO:0001895
+name: TFBS_ablation
+def: "A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]
+comment: Created in conjunction with the EBI.
+synonym: "TFBS ablation" EXACT []
+synonym: "transcription factor binding site ablation" EXACT []
+is_a: SO:0001894 ! regulatory_region_ablation
+created_by: kareneilbeck
+creation_date: 2012-04-03T12:45:56Z
+
+[Term]
+id: SO:0001896
+name: transposable_element_CDS
+def: "A CDS that is part of a transposable element." [SO:ke]
+synonym: "transposable element CDS" EXACT []
+is_a: SO:0000316 ! CDS
+relationship: part_of SO:0000101 ! transposable_element
+created_by: kareneilbeck
+creation_date: 2012-04-05T01:57:04Z
+
+[Term]
+id: SO:0001897
+name: transposable_element_pseudogene
+def: "A pseudogene contained within a transposable element." [SO:ke]
+synonym: "transposable element pseudogene" EXACT []
+is_a: SO:0000336 ! pseudogene
+relationship: part_of SO:0000101 ! transposable_element
+created_by: kareneilbeck
+creation_date: 2012-04-05T04:09:45Z
+
+[Term]
+id: SO:0001898
+name: dg_repeat
+def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]
+comment: For the S. pombe project - requested by Val Wood.
+synonym: "dg repeat" EXACT []
+is_a: SO:0001797 ! centromeric_repeat
+relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region
+created_by: kareneilbeck
+creation_date: 2012-04-06T11:48:48Z
+
+[Term]
+id: SO:0001899
+name: dh_repeat
+def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]
+comment: For the S. pombe project - requested by Val Wood.
+synonym: "dh repeat" EXACT []
+is_a: SO:0001797 ! centromeric_repeat
+relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region
+created_by: kareneilbeck
+creation_date: 2012-04-06T11:50:07Z
+
+[Term]
+id: SO:0001900
+name: M26_binding_site
+def: "A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]
+synonym: "m26 site" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2012-04-06T12:02:10Z
+
+[Term]
+id: SO:0001901
+name: AACCCT_box
+def: "A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]
+synonym: "AACCCT box" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+created_by: kareneilbeck
+creation_date: 2012-04-06T12:05:24Z
+
+[Term]
+id: SO:0001902
+name: splice_region
+def: "A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]
+synonym: "splice region" RELATED []
+is_a: SO:0000835 ! primary_transcript_region
+relationship: part_of SO:0000185 ! primary_transcript
+created_by: kareneilbeck
+creation_date: 2012-04-06T12:23:32Z
+
+[Term]
+id: SO:0001903
+name: intronic_lncRNA
+def: "A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]
+synonym: "intronic lncRNA" EXACT []
+is_a: SO:0001877 ! lnc_RNA
+created_by: kareneilbeck
+creation_date: 2012-04-06T04:34:17Z
+
+[Term]
+id: SO:0001904
+name: antisense_lncRNA
+def: "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]
+synonym: "antisense lncRNA" RELATED []
+synonym: "natural antisense transcript" EXACT []
+is_a: SO:0001877 ! lnc_RNA
+created_by: kareneilbeck
+creation_date: 2012-04-06T04:36:44Z
+
+[Term]
+id: SO:0001905
+name: regional_centromere_outer_repeat_transcript
+def: "A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]
+synonym: "centromere outer repeat transcript" EXACT []
+synonym: "regional centromere outer repeat region transcript" EXACT []
+synonym: "regional_centromere_outer_repeat_region_transcript" EXACT []
+is_a: SO:0000185 ! primary_transcript
+relationship: derives_from SO:0001799 ! regional_centromere_outer_repeat_region
+created_by: kareneilbeck
+creation_date: 2012-04-11T04:54:22Z
+
+[Term]
+id: SO:0001906
+name: feature_truncation
+def: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]
+synonym: "feature truncation" EXACT []
+is_a: SO:0001878 ! feature_variant
+created_by: kareneilbeck
+creation_date: 2012-04-12T05:05:28Z
+
+[Term]
+id: SO:0001907
+name: feature_elongation
+def: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]
+synonym: "feature elongation" EXACT []
+is_a: SO:0001878 ! feature_variant
+created_by: kareneilbeck
+creation_date: 2012-04-12T05:05:56Z
+
+[Term]
+id: SO:0001908
+name: internal_feature_elongation
+def: "A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]
+synonym: "internal feature elongation" EXACT []
+is_a: SO:0001907 ! feature_elongation
+created_by: kareneilbeck
+creation_date: 2012-04-12T05:06:20Z
+
+[Term]
+id: SO:0001909
+name: frameshift_elongation
+def: "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]
+synonym: "ANNOVAR:frameshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "frameshift elongation" EXACT []
+is_a: SO:0001589 ! frameshift_variant
+is_a: SO:0001908 ! internal_feature_elongation
+created_by: kareneilbeck
+creation_date: 2012-04-12T05:10:05Z
+
+[Term]
+id: SO:0001910
+name: frameshift_truncation
+def: "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]
+synonym: "ANNOVAR:frameshit deletion" EXACT ebi_variants [http://www.openbioinformatics.org/annovar/annovar_download.html]
+synonym: "frameshft truncation" EXACT []
+is_a: SO:0001589 ! frameshift_variant
+is_a: SO:0001906 ! feature_truncation
+created_by: kareneilbeck
+creation_date: 2012-04-12T05:10:45Z
+
+[Term]
+id: SO:0001911
+name: copy_number_increase
+def: "A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]
+synonym: "copy number increase" EXACT []
+is_a: SO:0001563 ! copy_number_change
+created_by: kareneilbeck
+creation_date: 2012-04-13T11:26:32Z
+
+[Term]
+id: SO:0001912
+name: copy_number_decrease
+def: "A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]
+is_a: SO:0001563 ! copy_number_change
+created_by: kareneilbeck
+creation_date: 2012-04-13T11:27:52Z
+
+[Term]
+id: SO:0001913
+name: bacterial_RNApol_promoter_sigma_ecf
+def: "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]
+comment: Requested by Kevin Clancy - invitrogen -May 2012.
+synonym: "bacterial RNApol promoter sigma ecf " EXACT []
+is_a: SO:0000613 ! bacterial_RNApol_promoter
+created_by: kareneilbeck
+creation_date: 2012-06-11T02:41:33Z
+
+[Term]
+id: SO:0001914
+name: rDNA_replication_fork_barrier
+def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]
+comment: Requested by Midori - June 2012.
+synonym: "DNA spacer replication fork barrier" EXACT []
+synonym: "rDNA replication fork barrier" EXACT []
+synonym: "RFB" EXACT []
+synonym: "RTS1 barrier" EXACT []
+synonym: "RTS1 element" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2012-06-11T02:55:02Z
+
+[Term]
+id: SO:0001915
+name: transcription_start_cluster
+def: "A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]
+synonym: "transcriptional initiation cluster" EXACT []
+synonym: "transcriptional start site cluster" EXACT []
+synonym: "TSC" EXACT []
+synonym: "TSS cluster" EXACT []
+is_a: SO:0001410 ! experimental_feature
+created_by: kareneilbeck
+creation_date: 2012-10-17T12:09:50Z
+
+[Term]
+id: SO:0001916
+name: CAGE_tag
+def: "A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]
+synonym: "CAGE tag" EXACT []
+is_a: SO:0000324 ! tag
+created_by: kareneilbeck
+creation_date: 2012-10-17T12:36:58Z
+
+[Term]
+id: SO:0001917
+name: CAGE_cluster
+def: "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]
+synonym: "CAGE cluster" EXACT []
+synonym: "CAGE peak" EXACT []
+synonym: "CAGE_peak" EXACT []
+is_a: SO:0001915 ! transcription_start_cluster
+created_by: kareneilbeck
+creation_date: 2012-10-17T12:42:03Z
+
+[Term]
+id: SO:0001918
+name: 5_methylcytosine
+def: "A cytosine methylated at the 5 carbon." [SO:rtapella]
+synonym: "5 methylcytosine" EXACT []
+synonym: "5-mC" EXACT []
+synonym: "m-5C" EXACT []
+synonym: "m5c" EXACT []
+xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
+xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
+is_a: SO:0000114 ! methylated_cytosine
+created_by: kareneilbeck
+creation_date: 2012-10-17T12:46:10Z
+
+[Term]
+id: SO:0001919
+name: 4_methylcytosine
+def: "A cytosine methylated at the 4 nitrogen." [SO:rtapella]
+synonym: "4-mC" EXACT []
+synonym: "4-methylcytosine" EXACT []
+synonym: "m-4C" EXACT []
+synonym: "m4c" EXACT []
+synonym: "N4 methylcytosine" EXACT []
+synonym: "N4-methylcytosine" EXACT []
+synonym: "N4_methylcytosine" EXACT []
+xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
+xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
+is_a: SO:0000114 ! methylated_cytosine
+created_by: kareneilbeck
+creation_date: 2012-10-17T12:50:40Z
+
+[Term]
+id: SO:0001920
+name: N6_methyladenine
+def: "An adenine methylated at the 6 nitrogen." [SO:rtapella]
+synonym: "6-mA" EXACT []
+synonym: "6-methyladenine" EXACT []
+synonym: "6mA" EXACT []
+synonym: "m-6A" EXACT []
+synonym: "m6a" EXACT []
+synonym: "N6-methyladenine" EXACT []
+xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
+is_a: SO:0000161 ! methylated_adenine
+created_by: kareneilbeck
+creation_date: 2012-10-17T12:54:23Z
+
+[Term]
+id: SO:0001921
+name: mitochondrial_contig
+def: "A contig of mitochondria derived sequences." [GMOD:ea]
+comment: Requested by Bayer Cropscience, October, 2012.
+synonym: "mitochondrial contig" EXACT []
+is_a: SO:0000149 ! contig
+relationship: has_origin SO:0000737 ! mitochondrial_sequence
+created_by: kareneilbeck
+creation_date: 2012-10-31T12:34:38Z
+
+[Term]
+id: SO:0001922
+name: mitochondrial_supercontig
+def: "A scaffold composed of mitochondrial contigs." [GMOD:ea]
+synonym: "mitochondrial scaffold" EXACT []
+synonym: "mitochondrial supercontig" EXACT []
+synonym: "mitochondrial_scaffold" EXACT []
+is_a: SO:0000148 ! supercontig
+created_by: kareneilbeck
+creation_date: 2012-10-31T12:42:45Z
+
+[Term]
+id: SO:0001923
+name: TERRA
+def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]
+comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
+synonym: "telomeric repeat containing RNA" RELATED []
+is_a: SO:0001927 ! telomeric_transcript
+created_by: kareneilbeck
+creation_date: 2012-10-31T01:06:40Z
+
+[Term]
+id: SO:0001924
+name: ARRET
+def: "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]
+comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
+is_a: SO:0001927 ! telomeric_transcript
+created_by: kareneilbeck
+creation_date: 2012-10-31T01:11:49Z
+
+[Term]
+id: SO:0001925
+name: ARIA
+def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats." [PMID:22139915]
+comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
+is_a: SO:0001927 ! telomeric_transcript
+created_by: kareneilbeck
+creation_date: 2012-10-31T01:24:37Z
+
+[Term]
+id: SO:0001926
+name: anti_ARRET
+def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts." [PMID:22139915]
+comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
+synonym: "anti-ARRET" EXACT []
+is_a: SO:0001927 ! telomeric_transcript
+created_by: kareneilbeck
+creation_date: 2012-10-31T01:40:22Z
+
+[Term]
+id: SO:0001927
+name: telomeric_transcript
+def: "A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]
+synonym: "telomeric transcript" EXACT []
+is_a: SO:0000655 ! ncRNA
+created_by: kareneilbeck
+creation_date: 2012-10-31T01:42:15Z
+
+[Term]
+id: SO:0001928
+name: distal_duplication
+def: "A duplication of the distal region of a chromosome." [SO:bm]
+comment: This term is used by Complete Genomics in the structural variant analysis files.
+synonym: "distal duplication" EXACT []
+is_a: SO:1000035 ! duplication
+created_by: kareneilbeck
+creation_date: 2012-10-31T01:56:44Z
+
+[Term]
+id: SO:0001929
+name: mitochondrial_DNA_read
+def: "A sequencer read of a mitochondrial DNA sample." [GMOD:ea]
+comment: Requested by Bayer Cropscience, October, 2012.
+synonym: "mitochondrial DNA read" EXACT []
+is_a: SO:0000150 ! read
+relationship: has_origin SO:0001032 ! mitochondrial_DNA
+created_by: kareneilbeck
+creation_date: 2012-11-14T04:39:56Z
+
+[Term]
+id: SO:0001930
+name: chloroplast_DNA_read
+def: "A sequencer read of a chloroplast DNA sample." [GMOD:ea]
+comment: Requested by Bayer Cropscience, October, 2012.
+synonym: "chloroplast DNA read" EXACT []
+is_a: SO:0000150 ! read
+relationship: has_origin SO:0001033 ! chloroplast_DNA
+created_by: kareneilbeck
+creation_date: 2012-11-14T04:43:45Z
+
+[Term]
+id: SO:0001931
+name: consensus_gDNA
+def: "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]
+comment: Requested by Bayer Cropscience November, 2012.
+synonym: "consensus gDNA" EXACT []
+synonym: "consensus genomic DNA" EXACT []
+is_a: SO:0000994 ! consensus_region
+created_by: kareneilbeck
+creation_date: 2012-11-28T12:53:14Z
+
+[Term]
+id: SO:0001932
+name: restriction_enzyme_five_prime_single_strand_overhang
+def: "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]
+synonym: "restriction enzyme five prime single strand overhang" EXACT []
+is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang
+created_by: kareneilbeck
+creation_date: 2013-03-06T09:50:44Z
+
+[Term]
+id: SO:0001933
+name: restriction_enzyme_three_prime_single_strand_overhang
+def: "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]
+synonym: "restriction enzyme three prime single strand overhang" EXACT []
+is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang
+created_by: kareneilbeck
+creation_date: 2013-03-06T09:52:14Z
+
+[Term]
+id: SO:0001934
+name: monomeric_repeat
+def: "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]
+synonym: "monomeric repeat" EXACT []
+is_a: SO:0000705 ! tandem_repeat
+created_by: kareneilbeck
+creation_date: 2013-03-06T09:59:15Z
+
+[Term]
+id: SO:0001935
+name: H3K20_trimethylation_site
+def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]
+synonym: "H3K20 trimethylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:13:48Z
+
+[Term]
+id: SO:0001936
+name: H3K36_acetylation_site
+def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]
+synonym: "H3K36 acetylation site" EXACT []
+synonym: "H3K36ac" EXACT []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:16:55Z
+
+[Term]
+id: SO:0001937
+name: H2BK12_acetylation_site
+def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]
+synonym: "H2BK12 acetylation site" EXACT []
+synonym: "H2BK12ac" RELATED []
+is_a: SO:0001702 ! histone_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:19:13Z
+
+[Term]
+id: SO:0001938
+name: H2AK5_acetylation_site
+def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
+synonym: "H2AK5 acetylation site" EXACT []
+synonym: "H2AK5ac" EXACT []
+is_a: SO:0001702 ! histone_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:20:57Z
+
+[Term]
+id: SO:0001939
+name: H4K12_acetylation_site
+def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
+synonym: "H4K12 acetylation site" EXACT []
+synonym: "H4K12ac" EXACT []
+is_a: SO:0001972 ! histone_4_acylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:26:15Z
+
+[Term]
+id: SO:0001940
+name: H2BK120_acetylation_site
+def: "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
+synonym: "H2BK120 acetylation site" EXACT []
+synonym: "H2BK120ac" EXACT []
+is_a: SO:0001702 ! histone_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:28:38Z
+
+[Term]
+id: SO:0001941
+name: H4K91_acetylation_site
+def: "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
+synonym: "H4K91 acetylation site" EXACT []
+is_a: SO:0001972 ! histone_4_acylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:41:04Z
+
+[Term]
+id: SO:0001942
+name: H2BK20_acetylation_site
+def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
+synonym: "H2BK20 acetylation site" RELATED []
+synonym: "H2BK20ac" EXACT []
+is_a: SO:0001702 ! histone_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:44:31Z
+
+[Term]
+id: SO:0001943
+name: H3K4ac_acetylation_site
+def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
+synonym: "H3K4ac" EXACT []
+synonym: "H3K4ac acetylation site" EXACT []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:46:32Z
+
+[Term]
+id: SO:0001944
+name: H2AK9_acetylation_site
+def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
+synonym: "H2AK9 acetylation site" EXACT []
+synonym: "H2AK9ac" EXACT []
+is_a: SO:0001702 ! histone_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:48:11Z
+
+[Term]
+id: SO:0001945
+name: H3K56_acetylation_site
+def: "A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
+synonym: "H3K56 acetylation site" EXACT []
+synonym: "H3K56ac" EXACT []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:51:14Z
+
+[Term]
+id: SO:0001946
+name: H2BK15_acetylation_site
+def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
+synonym: "H2BK15 acetylation site" EXACT []
+synonym: "H2BK15ac" EXACT []
+is_a: SO:0001702 ! histone_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:53:23Z
+
+[Term]
+id: SO:0001947
+name: H3R2_monomethylation_site
+def: "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]
+synonym: " H3R2me1" EXACT []
+synonym: "H3R2 monomethylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:57:13Z
+
+[Term]
+id: SO:0001948
+name: H3R2_dimethylation_site
+def: "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]
+synonym: "H3R2 dimethylation site" EXACT []
+synonym: "H3R2me2" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T10:59:17Z
+
+[Term]
+id: SO:0001949
+name: H4R3_dimethylation_site
+def: "A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]
+synonym: "H4R3 dimethylation site" EXACT []
+synonym: "H4R3me2" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T11:01:27Z
+
+[Term]
+id: SO:0001950
+name: H4K4_trimethylation_site
+def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]
+synonym: " H4K4me3" EXACT []
+synonym: "H4K4 trimethylation site" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T11:03:29Z
+
+[Term]
+id: SO:0001951
+name: H3K23_dimethylation_site
+def: "A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]
+synonym: "H3K23 dimethylation site" EXACT []
+synonym: "H3K23me2" EXACT []
+is_a: SO:0001701 ! histone_methylation_site
+created_by: kareneilbeck
+creation_date: 2013-03-06T11:05:33Z
+
+[Term]
+id: SO:0001952
+name: promoter_flanking_region
+def: "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]
+synonym: "promoter flanking region" EXACT []
+is_a: SO:0001055 ! transcriptional_cis_regulatory_region
+created_by: kareneilbeck
+creation_date: 2013-03-06T11:36:25Z
+
+[Term]
+id: SO:0001953
+name: restriction_enzyme_assembly_scar
+def: "A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]
+is_a: SO:0001954 ! restriction_enzyme_region
+created_by: kareneilbeck
+creation_date: 2013-03-06T03:18:11Z
+
+[Term]
+id: SO:0001954
+name: restriction_enzyme_region
+def: "A region related to restriction enzyme function." [SO:ke]
+comment: Not a great term for annotation, but used to classify the various regions related to restriction enzymes.
+synonym: "restriction enzyme region" RELATED []
+is_a: SO:0001411 ! biological_region
+created_by: kareneilbeck
+creation_date: 2013-03-06T03:23:34Z
+
+[Term]
+id: SO:0001955
+name: protein_stability_element
+def: "A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]
+synonym: "protein stability element" RELATED []
+is_a: SO:0000839 ! polypeptide_region
+created_by: kareneilbeck
+creation_date: 2013-03-06T03:32:47Z
+
+[Term]
+id: SO:0001956
+name: protease_site
+def: "A polypeptide_region that codes for a protease cleavage site." [SO:ke]
+synonym: "protease site" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+created_by: kareneilbeck
+creation_date: 2013-03-06T03:36:28Z
+
+[Term]
+id: SO:0001957
+name: RNA_stability_element
+def: "RNA secondary structure that affects the stability of an RNA molecule." [SO:ke]
+synonym: "rna stability element" RELATED []
+created_by: kareneilbeck
+creation_date: 2013-03-06T03:38:35Z
+is_obsolete: true
+
+[Term]
+id: SO:0001958
+name: lariat_intron
+def: "A kind of intron whereby the excision is driven by lariat formation." [SO:ke]
+comment: Requested by PomBase 3604508.
+synonym: "lariat intron" EXACT []
+is_a: SO:0000188 ! intron
+created_by: kareneilbeck
+creation_date: 2013-03-07T10:58:40Z
+
+[Term]
+id: SO:0001959
+name: TCT_motif
+def: "A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]
+synonym: "polypyrimidine initiator" EXACT []
+synonym: "TCT element" EXACT []
+is_a: SO:0001660 ! core_promoter_element
+created_by: kareneilbeck
+creation_date: 2013-05-17T04:38:48Z
+
+[Term]
+id: SO:0001960
+name: 5_hydroxymethylcytosine
+def: "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]
+synonym: "5-hmC" EXACT []
+synonym: "5-hydroxymethylcytosine" EXACT []
+xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
+is_a: SO:0000114 ! methylated_cytosine
+created_by: kareneilbeck
+creation_date: 2013-05-17T05:05:31Z
+
+[Term]
+id: SO:0001961
+name: 5_formylcytosine
+def: "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]
+synonym: "5-fC" EXACT []
+synonym: "5-formylcytosine" EXACT []
+xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
+is_a: SO:0001963 ! modified_cytosine
+created_by: kareneilbeck
+creation_date: 2013-05-17T05:06:13Z
+
+[Term]
+id: SO:0001962
+name: modified_adenine
+def: "A modified adenine DNA base feature." [SO:ke]
+is_a: SO:0000305 ! modified_DNA_base
+created_by: kareneilbeck
+creation_date: 2013-05-20T01:22:30Z
+
+[Term]
+id: SO:0001963
+name: modified_cytosine
+def: "A modified cytosine DNA base feature." [SO:ke]
+is_a: SO:0000305 ! modified_DNA_base
+created_by: kareneilbeck
+creation_date: 2013-05-20T01:23:47Z
+
+[Term]
+id: SO:0001964
+name: modified_guanine
+def: "A modified guanine DNA base feature." [SO:ke]
+is_a: SO:0000305 ! modified_DNA_base
+created_by: kareneilbeck
+creation_date: 2013-05-20T01:25:31Z
+
+[Term]
+id: SO:0001965
+name: 8_oxoguanine
+def: "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
+synonym: "8-oxoG" EXACT []
+synonym: "8-oxoguanine" EXACT []
+xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
+is_a: SO:0001964 ! modified_guanine
+created_by: kareneilbeck
+creation_date: 2013-05-20T01:27:51Z
+
+[Term]
+id: SO:0001966
+name: 5_carboxylcytosine
+def: "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]
+synonym: "5-caC" EXACT []
+synonym: "5-carboxycytosine" EXACT []
+xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
+is_a: SO:0001963 ! modified_cytosine
+created_by: kareneilbeck
+creation_date: 2013-05-20T01:30:01Z
+
+[Term]
+id: SO:0001967
+name: 8_oxoadenine
+def: "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
+synonym: "8-oxoA" EXACT []
+synonym: "8-oxoadenine" EXACT []
+xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
+is_a: SO:0001962 ! modified_adenine
+created_by: kareneilbeck
+creation_date: 2013-05-20T01:31:05Z
+
+[Term]
+id: SO:0001968
+name: coding_transcript_variant
+def: "A transcript variant of a protein coding gene." [SO:ke]
+synonym: "coding transcript variant" EXACT []
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2013-05-22T04:34:49Z
+
+[Term]
+id: SO:0001969
+name: coding_transcript_intron_variant
+def: "A transcript variant occurring within an intron of a coding transcript." [SO:ke]
+synonym: "coding sequence intron variant" EXACT []
+is_a: SO:0001627 ! intron_variant
+is_a: SO:0001968 ! coding_transcript_variant
+created_by: kareneilbeck
+creation_date: 2013-05-23T10:54:17Z
+
+[Term]
+id: SO:0001970
+name: non_coding_transcript_intron_variant
+def: "A transcript variant occurring within an intron of a non coding transcript." [SO:ke]
+synonym: "non coding transcript intron variant" EXACT []
+is_a: SO:0001619 ! non_coding_transcript_variant
+is_a: SO:0001627 ! intron_variant
+created_by: kareneilbeck
+creation_date: 2013-05-23T10:55:03Z
+
+[Term]
+id: SO:0001971
+name: zinc_finger_binding_site
+synonym: "zinc finger binding site" EXACT []
+synonym: "zinc_fing" EXACT BS [unirot:features]
+is_a: SO:0001429 ! DNA_binding_site
+created_by: kareneilbeck
+creation_date: 2013-07-29T04:41:53Z
+
+[Term]
+id: SO:0001972
+name: histone_4_acylation_site
+def: "A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
+synonym: "H4ac" EXACT []
+is_a: SO:0001702 ! histone_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-07-30T10:43:04Z
+
+[Term]
+id: SO:0001973
+name: histone_3_acetylation_site
+def: "A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
+synonym: "H3ac" EXACT []
+is_a: SO:0001702 ! histone_acetylation_site
+created_by: kareneilbeck
+creation_date: 2013-07-30T10:46:42Z
+
+[Term]
+id: SO:0001974
+name: CTCF_binding_site
+def: "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]
+synonym: "CCCTF binding site" EXACT []
+synonym: "CTCF binding site" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2013-07-30T10:59:11Z
+
+[Term]
+id: SO:0001975
+name: five_prime_sticky_end_restriction_enzyme_cleavage_site
+def: "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]
+comment: Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
+synonym: "five prime sticky end restriction enzyme cleavage site" EXACT []
+is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
+created_by: kareneilbeck
+creation_date: 2013-07-30T11:32:16Z
+
+[Term]
+id: SO:0001976
+name: three_prime_sticky_end_restriction_enzyme_cleavage_site
+def: "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]
+comment: Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
+synonym: "three prime sticky end restriction enzyme cleavage site" EXACT []
+is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
+created_by: kareneilbeck
+creation_date: 2013-07-30T11:37:19Z
+
+[Term]
+id: SO:0001977
+name: ribonuclease_site
+def: "A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]
+synonym: "ribonuclease site" EXACT []
+is_a: SO:0000833 ! transcript_region
+created_by: kareneilbeck
+creation_date: 2013-07-30T11:41:06Z
+
+[Term]
+id: SO:0001978
+name: signature
+def: "A region of sequence where developer information is encoded." [SO:ke]
+comment: Requested by Jackie Quinn for use in synthetic biology.
+synonym: "DNA signature" EXACT []
+is_a: SO:0000804 ! engineered_region
+created_by: kareneilbeck
+creation_date: 2013-07-30T11:49:22Z
+
+[Term]
+id: SO:0001979
+name: RNA_stability_element
+def: "A motif that affects the stability of RNA." [PMID:22495308, SO:ke]
+synonym: "RNA stability element" EXACT []
+is_a: SO:0000715 ! RNA_motif
+created_by: kareneilbeck
+creation_date: 2013-07-30T03:33:53Z
+
+[Term]
+id: SO:0001980
+name: G_box
+def: "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]
+comment: A plant specific region.
+synonym: "G-box" EXACT []
+synonym: "GBF binding sequence" EXACT []
+is_a: SO:0001678 ! regulatory_promoter_element
+created_by: kareneilbeck
+creation_date: 2013-07-30T04:00:50Z
+
+[Term]
+id: SO:0001981
+name: L_box
+def: "An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]
+synonym: "L-box" EXACT []
+synonym: "L-box promoter element" EXACT []
+is_a: SO:0001678 ! regulatory_promoter_element
+created_by: kareneilbeck
+creation_date: 2013-07-30T04:12:19Z
+
+[Term]
+id: SO:0001982
+name: I-box
+def: "A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]
+synonym: "I-box promoter motif" EXACT []
+is_a: SO:0001678 ! regulatory_promoter_element
+created_by: kareneilbeck
+creation_date: 2013-07-30T04:17:55Z
+
+[Term]
+id: SO:0001983
+name: 5_prime_UTR_premature_start_codon_variant
+def: "A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]
+comment: Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia.
+synonym: "5' UTR premature start codon variant" EXACT []
+synonym: "snpEff:START_GAINED" EXACT VAR []
+is_a: SO:0001623 ! 5_prime_UTR_variant
+created_by: kareneilbeck
+creation_date: 2013-07-30T04:36:25Z
+
+[Term]
+id: SO:0001984
+name: silent_mating_type_cassette_array
+def: "A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]
+synonym: "silent mating-type cassette" RELATED []
+is_a: SO:0005854 ! gene_cassette_array
+created_by: kareneilbeck
+creation_date: 2013-07-31T02:40:38Z
+
+[Term]
+id: SO:0001985
+name: Okazaki_fragment
+def: "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]
+comment: Requested by Midori Harris, 2013.
+synonym: "Okazaki fragment" EXACT []
+is_a: SO:0001411 ! biological_region
+created_by: kareneilbeck
+creation_date: 2013-07-31T02:57:55Z
+
+[Term]
+id: SO:0001986
+name: upstream_transcript_variant
+def: "A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]
+comment: Requested by Graham Ritchie, EBI/Sanger.
+synonym: "upstream transcript variant" EXACT []
+is_a: SO:0001628 ! intergenic_variant
+created_by: kareneilbeck
+creation_date: 2013-07-31T03:46:14Z
+
+[Term]
+id: SO:0001987
+name: downstream_transcript_variant
+comment: Requested by Graham Ritchie, EBI/Sanger.
+synonym: "downstream transcript variant" EXACT []
+is_a: SO:0001628 ! intergenic_variant
+created_by: kareneilbeck
+creation_date: 2013-07-31T03:47:51Z
+
+[Term]
+id: SO:0001988
+name: 5_prime_UTR_premature_start_codon_gain_variant
+def: "A 5' UTR variant where a premature start codon is gained." [Sanger:am]
+synonym: "5 prime UTR premature start codon gain variant" EXACT []
+is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
+created_by: kareneilbeck
+creation_date: 2013-07-31T03:53:06Z
+
+[Term]
+id: SO:0001989
+name: 5_prime_UTR_premature_start_codon_loss_variant
+def: "A 5' UTR variant where a premature start codon is lost." [SANGER:am]
+is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
+created_by: kareneilbeck
+creation_date: 2013-07-31T03:56:48Z
+
+[Term]
+id: SO:0001990
+name: five_prime_UTR_premature_start_codon_location_variant
+def: "A 5' UTR variant where a premature start codon is moved." [SANGER:am]
+is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
+created_by: kareneilbeck
+creation_date: 2013-07-31T03:57:47Z
+
+[Term]
+id: SO:0001991
+name: consensus_AFLP_fragment
+def: "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]
+comment: Requested by Bayer Cropscience September, 2013.
+synonym: "consensus AFLP fragment" EXACT []
+synonym: "consensus amplified fragment length polymorphism fragment" EXACT []
+is_a: SO:0000994 ! consensus_region
+created_by: kareneilbeck
+creation_date: 2013-09-24T10:43:41Z
+
+[Term]
+id: SO:0001992
+name: nonsynonymous_variant
+def: "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]
+synonym: "non_synonymous_coding" EXACT [http://ensembl.org/info/docs/variation/index.html]
+synonym: "nonsynonymous variant" EXACT []
+is_a: SO:0001650 ! inframe_variant
+created_by: kareneilbeck
+creation_date: 2013-10-16T11:47:51Z
+
+[Term]
+id: SO:0001993
+name: extended_cis_splice_site
+def: "Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]
+comment: Added by Andy Menzies (Sanger).
+synonym: "extended cis splice site" EXACT []
+is_a: SO:0001419 ! cis_splice_site
+created_by: kareneilbeck
+creation_date: 2014-01-04T06:20:00Z
+
+[Term]
+id: SO:0001994
+name: intron_base_5
+def: "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]
+synonym: "intron base 5" EXACT []
+is_a: SO:0001014 ! intron_domain
+relationship: part_of SO:0001993 ! extended_cis_splice_site
+created_by: kareneilbeck
+creation_date: 2014-01-04T06:26:02Z
+
+[Term]
+id: SO:0001995
+name: extended_intronic_splice_region_variant
+def: "A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]
+comment: Added by Andy Menzies (Sanger).
+synonym: "extended intronic splice region variant" EXACT []
+is_a: SO:0001568 ! splicing_variant
+created_by: kareneilbeck
+creation_date: 2014-01-04T06:37:27Z
+
+[Term]
+id: SO:0001996
+name: extended_intronic_splice_region
+def: "Region of intronic sequence within 10 bases of an exon." [SANGER:am]
+synonym: "extended intronic splice region " EXACT []
+is_a: SO:0001014 ! intron_domain
+created_by: kareneilbeck
+creation_date: 2014-01-04T06:41:23Z
+
+[Term]
+id: SO:0001997
+name: subtelomere
+def: "A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]
+is_a: SO:0000628 ! chromosomal_structural_element
+created_by: kareneilbeck
+creation_date: 2014-01-05T07:02:01Z
+
+[Term]
+id: SO:0001998
+name: sgRNA
+def: "A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]
+synonym: "gRNA" RELATED []
+synonym: "guide RNA" RELATED []
+synonym: "small guide RNA" EXACT []
+is_a: SO:0000696 ! oligo
+created_by: kareneilbeck
+creation_date: 2014-01-05T07:25:08Z
+
+[Term]
+id: SO:0001999
+name: mating_type_region_motif
+def: "DNA motif that is a component of a mating type region." [SO:ke]
+synonym: "mating type region motif" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0001789 ! mating_type_region
+created_by: kareneilbeck
+creation_date: 2014-01-05T07:30:17Z
+
+[Term]
+id: SO:0002001
+name: Y_region
+def: "A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]
+comment: Requested by Janos Demeter, SGD.
+synonym: "Y-region" EXACT []
+is_a: SO:0001999 ! mating_type_region_motif
+created_by: kareneilbeck
+creation_date: 2014-01-05T07:33:30Z
+
+[Term]
+id: SO:0002002
+name: Z1_region
+def: "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]
+comment: Requested by Janos Demeter, SGD.
+synonym: "Z1-region" EXACT []
+is_a: SO:0001999 ! mating_type_region_motif
+created_by: kareneilbeck
+creation_date: 2014-01-05T07:34:59Z
+
+[Term]
+id: SO:0002003
+name: Z2_region
+def: "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]
+comment: Requested by Janos Demeter, SGD.
+synonym: "Z2-segment" EXACT []
+is_a: SO:0001999 ! mating_type_region_motif
+created_by: kareneilbeck
+creation_date: 2014-01-05T07:36:45Z
+
+[Term]
+id: SO:0002004
+name: ARS_consensus_sequence
+def: "The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]
+synonym: "ACS" EXACT []
+synonym: "ARS consensus sequence" EXACT []
+is_a: SO:0000713 ! DNA_motif
+relationship: part_of SO:0000436 ! ARS
+created_by: kareneilbeck
+creation_date: 2014-01-05T07:47:48Z
+
+[Term]
+id: SO:0002005
+name: DSR_motif
+def: "The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]
+comment: Requested by Antonia Locke, (Pombe).
+synonym: "DSR motif" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2014-01-05T07:51:27Z
+
+[Term]
+id: SO:0002006
+name: zinc_repressed_element
+def: "A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]
+comment: This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe.
+synonym: "zinc repressed element" EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2014-01-05T09:23:27Z
+
+[Term]
+id: SO:0002007
+name: MNV
+def: "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]
+synonym: "multiple nucleotide substitution" EXACT []
+synonym: "multiple nucleotide variant" EXACT []
+is_a: SO:1000002 ! substitution
+created_by: kareneilbeck
+creation_date: 2014-01-13T03:48:40Z
+
+[Term]
+id: SO:0002008
+name: rare_amino_acid_variant
+def: "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]
+comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
+synonym: "rare amino acid variant" EXACT []
+is_a: SO:0001586 ! non_conservative_missense_variant
+created_by: kareneilbeck
+creation_date: 2014-03-24T02:24:01Z
+
+[Term]
+id: SO:0002009
+name: selenocysteine_loss
+def: "A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid." [SO:ke]
+comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
+synonym: "selenocysteine loss" EXACT []
+is_a: SO:0002008 ! rare_amino_acid_variant
+created_by: kareneilbeck
+creation_date: 2014-03-24T02:29:44Z
+
+[Term]
+id: SO:0002010
+name: pyrrolysine_loss
+def: "A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]
+comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
+synonym: "pyrrolysine loss" EXACT []
+is_a: SO:0002008 ! rare_amino_acid_variant
+created_by: kareneilbeck
+creation_date: 2014-03-24T02:30:16Z
+
+[Term]
+id: SO:0002011
+name: intragenic_variant
+def: "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." [SO:ke]
+comment: Requested by Pablo Cingolani, for use in SnpEff.
+synonym: "intragenic variant" EXACT []
+synonym: "snpEff:INTRAGENIC" EXACT VAR []
+is_a: SO:0001576 ! transcript_variant
+created_by: kareneilbeck
+creation_date: 2014-03-24T02:33:13Z
+
+[Term]
+id: SO:0002012
+name: start_lost
+def: "A codon variant that changes at least one base of the canonical start codon." [SO:ke]
+comment: Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
+synonym: "snpEff:START_LOST" EXACT VAR []
+is_a: SO:0001582 ! initiator_codon_variant
+is_a: SO:0001992 ! nonsynonymous_variant
+created_by: kareneilbeck
+creation_date: 2014-03-24T02:41:28Z
+
+[Term]
+id: SO:0002013
+name: 5_prime_UTR_truncation
+def: "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence." [SO:ke]
+synonym: "5 prime UTR truncation" EXACT []
+synonym: "snpEff:UTR_5_DELETED" EXACT VAR []
+is_a: SO:0001623 ! 5_prime_UTR_variant
+created_by: kareneilbeck
+creation_date: 2014-03-25T10:46:42Z
+
+[Term]
+id: SO:0002014
+name: 5_prime_UTR_elongation
+def: "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]
+synonym: "5 prime UTR elongation" EXACT []
+is_a: SO:0001623 ! 5_prime_UTR_variant
+created_by: kareneilbeck
+creation_date: 2014-03-25T10:48:26Z
+
+[Term]
+id: SO:0002015
+name: 3_prime_UTR_truncation
+def: "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence." [SO:ke]
+synonym: "3 prime UTR truncation" EXACT []
+synonym: "snpEff:UTR_3_DELETED" EXACT VAR []
+is_a: SO:0001624 ! 3_prime_UTR_variant
+created_by: kareneilbeck
+creation_date: 2014-03-25T10:54:50Z
+
+[Term]
+id: SO:0002016
+name: 3_prime_UTR_elongation
+def: "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]
+synonym: "3 prime UTR elongation" EXACT []
+is_a: SO:0001624 ! 3_prime_UTR_variant
+created_by: kareneilbeck
+creation_date: 2014-03-25T10:55:33Z
+
+[Term]
+id: SO:0002017
+name: conserved_intergenic_variant
+def: "A sequence variant located in a conserved intergenic region, between genes." [SO:ke]
+comment: Requested by Uma Paila (UVA) for snpEff.
+synonym: "conserved intergenic variant" EXACT []
+synonym: "snpEff:INTERGENIC_CONSERVED" EXACT VAR []
+is_a: SO:0001628 ! intergenic_variant
+created_by: kareneilbeck
+creation_date: 2014-03-25T02:54:39Z
+
+[Term]
+id: SO:0002018
+name: conserved_intron_variant
+def: "A transcript variant occurring within a conserved region of an intron." [SO:ke]
+comment: Requested by Uma Paila (UVA) for snpEff.
+synonym: "conserved intron variant" EXACT []
+synonym: "snpEff:INTRON_CONSERVED" EXACT VAR []
+is_a: SO:0001627 ! intron_variant
+created_by: kareneilbeck
+creation_date: 2014-03-25T02:58:41Z
+
+[Term]
+id: SO:0002019
+name: start_retained_variant
+def: "A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]
+comment: Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
+is_a: SO:0001582 ! initiator_codon_variant
+is_a: SO:0001819 ! synonymous_variant
+created_by: kareneilbeck
+creation_date: 2014-03-28T10:08:41Z
+
+[Term]
+id: SO:0002020
+name: boundary_element
+def: "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]
+comment: Requested by Antonia Lock.
+synonym: "boundary element" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2014-05-30T14:45:37Z
+
+[Term]
+id: SO:0002021
+name: mating_type_region_replication_fork_barrier
+def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]
+comment: Requested by Midori Harris.
+synonym: "mating type region replication fork barrier" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2014-05-30T14:57:26Z
+
+[Term]
+id: SO:0002022
+name: priRNA
+def: "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]
+synonym: "primal small RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+created_by: kareneilbeck
+creation_date: 2014-05-30T15:01:24Z
+
+[Term]
+id: SO:0002023
+name: multiplexing_sequence_identifier
+def: "A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]
+synonym: "multiplexing sequence identifier" EXACT []
+is_a: SO:0000324 ! tag
+created_by: kareneilbeck
+creation_date: 2014-05-30T15:13:16Z
+
+[Term]
+id: SO:0002024
+name: W_region
+alt_id: SO:0002000
+def: "The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR." [SGD:jd]
+comment: MERGED COMMENT:\nTARGET COMMENT: Requested by Janos Demeter, SGD.\n--------------------\nSOURCE COMMENT: Requested by Janos Demeter, SGD.
+synonym: "W-region" EXACT []
+is_a: SO:0001999 ! mating_type_region_motif
+created_by: kareneilbeck
+creation_date: 2014-07-11T13:20:08Z
+
+[Term]
+id: SO:0002025
+name: cis_acting_homologous_chromosome_pairing_region
+def: "A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]
+comment: Comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the "Mei2 dot". This term was Requested by Val Wood, PomBase.
+synonym: "cis-acting homologous chromosome pairing region" EXACT []
+is_a: SO:0000713 ! DNA_motif
+created_by: kareneilbeck
+creation_date: 2014-07-14T11:40:34Z
+
+[Term]
+id: SO:0002026
+name: intein_encoding_region
+def: "The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]
+comment: Requested by Janos Demeter 2014.
+is_a: SO:0000842 ! gene_component_region
+created_by: kareneilbeck
+creation_date: 2014-07-14T11:53:21Z
+
+[Term]
+id: SO:0002027
+name: uORF
+def: "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]
+synonym: "upstream ORF" EXACT []
+is_a: SO:0000236 ! ORF
+created_by: kareneilbeck
+creation_date: 2014-07-14T11:59:23Z
+
+[Term]
+id: SO:0002028
+name: sORF
+def: "An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]
+synonym: "small ORF" EXACT []
+synonym: "smORF" EXACT []
+is_a: SO:0000236 ! ORF
+created_by: kareneilbeck
+creation_date: 2014-07-14T12:02:33Z
+
+[Term]
+id: SO:0002029
+name: tnaORF
+def: "A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]
+synonym: "translated nested antisense gene" EXACT []
+is_a: SO:0000236 ! ORF
+created_by: kareneilbeck
+creation_date: 2014-07-14T12:04:32Z
+
+[Term]
+id: SO:0002030
+name: X_region
+def: "One of two segments of homology found at all three mating loci (HML, MAT and HMR)." [SGD:jd]
+synonym: "x-region" EXACT []
+is_a: SO:0001999 ! mating_type_region_motif
+created_by: kareneilbeck
+creation_date: 2014-07-14T18:43:21Z
+
+[Term]
+id: SO:0002031
+name: shRNA
+def: "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]
+synonym: "short hairpin RNA" EXACT []
+synonym: "small hairpin RNA" EXACT []
+xref: http:http:en.wikipedia.org/wiki/Small_hairpin_RNA "wikipedia"
+is_a: SO:0000655 ! ncRNA
+created_by: kareneilbeck
+creation_date: 2014-10-23T09:16:29Z
+
+[Term]
+id: SO:0002032
+name: moR
+def: "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA." [SO:ke]
+comment: MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015.
+synonym: "microRNA-offset RNA" EXACT []
+is_a: SO:0000370 ! small_regulatory_ncRNA
+relationship: part_of SO:0001244 ! pre_miRNA
+created_by: kareneilbeck
+creation_date: 2015-01-09T13:57:43Z
+
+[Term]
+id: SO:0002033
+name: loR
+def: "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA." [SO:ke]
+comment: MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015.
+synonym: "loop-origin miRs" EXACT []
+is_a: SO:0000370 ! small_regulatory_ncRNA
+relationship: part_of SO:0001244 ! pre_miRNA
+created_by: kareneilbeck
+creation_date: 2015-01-09T14:02:02Z
+
+[Term]
+id: SO:0002034
+name: miR_encoding_snoRNA_primary_transcript
+def: "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
+synonym: "miR encoding snoRNA primary transcript" EXACT []
+is_a: SO:0000232 ! snoRNA_primary_transcript
+relationship: has_part SO:0001244 ! pre_miRNA
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:02:13Z
+
+[Term]
+id: SO:0002035
+name: lncRNA_primary_transcript
+def: "A primary transcript encoding a lncRNA." [SO:ke]
+synonym: "lncRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:23:03Z
+
+[Term]
+id: SO:0002036
+name: miR_encoding_lncRNA_primary_transcript
+def: "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
+synonym: "miR encoding lncRNA primary transcript" EXACT []
+is_a: SO:0002035 ! lncRNA_primary_transcript
+relationship: has_part SO:0001244 ! pre_miRNA
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:23:48Z
+
+[Term]
+id: SO:0002037
+name: miR_encoding_tRNA_primary_transcript
+def: "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
+synonym: "miR encoding tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+relationship: has_part SO:0001244 ! pre_miRNA
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:28:23Z
+
+[Term]
+id: SO:0002038
+name: shRNA_primary_transcript
+def: "A primary transcript encoding an shRNA." [SO:ke]
+synonym: "shRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:30:43Z
+
+[Term]
+id: SO:0002039
+name: miR_encoding_shRNA_primary_transcript
+def: "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
+synonym: "miR encoding shRNA primary transcript" EXACT []
+is_a: SO:0002038 ! shRNA_primary_transcript
+relationship: has_part SO:0001244 ! pre_miRNA
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:32:00Z
+
+[Term]
+id: SO:0002040
+name: vaultRNA_primary_transcript
+def: "A primary transcript encoding a vaultRNA." [SO:ke]
+synonym: "vaultRNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:33:33Z
+
+[Term]
+id: SO:0002041
+name: miR_encoding_vaultRNA_primary_transcript
+def: "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
+synonym: "miR encoding vaultRNA primary transcript" EXACT []
+is_a: SO:0002040 ! vaultRNA_primary_transcript
+relationship: has_part SO:0001244 ! pre_miRNA
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:34:32Z
+
+[Term]
+id: SO:0002042
+name: Y_RNA_primary_transcript
+def: "A primary transcript encoding a Y-RNA." [SO:ke]
+synonym: "Y-RNA primary transcript" EXACT []
+is_a: SO:0000483 ! nc_primary_transcript
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:36:51Z
+
+[Term]
+id: SO:0002043
+name: miR_encoding_Y_RNA_primary_transcript
+def: "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
+synonym: "miR encoding Y-RNA primary transcript" EXACT []
+is_a: SO:0002042 ! Y_RNA_primary_transcript
+relationship: has_part SO:0001244 ! pre_miRNA
+created_by: kareneilbeck
+creation_date: 2015-01-09T15:37:46Z
+
+[Term]
+id: SO:0002044
+name: TCS_element
+def: "A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT." [PMID:1489142, PMID:20118212, SO:ke]
+comment: Requested by Rama - SGD.
+synonym: "TCS element" EXACT []
+synonym: "TEA Consensus Sequence " EXACT []
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2015-02-09T15:02:53Z
+
+[Term]
+id: SO:0002045
+name: pheromone_response_element
+def: "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]." [PMID:1489142, SO:ke]
+comment: Requested by Rama, SGD.
+synonym: "pheromone response element" EXACT []
+synonym: "PRE" EXACT []
+is_a: SO:0000235 ! TF_binding_site
+is_a: SO:0001659 ! promoter_element
+created_by: kareneilbeck
+creation_date: 2015-02-09T15:05:43Z
+
+[Term]
+id: SO:0002046
+name: FRE
+def: "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae." [PMID:1489142, SO:ke]
+comment: Requested by Rama, SGD.
+synonym: "filamentation and invasion response element" EXACT []
+is_a: SO:0001461 ! enhancer_binding_site
+created_by: kareneilbeck
+creation_date: 2015-02-09T15:09:47Z
+
+[Term]
+id: SO:0002047
+name: transcription_pause_site
+def: "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli." [PMID:24789973, SO:ke]
+synonym: "transcription pause site" EXACT []
+is_a: SO:0001679 ! transcription_regulatory_region
+created_by: kareneilbeck
+creation_date: 2015-02-09T15:32:52Z
+
+[Term]
+id: SO:0002048
+name: disabled_reading_frame
+def: "A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons)." [SGD:se]
+synonym: "disabled ORF" EXACT []
+synonym: "disabled_reading frame" RELATED []
+synonym: "dORF" EXACT []
+is_a: SO:0000717 ! reading_frame
+created_by: kareneilbeck
+creation_date: 2015-02-09T16:15:46Z
+
+[Term]
+id: SO:0002049
+name: H3K27_acetylation_site
+def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:rs]
+comment: Requested by: Sagar Jain, Richard Scheuermann.
+synonym: "H3K27 acetylation site" EXACT []
+is_a: SO:0001973 ! histone_3_acetylation_site
+created_by: kareneilbeck
+creation_date: 2015-05-14T10:17:11Z
+
+[Term]
+id: SO:0002050
+name: constitutive_promoter
+def: "A promoter that allows for continual transcription of gene." [SO:ke]
+synonym: "constitutive promoter" EXACT []
+is_a: SO:0000167 ! promoter
+created_by: kareneilbeck
+creation_date: 2015-05-14T10:39:09Z
+
+[Term]
+id: SO:0002051
+name: inducible_promoter
+def: "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors." [SO:ke]
+synonym: "inducible promoter" EXACT []
+is_a: SO:0000167 ! promoter
+created_by: kareneilbeck
+creation_date: 2015-05-14T10:39:56Z
+
+[Term]
+id: SO:0002052
+name: dominant_negative_variant
+def: "A variant where the mutated gene product adversely affects the other (wild type) gene product." [SO:ke]
+comment: Requested by Deanna Church.
+synonym: "dominant negative" EXACT []
+synonym: "dominant negative variant" EXACT []
+is_a: SO:0001536 ! functional_variant
+created_by: kareneilbeck
+creation_date: 2015-05-14T11:16:28Z
+
+[Term]
+id: SO:0002053
+name: gain_of_function_variant
+def: "A sequence variant whereby new or enhanced function is conferred on the gene product." [SO:ke]
+synonym: "gain of function variant" EXACT []
+is_a: SO:0001536 ! functional_variant
+created_by: kareneilbeck
+creation_date: 2015-05-14T11:20:47Z
+
+[Term]
+id: SO:0002054
+name: loss_of_function_variant
+def: "A sequence variant whereby the gene product has diminished or abolished function." [SO:ke]
+synonym: "loss of function variant" EXACT []
+is_a: SO:0001536 ! functional_variant
+created_by: kareneilbeck
+creation_date: 2015-05-14T11:21:29Z
+
+[Term]
+id: SO:0002055
+name: null_mutation
+def: "A variant whereby the gene product is not functional or the gene product is not produced." [SO:ke]
+synonym: "null mutation" EXACT []
+is_a: SO:0001536 ! functional_variant
+created_by: kareneilbeck
+creation_date: 2015-05-14T11:21:57Z
+
+[Term]
+id: SO:0002056
+name: intronic_splicing_silencer
+def: "An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke]
+comment: Requested by Javier Diez Perez.
+synonym: "intronic splicing silencer" EXACT []
+synonym: "ISS" EXACT []
+is_a: SO:0000625 ! silencer
+relationship: part_of SO:0000188 ! intron
+created_by: kareneilbeck
+creation_date: 2015-05-14T12:24:10Z
+
+[Term]
+id: SO:0002057
+name: intronic_splicing_enhancer
+synonym: "ISE" EXACT []
+created_by: kareneilbeck
+creation_date: 2015-05-14T12:28:31Z
+is_obsolete: true
+
+[Term]
+id: SO:0002058
+name: exonic_splicing_silencer
+def: "An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke]
+comment: Requested by Javier Diez Perez.
+synonym: "ESS" EXACT []
+synonym: "exonic splicing silencer" EXACT []
+is_a: SO:0000625 ! silencer
+is_a: SO:0000852 ! exon_region
+created_by: kareneilbeck
+creation_date: 2015-05-14T12:42:12Z
+
+[Term]
+id: SO:0002059
+name: recombination_enhancer
+def: "A regulatory_region that promotes or induces the process of recombination." [PMID:8861911, SGD:se]
+synonym: "recombination enhancer" EXACT []
+is_a: SO:0001681 ! recombination_regulatory_region
+created_by: kareneilbeck
+creation_date: 2015-05-14T13:08:58Z
+
+[Term]
+id: SO:0002060
+name: interchomosomal_translocation
+def: "A translocation where the regions involved are from different chromosomes." [NCBI:th]
+is_a: SO:1000044 ! chromosomal_translocation
+created_by: kareneilbeck
+creation_date: 2015-06-18T11:10:30Z
+
+[Term]
+id: SO:0002061
+name: intrachomosomal_translocation
+def: "A translocation where the regions involved are from the same chromosome." [NCBI:th]
+is_a: SO:1000044 ! chromosomal_translocation
+created_by: kareneilbeck
+creation_date: 2015-06-18T11:10:51Z
+
+[Term]
+id: SO:0002062
+name: complex_chromosomal_rearrangement
+def: "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis." [NCBI:th]
+synonym: "complex chromosomal rearrangement" EXACT []
+is_a: SO:0001784 ! complex_structural_alteration
+created_by: kareneilbeck
+creation_date: 2015-06-18T11:24:55Z
+
+[Term]
+id: SO:0002063
+name: alu_insertion
+def: "An insertion of sequence from the Alu family of mobile elements." [NCBI:th]
+synonym: "alu insertion" EXACT []
+is_a: SO:0001837 ! mobile_element_insertion
+created_by: kareneilbeck
+creation_date: 2015-06-18T11:30:36Z
+
+[Term]
+id: SO:0002064
+name: LINE1_insertion
+def: "An insertion from the Line1 family of mobile elements." [NCBI:th]
+synonym: "line1 insertion" RELATED []
+is_a: SO:0001837 ! mobile_element_insertion
+created_by: kareneilbeck
+creation_date: 2015-06-18T11:34:44Z
+
+[Term]
+id: SO:0002065
+name: SVA_insertion
+def: "An insertion of sequence from the SVA family of mobile elements." [NCBI:th]
+is_a: SO:0001837 ! mobile_element_insertion
+created_by: kareneilbeck
+creation_date: 2015-06-18T11:36:12Z
+
+[Term]
+id: SO:0005836
+name: regulatory_region
+def: "A region of sequence that is involved in the control of a biological process." [SO:ke]
+subset: SOFA
+synonym: "regulatory region" EXACT []
+xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki"
+is_a: SO:0000831 ! gene_member_region
+
+[Term]
+id: SO:0005837
+name: U14_snoRNA_primary_transcript
+def: "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]
+synonym: "4.5S snRNA primary transcript" EXACT []
+synonym: "U14 snoRNA primary transcript" EXACT []
+is_a: SO:0000232 ! snoRNA_primary_transcript
+
+[Term]
+id: SO:0005841
+name: methylation_guide_snoRNA
+def: "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
+comment: Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
+synonym: "methylation guide snoRNA" EXACT []
+is_a: SO:0000593 ! C_D_box_snoRNA
+relationship: derives_from SO:0000580 ! methylation_guide_snoRNA_primary_transcript
+
+[Term]
+id: SO:0005843
+name: rRNA_cleavage_RNA
+def: "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]
+synonym: "rRNA cleavage RNA" EXACT []
+is_a: SO:0000655 ! ncRNA
+relationship: derives_from SO:0000582 ! rRNA_cleavage_snoRNA_primary_transcript
+
+[Term]
+id: SO:0005845
+name: exon_of_single_exon_gene
+def: "An exon that is the only exon in a gene." [RSC:cb]
+synonym: "exon of single exon gene" EXACT []
+synonym: "single_exon" RELATED []
+synonym: "singleton exon" EXACT []
+is_a: SO:0000147 ! exon
+
+[Term]
+id: SO:0005847
+name: cassette_array_member
+synonym: "cassette array member" EXACT []
+is_a: SO:0005848 ! gene_cassette_member
+
+[Term]
+id: SO:0005848
+name: gene_cassette_member
+synonym: "gene cassette member" EXACT []
+is_a: SO:0000081 ! gene_array_member
+
+[Term]
+id: SO:0005849
+name: gene_subarray_member
+synonym: "gene subarray member" EXACT []
+is_a: SO:0000081 ! gene_array_member
+
+[Term]
+id: SO:0005850
+name: primer_binding_site
+def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
+synonym: "primer binding site" EXACT []
+xref: http://en.wikipedia.org/wiki/Primer_binding_site "wiki"
+is_a: SO:0001655 ! nucleotide_binding_site
+relationship: part_of SO:0000186 ! LTR_retrotransposon
+
+[Term]
+id: SO:0005851
+name: gene_array
+def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]
+comment: This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
+synonym: "gene array" EXACT []
+is_a: SO:0005855 ! gene_group
+
+[Term]
+id: SO:0005852
+name: gene_subarray
+def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]
+comment: This would include, for example, a cluster of genes encoding different histones.
+synonym: "gene subarray" EXACT []
+is_a: SO:0005855 ! gene_group
+
+[Term]
+id: SO:0005853
+name: gene_cassette
+def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]
+comment: This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.
+synonym: "gene cassette" EXACT []
+xref: http://en.wikipedia.org/wiki/Gene_cassette "wiki"
+is_a: SO:0000704 ! gene
+
+[Term]
+id: SO:0005854
+name: gene_cassette_array
+def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]
+comment: This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
+synonym: "gene cassette array" EXACT []
+is_a: SO:0005855 ! gene_group
+relationship: has_part SO:0005853 ! gene_cassette
+
+[Term]
+id: SO:0005855
+name: gene_group
+def: "A collection of related genes." [SO:ma]
+subset: SOFA
+synonym: "gene group" EXACT []
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:0005856
+name: selenocysteine_tRNA_primary_transcript
+def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
+synonym: "selenocysteine tRNA primary transcript" EXACT []
+is_a: SO:0000210 ! tRNA_primary_transcript
+
+[Term]
+id: SO:0005857
+name: selenocysteinyl_tRNA
+def: "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]
+synonym: "selenocysteinyl tRNA" EXACT []
+synonym: "selenocysteinyl-transfer ribonucleic acid" EXACT []
+synonym: "selenocysteinyl-transfer RNA" EXACT []
+is_a: SO:0000253 ! tRNA
+relationship: derives_from SO:0005856 ! selenocysteine_tRNA_primary_transcript
+
+[Term]
+id: SO:0005858
+name: syntenic_region
+def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]
+synonym: "syntenic region" EXACT []
+is_a: SO:0000330 ! conserved_region
+relationship: has_quality SO:0000860 ! syntenic
+
+[Term]
+id: SO:0100001
+name: biochemical_region_of_peptide
+def: "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "biochemical motif" EXACT []
+synonym: "biochemical region of peptide" EXACT []
+synonym: "biochemical_region" RELATED []
+is_a: SO:0001067 ! polypeptide_motif
+
+[Term]
+id: SO:0100002
+name: molecular_contact_region
+def: "A region that is involved a contact with another molecule." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "molecular contact region" RELATED []
+is_a: SO:0100001 ! biochemical_region_of_peptide
+
+[Term]
+id: SO:0100003
+name: intrinsically_unstructured_polypeptide_region
+def: "A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]
+subset: biosapiens
+synonym: "disordered region" RELATED BS []
+synonym: "intrinsically unstructured polypeptide region" EXACT []
+is_a: SO:0001070 ! polypeptide_structural_region
+
+[Term]
+id: SO:0100004
+name: catmat_left_handed_three
+def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "catmat-3l" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0100005
+name: catmat_left_handed_four
+def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "catmat-4l" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0100006
+name: catmat_right_handed_three
+def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "catmat-3r" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0100007
+name: catmat_right_handed_four
+def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "catmat-4r" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0100008
+name: alpha_beta_motif
+def: "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
+subset: biosapiens
+synonym: "alpha beta motif" EXACT []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0100009
+name: lipoprotein_signal_peptide
+def: "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]
+subset: biosapiens
+synonym: "lipoprotein signal peptide" EXACT []
+synonym: "prokaryotic membrane lipoprotein lipid attachment site" EXACT []
+is_a: SO:0100011 ! cleaved_peptide_region
+
+[Term]
+id: SO:0100010
+name: no_output
+def: "An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]
+subset: biosapiens
+synonym: "no output" EXACT BS []
+is_a: SO:0000703 ! experimental_result_region
+
+[Term]
+id: SO:0100011
+name: cleaved_peptide_region
+def: "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+subset: SOFA
+synonym: "cleaved peptide region" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+relationship: part_of SO:0001063 ! immature_peptide_region
+
+[Term]
+id: SO:0100012
+name: peptide_coil
+def: "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]
+subset: biosapiens
+synonym: "coil" RELATED BS []
+synonym: "peptide coil" EXACT []
+synonym: "random coil" RELATED BS []
+is_a: SO:0001078 ! polypeptide_secondary_structure
+
+[Term]
+id: SO:0100013
+name: hydrophobic_region_of_peptide
+def: "Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]
+comment: Range.
+subset: biosapiens
+synonym: "hydropathic" RELATED []
+synonym: "hydrophobic region of peptide" RELATED []
+synonym: "hydrophobic_region" EXACT []
+synonym: "hydrophobicity" RELATED []
+is_a: SO:0000839 ! polypeptide_region
+
+[Term]
+id: SO:0100014
+name: n_terminal_region
+def: "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]
+subset: biosapiens
+synonym: "N-region" RELATED []
+is_a: SO:0100011 ! cleaved_peptide_region
+relationship: part_of SO:0000418 ! signal_peptide
+
+[Term]
+id: SO:0100015
+name: c_terminal_region
+def: "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]
+subset: biosapiens
+synonym: "C-region" RELATED []
+is_a: SO:0100011 ! cleaved_peptide_region
+relationship: part_of SO:0000418 ! signal_peptide
+
+[Term]
+id: SO:0100016
+name: central_hydrophobic_region_of_signal_peptide
+def: "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]
+subset: biosapiens
+synonym: "central hydrophobic region of signal peptide" EXACT []
+synonym: "central_hydrophobic_region" RELATED []
+synonym: "H-region" RELATED []
+is_a: SO:0100011 ! cleaved_peptide_region
+relationship: part_of SO:0000418 ! signal_peptide
+
+[Term]
+id: SO:0100017
+name: polypeptide_conserved_motif
+def: "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]
+subset: biosapiens
+synonym: "motif" RELATED []
+is_a: SO:0001067 ! polypeptide_motif
+
+[Term]
+id: SO:0100018
+name: polypeptide_binding_motif
+def: "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]
+subset: biosapiens
+synonym: "binding" RELATED [uniprot:feature_type]
+synonym: "polypeptide binding motif" EXACT []
+is_a: SO:0100001 ! biochemical_region_of_peptide
+
+[Term]
+id: SO:0100019
+name: polypeptide_catalytic_motif
+def: "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]
+subset: biosapiens
+synonym: "catalytic_motif" RELATED []
+synonym: "polypeptide catalytic motif" EXACT []
+is_a: SO:0100001 ! biochemical_region_of_peptide
+
+[Term]
+id: SO:0100020
+name: polypeptide_DNA_contact
+def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]
+subset: biosapiens
+synonym: "DNA_bind" EXACT BS [uniprot:feature]
+synonym: "polypeptide DNA contact" EXACT []
+is_a: SO:0001429 ! DNA_binding_site
+is_a: SO:0100002 ! molecular_contact_region
+
+[Term]
+id: SO:0100021
+name: polypeptide_conserved_region
+def: "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]
+subset: biosapiens
+synonym: "polypeptide conserved region" EXACT []
+is_a: SO:0000839 ! polypeptide_region
+
+[Term]
+id: SO:1000002
+name: substitution
+def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]
+subset: SOFA
+xref: loinc:LA6690-7 "Substitution"
+is_a: SO:0001059 ! sequence_alteration
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:1000005
+name: complex_substitution
+def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+subset: SOFA
+synonym: "complex substitution" EXACT []
+is_a: SO:1000002 ! substitution
+
+[Term]
+id: SO:1000008
+name: point_mutation
+def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]
+subset: SOFA
+synonym: "point mutation" EXACT []
+xref: http://en.wikipedia.org/wiki/Point_mutation "wiki"
+is_a: SO:0001483 ! SNV
+
+[Term]
+id: SO:1000009
+name: transition
+def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+is_a: SO:0001483 ! SNV
+
+[Term]
+id: SO:1000010
+name: pyrimidine_transition
+def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]
+synonym: "pyrimidine transition" EXACT []
+is_a: SO:1000009 ! transition
+
+[Term]
+id: SO:1000011
+name: C_to_T_transition
+def: "A transition of a cytidine to a thymine." [SO:ke]
+synonym: "C to T transition" EXACT []
+is_a: SO:1000010 ! pyrimidine_transition
+
+[Term]
+id: SO:1000012
+name: C_to_T_transition_at_pCpG_site
+def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+synonym: "C to T transition at pCpG site" EXACT []
+is_a: SO:1000011 ! C_to_T_transition
+
+[Term]
+id: SO:1000013
+name: T_to_C_transition
+synonym: "T to C transition" EXACT []
+is_a: SO:1000010 ! pyrimidine_transition
+
+[Term]
+id: SO:1000014
+name: purine_transition
+def: "A substitution of a purine, A or G, for another purine." [SO:ke]
+synonym: "purine transition" EXACT []
+is_a: SO:1000009 ! transition
+
+[Term]
+id: SO:1000015
+name: A_to_G_transition
+def: "A transition of an adenine to a guanine." [SO:ke]
+synonym: "A to G transition" EXACT []
+is_a: SO:1000014 ! purine_transition
+
+[Term]
+id: SO:1000016
+name: G_to_A_transition
+def: "A transition of a guanine to an adenine." [SO:ke]
+synonym: "G to A transition" EXACT []
+is_a: SO:1000014 ! purine_transition
+
+[Term]
+id: SO:1000017
+name: transversion
+def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+xref: http://en.wikipedia.org/wiki/Transversion "wiki"
+is_a: SO:0001483 ! SNV
+
+[Term]
+id: SO:1000018
+name: pyrimidine_to_purine_transversion
+def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]
+synonym: "pyrimidine to purine transversion" EXACT []
+is_a: SO:1000017 ! transversion
+
+[Term]
+id: SO:1000019
+name: C_to_A_transversion
+def: "A transversion from cytidine to adenine." [SO:ke]
+synonym: "C to A transversion" EXACT []
+is_a: SO:1000018 ! pyrimidine_to_purine_transversion
+
+[Term]
+id: SO:1000020
+name: C_to_G_transversion
+synonym: "C to G transversion" EXACT []
+is_a: SO:1000018 ! pyrimidine_to_purine_transversion
+
+[Term]
+id: SO:1000021
+name: T_to_A_transversion
+def: "A transversion from T to A." [SO:ke]
+synonym: "T to A transversion" EXACT []
+is_a: SO:1000018 ! pyrimidine_to_purine_transversion
+
+[Term]
+id: SO:1000022
+name: T_to_G_transversion
+def: "A transversion from T to G." [SO:ke]
+synonym: "T to G transversion" EXACT []
+is_a: SO:1000018 ! pyrimidine_to_purine_transversion
+
+[Term]
+id: SO:1000023
+name: purine_to_pyrimidine_transversion
+def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]
+synonym: "purine to pyrimidine transversion" EXACT []
+is_a: SO:1000017 ! transversion
+
+[Term]
+id: SO:1000024
+name: A_to_C_transversion
+def: "A transversion from adenine to cytidine." [SO:ke]
+synonym: "A to C transversion" EXACT []
+is_a: SO:1000023 ! purine_to_pyrimidine_transversion
+
+[Term]
+id: SO:1000025
+name: A_to_T_transversion
+def: "A transversion from adenine to thymine." [SO:ke]
+synonym: "A to T transversion" EXACT []
+is_a: SO:1000023 ! purine_to_pyrimidine_transversion
+
+[Term]
+id: SO:1000026
+name: G_to_C_transversion
+def: "A transversion from guanine to cytidine." [SO:ke]
+synonym: "G to C transversion" EXACT []
+is_a: SO:1000023 ! purine_to_pyrimidine_transversion
+
+[Term]
+id: SO:1000027
+name: G_to_T_transversion
+def: "A transversion from guanine to thymine." [SO:ke]
+synonym: "G to T transversion" EXACT []
+is_a: SO:1000023 ! purine_to_pyrimidine_transversion
+
+[Term]
+id: SO:1000028
+name: intrachromosomal_mutation
+def: "A chromosomal structure variation within a single chromosome." [SO:ke]
+synonym: "intrachromosomal mutation" EXACT []
+is_a: SO:1000183 ! chromosome_structure_variation
+relationship: has_quality SO:0001510 ! intrachromosomal
+
+[Term]
+id: SO:1000029
+name: chromosomal_deletion
+def: "An incomplete chromosome." [SO:ke]
+synonym: "(bacteria)&Dgr;" RELATED []
+synonym: "(Drosophila)Df" RELATED []
+synonym: "(fungi)D" RELATED []
+synonym: "chromosomal deletion" EXACT []
+synonym: "deficiency" EXACT []
+xref: http://en.wikipedia.org/wiki/Chromosomal_deletion "wiki"
+is_a: SO:1000028 ! intrachromosomal_mutation
+relationship: has_part SO:0000159 ! deletion
+
+[Term]
+id: SO:1000030
+name: chromosomal_inversion
+def: "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]
+synonym: "(bacteria)IN" RELATED []
+synonym: "(Drosophila)In" RELATED []
+synonym: "(fungi)In" RELATED []
+synonym: "chromosomal inversion" EXACT []
+xref: http://en.wikipedia.org/wiki/Chromosomal_inversion "wiki"
+is_a: SO:1000028 ! intrachromosomal_mutation
+relationship: has_part SO:1000036 ! inversion
+
+[Term]
+id: SO:1000031
+name: interchromosomal_mutation
+def: "A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]
+synonym: "interchromosomal mutation" EXACT []
+is_a: SO:1000183 ! chromosome_structure_variation
+relationship: has_quality SO:0001511 ! interchromosomal
+
+[Term]
+id: SO:1000032
+name: indel
+def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel]
+comment: Indels can have a different number of bases than the corresponding reference sequence.
+xref: http://en.wikipedia.org/wiki/Indel "wiki"
+xref: loinc:LA9659-9 "Insertion and Deletion"
+is_a: SO:0001059 ! sequence_alteration
+
+[Term]
+id: SO:1000035
+name: duplication
+def: "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]
+synonym: "nucleotide duplication" EXACT []
+synonym: "nucleotide_duplication" RELATED []
+xref: loinc:LA6686-5 "Duplication"
+is_a: SO:0000667 ! insertion
+
+[Term]
+id: SO:1000036
+name: inversion
+def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+subset: DBVAR
+subset: SOFA
+synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
+xref: loinc:LA6689-9 "Inversion"
+is_a: SO:0001059 ! sequence_alteration
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:1000037
+name: chromosomal_duplication
+def: "An extra chromosome." [SO:ke]
+synonym: "(Drosophila)Dp" RELATED []
+synonym: "(fungi)Dp" RELATED []
+synonym: "chromosomal duplication" EXACT []
+xref: http://en.wikipedia.org/wiki/Chromosomal_duplication "wiki"
+is_a: SO:1000183 ! chromosome_structure_variation
+
+[Term]
+id: SO:1000038
+name: intrachromosomal_duplication
+def: "A duplication that occurred within a chromosome." [SO:ke]
+synonym: "intrachromosomal duplication" EXACT []
+is_a: SO:1000028 ! intrachromosomal_mutation
+is_a: SO:1000037 ! chromosomal_duplication
+relationship: has_part SO:1000035 ! duplication
+
+[Term]
+id: SO:1000039
+name: direct_tandem_duplication
+def: "A tandem duplication where the individual regions are in the same orientation." [SO:ke]
+synonym: "direct tandem duplication" EXACT []
+is_a: SO:1000173 ! tandem_duplication
+
+[Term]
+id: SO:1000040
+name: inverted_tandem_duplication
+def: "A tandem duplication where the individual regions are not in the same orientation." [SO:ke]
+synonym: "inverted tandem duplication" EXACT []
+synonym: "mirror duplication" RELATED []
+is_a: SO:1000173 ! tandem_duplication
+
+[Term]
+id: SO:1000041
+name: intrachromosomal_transposition
+def: "A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]
+synonym: "(Drosophila)Tp" RELATED []
+synonym: "intrachromosomal transposition" EXACT []
+is_a: SO:0000453 ! chromosomal_transposition
+is_a: SO:1000038 ! intrachromosomal_duplication
+relationship: has_part SO:0000199 ! translocation
+relationship: has_part SO:1000035 ! duplication
+
+[Term]
+id: SO:1000042
+name: compound_chromosome
+def: "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]
+synonym: "compound chromosome" EXACT []
+is_a: SO:1000183 ! chromosome_structure_variation
+
+[Term]
+id: SO:1000043
+name: Robertsonian_fusion
+def: "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]
+synonym: "centric-fusion translocations" EXACT []
+synonym: "Robertsonian fusion" EXACT []
+synonym: "whole-arm translocations" EXACT []
+xref: http://en.wikipedia.org/wiki/Robertsonian_fusion "wiki"
+is_a: SO:1000044 ! chromosomal_translocation
+
+[Term]
+id: SO:1000044
+name: chromosomal_translocation
+def: "An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]
+synonym: "(Drosophila)T" RELATED []
+synonym: "(fungi)T" RELATED []
+synonym: "chromosomal translocation" EXACT []
+xref: http://en.wikipedia.org/wiki/Chromosomal_translocation "wiki"
+is_a: SO:0000199 ! translocation
+is_a: SO:1000031 ! interchromosomal_mutation
+
+[Term]
+id: SO:1000045
+name: ring_chromosome
+def: "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]
+synonym: "(Drosophila)R" RELATED []
+synonym: "(fungi)C" RELATED []
+synonym: "ring chromosome" EXACT []
+xref: http://en.wikipedia.org/wiki/Ring_chromosome "wiki"
+is_a: SO:1000028 ! intrachromosomal_mutation
+relationship: has_quality SO:0000988 ! circular
+
+[Term]
+id: SO:1000046
+name: pericentric_inversion
+def: "A chromosomal inversion that includes the centromere." [FB:reference_manual]
+synonym: "pericentric inversion" EXACT []
+is_a: SO:1000030 ! chromosomal_inversion
+relationship: has_quality SO:0001518 ! pericentric
+
+[Term]
+id: SO:1000047
+name: paracentric_inversion
+def: "A chromosomal inversion that does not include the centromere." [FB:reference_manual]
+synonym: "paracentric inversion" EXACT []
+is_a: SO:1000030 ! chromosomal_inversion
+relationship: has_quality SO:0001519 ! paracentric
+
+[Term]
+id: SO:1000048
+name: reciprocal_chromosomal_translocation
+def: "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]
+synonym: "reciprocal chromosomal translocation" EXACT []
+is_a: SO:1000044 ! chromosomal_translocation
+
+[Term]
+id: SO:1000049
+name: sequence_variation_affecting_transcript
+alt_id: SO:1000177
+alt_id: SO:1000179
+def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting transcript" EXACT []
+synonym: "mutation causing partially characterised change in transcript" RELATED []
+synonym: "mutation causing uncharacterised change in transcript" RELATED []
+synonym: "sequence variant causing partially characterised change in transcript" EXACT []
+synonym: "sequence variant causing uncharacterised change in transcript" EXACT []
+synonym: "sequence variation affecting transcript" EXACT []
+synonym: "sequence_variant_causing_partially_characterised_change_in_transcript" EXACT []
+synonym: "sequence_variant_causing_uncharacterised_change_in_transcript" EXACT []
+is_obsolete: true
+replaced_by: SO:0001576
+
+[Term]
+id: SO:1000050
+name: sequence_variant_causing_no_change_in_transcript
+def: "No effect on the state of the RNA." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term.
+synonym: "mutation causing no change in transcript" RELATED []
+synonym: "sequence variant causing no change in transcript" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000054
+name: sequence_variation_affecting_coding_sequence
+def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting coding sequence" EXACT []
+synonym: "sequence variation affecting coding sequence" RELATED []
+is_obsolete: true
+replaced_by: SO:0001580
+
+[Term]
+id: SO:1000055
+name: sequence_variant_causing_initiator_codon_change_in_transcript
+def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing initiator codon change in transcript" RELATED []
+synonym: "sequence variant causing initiator codon change in transcript" EXACT []
+is_obsolete: true
+replaced_by: SO:0001582
+
+[Term]
+id: SO:1000056
+name: sequence_variant_causing_amino_acid_coding_codon_change_in_transcript
+def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutaton causing amino acid coding codon change in transcript" RELATED []
+synonym: "sequence variant causing amino acid coding codon change in transcript" EXACT []
+is_obsolete: true
+consider: SO:0001606
+
+[Term]
+id: SO:1000057
+name: sequence_variant_causing_synonymous_codon_change_in_transcript
+def: "The changed codon has the same translation product as the original codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing synonymous codon change in transcript" RELATED []
+synonym: "sequence variant causing synonymous codon change in transcript" EXACT []
+is_obsolete: true
+replaced_by: SO:0001819
+
+[Term]
+id: SO:1000058
+name: sequence_variant_causing_non_synonymous_codon_change_in_transcript
+def: "A DNA point mutation that causes a substitution of an amino acid by an other." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing non synonymous codon change in transcript" RELATED []
+synonym: "non-synonymous codon change in transcript" EXACT []
+synonym: "sequence variant causing non synonymous codon change in transcript" EXACT []
+is_obsolete: true
+consider: SO:0001583
+
+[Term]
+id: SO:1000059
+name: sequence_variant_causing_missense_codon_change_in_transcript
+def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing missense codon change in transcript" RELATED []
+synonym: "sequence variant causing missense codon change in transcript" EXACT []
+is_obsolete: true
+consider: SO:0001583
+
+[Term]
+id: SO:1000060
+name: sequence_variant_causing_conservative_missense_codon_change_in_transcript
+def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
+synonym: "mutation causing conservative missense codon change in transcript" RELATED []
+synonym: "sequence variant causing conservative missense codon change in transcript" EXACT []
+is_obsolete: true
+replaced_by: SO:0001585
+
+[Term]
+id: SO:1000061
+name: sequence_variant_causing_nonconservative_missense_codon_change_in_transcript
+def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
+synonym: "mutation causing nonconservative missense codon change in transcript" RELATED []
+synonym: "sequence variant causing nonconservative missense codon change in transcript" EXACT []
+is_obsolete: true
+consider: SO:0001586
+
+[Term]
+id: SO:1000062
+name: sequence_variant_causing_nonsense_codon_change_in_transcript
+def: "The nucleotide change in the codon triplet creates a terminator codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing nonsense codon change in transcript" RELATED []
+synonym: "sequence variant causing nonsense codon change in transcript" EXACT []
+is_obsolete: true
+consider: SO:0001587
+
+[Term]
+id: SO:1000063
+name: sequence_variant_causing_terminator_codon_change_in_transcript
+def: "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing terminator codon change in transcript" RELATED []
+synonym: "sequence variant causing terminator codon change in transcript" EXACT []
+is_obsolete: true
+consider: SO:0001590
+
+[Term]
+id: SO:1000064
+name: sequence_variation_affecting_reading_frame
+def: "An umbrella term for terms describing an effect of a sequence variation on the frame of translation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting reading frame" EXACT []
+synonym: "sequence variation affecting reading frame" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:1000065
+name: frameshift_sequence_variation
+def: "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]
+synonym: "frameshift mutation" EXACT []
+synonym: "frameshift sequence variation" RELATED []
+synonym: "out of frame mutation" RELATED []
+xref: http://en.wikipedia.org/wiki/Frameshift_mutation "wiki"
+is_obsolete: true
+
+[Term]
+id: SO:1000066
+name: sequence_variant_causing_plus_1_frameshift_mutation
+def: "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "plus 1 frameshift mutation" EXACT []
+synonym: "sequence variant causing plus 1 frameshift mutation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001594
+
+[Term]
+id: SO:1000067
+name: sequence_variant_causing_minus_1_frameshift
+def: "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "minus 1 frameshift mutation" EXACT []
+synonym: "sequence variant causing minus 1 frameshift" EXACT []
+is_obsolete: true
+replaced_by: SO:0001592
+
+[Term]
+id: SO:1000068
+name: sequence_variant_causing_plus_2_frameshift
+def: "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "plus 2 frameshift mutation" EXACT []
+synonym: "sequence variant causing plus 2 frameshift" EXACT []
+is_obsolete: true
+replaced_by: SO:0001595
+
+[Term]
+id: SO:1000069
+name: sequence_variant_causing_minus_2_frameshift
+def: "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "minus 2 frameshift mutation" EXACT []
+synonym: "sequence variant causing minus 2 frameshift" EXACT []
+is_obsolete: true
+replaced_by: SO:0001593
+
+[Term]
+id: SO:1000070
+name: sequence_variant_affecting_transcript_processing
+def: "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting transcript processing" RELATED []
+synonym: "sequence variant affecting transcript processing" EXACT []
+is_obsolete: true
+replaced_by: SO:0001543
+
+[Term]
+id: SO:1000071
+name: sequence_variant_affecting_splicing
+def: "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting splicing" RELATED []
+synonym: "sequence variant affecting splicing" EXACT []
+is_obsolete: true
+replaced_by: SO:0001568
+
+[Term]
+id: SO:1000072
+name: sequence_variant_affecting_splice_donor
+def: "A sequence_variant_effect that changes the splice donor sequence." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting splice donor" RELATED []
+synonym: "sequence variant affecting splice donor" RELATED []
+synonym: "splice donor mutation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001575
+
+[Term]
+id: SO:1000073
+name: sequence_variant_affecting_splice_acceptor
+def: "A sequence_variant_effect that changes the splice acceptor sequence." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting splicing" RELATED []
+synonym: "sequence variant affecting splice acceptor" RELATED []
+synonym: "splice acceptor mutation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001574
+
+[Term]
+id: SO:1000074
+name: sequence_variant_causing_cryptic_splice_activation
+def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.
+synonym: "cryptic splice activator sequence variant" EXACT []
+synonym: "mutation causing cryptic splice activator" RELATED []
+synonym: "sequence variant causing cryptic splice activator" EXACT []
+is_obsolete: true
+replaced_by: SO:0001569
+
+[Term]
+id: SO:1000075
+name: sequence_variant_affecting_editing
+def: "Sequence variant affects the editing of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting editing" RELATED []
+synonym: "sequence variant affecting editing" EXACT []
+is_obsolete: true
+replaced_by: SO:0001544
+
+[Term]
+id: SO:1000076
+name: sequence_variant_affecting_transcription
+def: "Mutation affects the process of transcription, its initiation, progression or termination." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting transcription" RELATED []
+synonym: "sequence variant affecting transcription" EXACT []
+is_obsolete: true
+replaced_by: SO:0001549
+
+[Term]
+id: SO:1000078
+name: sequence_variant_decreasing_rate_of_transcription
+def: "A sequence variation that decreases the rate a which transcription of the sequence occurs." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation decreasing rate of transcription" RELATED []
+synonym: "sequence variation decreasing rate of transcription" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000079
+name: sequence_variation_affecting_transcript_sequence
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting transcript sequence" EXACT []
+synonym: "sequence variation affecting transcript sequence" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000080
+name: sequence_variant_increasing_rate_of_transcription
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation increasing rate of transcription" RELATED []
+synonym: "sequence variation increasing rate of transcription" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000081
+name: sequence_variant_affecting_rate_of_transcription
+def: "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting rate of transcription" RELATED []
+synonym: "sequence variant affecting rate of transcription" EXACT []
+is_obsolete: true
+replaced_by: SO:0001550
+
+[Term]
+id: SO:1000082
+name: sequence variant_affecting_transcript_stability
+def: "Sequence variant affects the stability of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting transcript stability" RELATED []
+synonym: "sequence variant affecting transcript stability" EXACT []
+is_obsolete: true
+replaced_by: SO:0001546
+
+[Term]
+id: SO:1000083
+name: sequence_variant_increasing_transcript_stability
+def: "Sequence variant increases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation increasing transcript stability" RELATED []
+synonym: "sequence variant increasing transcript stability" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000084
+name: sequence_variant_decreasing_transcript_stability
+def: "Sequence variant decreases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation decreasing transcript stability" RELATED []
+synonym: "sequence variant decreasing transcript stability" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000085
+name: sequence_variation_affecting_level_of_transcript
+def: "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting level of transcript" RELATED []
+synonym: "sequence variation affecting level of transcript" EXACT []
+is_obsolete: true
+replaced_by: SO:0001540
+
+[Term]
+id: SO:1000086
+name: sequence_variation_decreasing_level_of_transcript
+def: "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation decreasing level of transcript" EXACT []
+synonym: "sequence variation decreasing level of transcript" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:1000087
+name: sequence_variation_increasing_level_of_transcript
+def: "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation increasing level of transcript" EXACT []
+synonym: "sequence variation increasing level of transcript" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000088
+name: sequence_variant_affecting_translational_product
+alt_id: SO:1000090
+alt_id: SO:1000091
+def: "A sequence variant causing a change in primary translation product of a transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting translational product" RELATED []
+synonym: "mutation causing partially characterised change of translational product" RELATED []
+synonym: "mutation causing uncharacterised change of translational product" RELATED []
+synonym: "sequence variant affecting translational product" EXACT []
+synonym: "sequence variant causing partially characterised change of translational product" EXACT []
+synonym: "sequence variant causing uncharacterised change of translational product" EXACT []
+synonym: "sequence_variant_causing_partially_characterised_change_of_translational_product" EXACT []
+synonym: "sequence_variant_causing_uncharacterised_change_of_translational_product" EXACT []
+is_obsolete: true
+replaced_by: SO:0001553
+
+[Term]
+id: SO:1000089
+name: sequence_variant_causing_no_change_of_translational_product
+def: "The sequence variant at RNA level does not lead to any change in polypeptide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term.
+synonym: "mutation causing no change of translational product" RELATED []
+synonym: "sequence variant causing no change of translational product" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000092
+name: sequence_variant_causing_complex_change_of_translational_product
+def: "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing complex change of translational product" RELATED []
+synonym: "sequence variant causing complex change of translational product" EXACT []
+is_obsolete: true
+consider: SO:0001539
+
+[Term]
+id: SO:1000093
+name: sequence_variant_causing_amino_acid_substitution
+def: "The replacement of a single amino acid by another." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing amino acid substitution" RELATED []
+synonym: "sequence variant causing amino acid substitution" EXACT []
+is_obsolete: true
+replaced_by: SO:0001606
+
+[Term]
+id: SO:1000094
+name: sequence_variant_causing_conservative_amino_acid_substitution
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing conservative amino acid substitution" RELATED []
+synonym: "sequence variant causing conservative amino acid substitution" EXACT []
+is_obsolete: true
+replaced_by: SO:0001607
+
+[Term]
+id: SO:1000095
+name: sequence_variant_causing_nonconservative_amino_acid_substitution
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing nonconservative amino acid substitution" RELATED []
+synonym: "sequence variant causing nonconservative amino acid substitution" EXACT []
+is_obsolete: true
+replaced_by: SO:0001607
+
+[Term]
+id: SO:1000096
+name: sequence_variant_causing_amino_acid_insertion
+def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing amino acid insertion" RELATED []
+synonym: "sequence variant causing amino acid insertion" EXACT []
+is_obsolete: true
+replaced_by: SO:0001605
+
+[Term]
+id: SO:1000097
+name: sequence_variant_causing_amino_acid_deletion
+def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing amino acid deletion" RELATED []
+synonym: "sequence variant causing amino acid deletion" EXACT []
+is_obsolete: true
+consider: SO:0001825
+
+[Term]
+id: SO:1000098
+name: sequence_variant_causing_polypeptide_truncation
+def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing polypeptide truncation" RELATED []
+synonym: "sequence variant causing polypeptide truncation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001587
+
+[Term]
+id: SO:1000099
+name: sequence_variant_causing_polypeptide_elongation
+def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing polypeptide elongation" RELATED []
+synonym: "sequence variant causing polypeptide elongation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001609
+
+[Term]
+id: SO:1000100
+name: mutation_causing_polypeptide_N_terminal_elongation
+def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing polypeptide N terminal elongation" EXACT []
+synonym: "polypeptide N-terminal elongation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001611
+
+[Term]
+id: SO:1000101
+name: mutation_causing_polypeptide_C_terminal_elongation
+def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing polypeptide C terminal elongation" EXACT []
+synonym: "polypeptide C-terminal elongation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001610
+
+[Term]
+id: SO:1000102
+name: sequence_variant_affecting_level_of_translational_product
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting level of translational product" RELATED []
+synonym: "sequence variant affecting level of translational product" EXACT []
+is_obsolete: true
+replaced_by: SO:0001553
+
+[Term]
+id: SO:1000103
+name: sequence_variant_decreasing_level_of_translation_product
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutationdecreasing level of translation product" RELATED []
+synonym: "sequence variant decreasing level of translation product" EXACT []
+is_obsolete: true
+replaced_by: SO:0001555
+
+[Term]
+id: SO:1000104
+name: sequence_variant_increasing_level_of_translation_product
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutationt increasing level of translation product" RELATED []
+synonym: "sequence variant increasing level of translation product" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000105
+name: sequence_variant_affecting_polypeptide_amino_acid_sequence
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting polypeptide amino acid sequence" RELATED []
+synonym: "sequence variant affecting polypeptide amino acid sequence" EXACT []
+is_obsolete: true
+replaced_by: SO:0001603
+
+[Term]
+id: SO:1000106
+name: mutation_causing_inframe_polypeptide_N_terminal_elongation
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "inframe polypeptide N-terminal elongation" EXACT []
+synonym: "mutation causing inframe polypeptide N terminal elongation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001614
+
+[Term]
+id: SO:1000107
+name: mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing out of frame polypeptide N terminal elongation" EXACT []
+synonym: "out of frame polypeptide N-terminal elongation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001615
+
+[Term]
+id: SO:1000108
+name: mutaton_causing_inframe_polypeptide_C_terminal_elongation
+synonym: "inframe_polypeptide C-terminal elongation" EXACT []
+synonym: "mutaton causing inframe polypeptide C terminal elongation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001612
+
+[Term]
+id: SO:1000109
+name: mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing out of frame polypeptide C terminal elongation" EXACT []
+synonym: "out of frame polypeptide C-terminal elongation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001613
+
+[Term]
+id: SO:1000110
+name: frame_restoring_sequence_variant
+def: "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
+synonym: "frame restoring mutation" EXACT []
+synonym: "frame restoring sequence variant" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000111
+name: sequence_variant_affecting_3D_structure_of_polypeptide
+alt_id: SO:1000113
+alt_id: SO:1000114
+def: "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting 3D structure of polypeptide" RELATED []
+synonym: "mutation causing partially characterised 3D structural change" RELATED []
+synonym: "mutation causing uncharacterised 3D structural change" RELATED []
+synonym: "sequence variant affecting 3D structure of polypeptide" EXACT []
+synonym: "sequence variant affecting 3D-structure of polypeptide" EXACT []
+synonym: "sequence variant causing partially characterised 3D structural change" EXACT []
+synonym: "sequence variant causing uncharacterised 3D structural change" EXACT []
+synonym: "sequence_variant_causing_partially_characterised_3D_structural_change" EXACT []
+synonym: "sequence_variant_causing_uncharacterised_3D_structural_change" EXACT []
+is_obsolete: true
+replaced_by: SO:0001599
+
+[Term]
+id: SO:1000112
+name: sequence_variant_causing_no_3D_structural_change
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term.
+synonym: "mutation causing no 3D structural change" RELATED []
+synonym: "sequence variant causing no 3D structural change" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000115
+name: sequence_variant_causing_complex_3D_structural_change
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing complex 3D structural change" RELATED []
+synonym: "sequence variant causing complex 3D structural change" EXACT []
+is_obsolete: true
+replaced_by: SO:0001600
+
+[Term]
+id: SO:1000116
+name: sequence_variant_causing_conformational_change
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing conformational change" RELATED []
+synonym: "sequence variant causing conformational change" EXACT []
+is_obsolete: true
+replaced_by: SO:0001601
+
+[Term]
+id: SO:1000117
+name: sequence_variant_affecting_polypeptide_function
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting polypeptide function" RELATED []
+synonym: "sequence variant affecting polypeptide function" EXACT []
+is_obsolete: true
+replaced_by: SO:0001554
+
+[Term]
+id: SO:1000118
+name: sequence_variant_causing_loss_of_function_of_polypeptide
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "loss of function of polypeptide" RELATED []
+synonym: "mutation causing loss of function of polypeptide" RELATED []
+synonym: "sequence variant causing loss of function of polypeptide" EXACT []
+is_obsolete: true
+replaced_by: SO:0001559
+
+[Term]
+id: SO:1000119
+name: sequence_variant_causing_inactive_ligand_binding_site
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing inactive ligand binding site" RELATED []
+synonym: "sequence variant causing inactive ligand binding site" EXACT []
+is_obsolete: true
+replaced_by: SO:0001560
+
+[Term]
+id: SO:1000120
+name: sequence_variant_causing_inactive_catalytic_site
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing inactive catalytic site" RELATED []
+synonym: "sequence variant causing inactive catalytic site" EXACT []
+is_obsolete: true
+replaced_by: SO:0001618
+
+[Term]
+id: SO:1000121
+name: sequence_variant_causing_polypeptide_localization_change
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing polypeptide localization change" RELATED []
+synonym: "sequence variant causing polypeptide localization change" EXACT []
+is_obsolete: true
+replaced_by: SO:0001558
+
+[Term]
+id: SO:1000122
+name: sequence_variant_causing_polypeptide_post_translational_processing_change
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing polypeptide post translational processing change" RELATED []
+synonym: "polypeptide post-translational processing affected" EXACT []
+synonym: "sequence variant causing polypeptide post translational processing change" EXACT []
+is_obsolete: true
+replaced_by: SO:0001562
+
+[Term]
+id: SO:1000123
+name: polypeptide_post_translational_processing_affected
+synonym: "polypeptide_post-translational_processing_affected" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:1000124
+name: sequence_variant_causing_partial_loss_of_function_of_polypeptide
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing partial loss of function of polypeptide" RELATED []
+synonym: "partial loss of function of polypeptide" EXACT []
+synonym: "sequence variant causing partial loss of function of polypeptide" EXACT []
+is_obsolete: true
+replaced_by: SO:0001561
+
+[Term]
+id: SO:1000125
+name: sequence_variant_causing_gain_of_function_of_polypeptide
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "gain of function of polypeptide" EXACT []
+synonym: "mutation causing gain of function of polypeptide" RELATED []
+synonym: "sequence variant causing gain of function of polypeptide" EXACT []
+is_obsolete: true
+replaced_by: SO:0001557
+
+[Term]
+id: SO:1000126
+name: sequence_variant_affecting_transcript_secondary_structure
+def: "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting transcript secondary structure" RELATED []
+synonym: "sequence variant affecting transcript secondary structure" EXACT []
+is_obsolete: true
+replaced_by: SO:0001596
+
+[Term]
+id: SO:1000127
+name: sequence_variant_causing_compensatory_transcript_secondary_structure_mutation
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing compensatory transcript secondary structure mutation" RELATED []
+synonym: "sequence variant causing compensatory transcript secondary structure mutation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001597
+
+[Term]
+id: SO:1000132
+name: sequence_variant_effect
+def: "The effect of a change in nucleotide sequence." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.\nUpdated after discussion with Peter Taschner - Feb 09.
+synonym: "sequence variant effect" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:1000134
+name: sequence_variant_causing_polypeptide_fusion
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing polypeptide fusion" RELATED []
+synonym: "sequence variant causing polypeptide fusion" EXACT []
+is_obsolete: true
+replaced_by: SO:0001616
+
+[Term]
+id: SO:1000136
+name: autosynaptic_chromosome
+def: "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]
+synonym: "(Drosophila)A" RELATED []
+synonym: "autosynaptic chromosome" EXACT []
+is_a: SO:1000183 ! chromosome_structure_variation
+
+[Term]
+id: SO:1000138
+name: homo_compound_chromosome
+def: "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]
+synonym: "homo compound chromosome" EXACT []
+synonym: "homo-compound chromosome" EXACT []
+is_a: SO:1000042 ! compound_chromosome
+
+[Term]
+id: SO:1000140
+name: hetero_compound_chromosome
+def: "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]
+synonym: "hetero compound chromosome" EXACT []
+synonym: "hetero-compound chromosome" EXACT []
+is_a: SO:1000042 ! compound_chromosome
+
+[Term]
+id: SO:1000141
+name: chromosome_fission
+def: "A chromosome that occurred by the division of a larger chromosome." [SO:ke]
+synonym: "chromosome fission" EXACT []
+is_a: SO:1000028 ! intrachromosomal_mutation
+
+[Term]
+id: SO:1000142
+name: dexstrosynaptic_chromosome
+def: "An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]
+synonym: "dexstrosynaptic chromosome" EXACT []
+is_a: SO:1000136 ! autosynaptic_chromosome
+
+[Term]
+id: SO:1000143
+name: laevosynaptic_chromosome
+def: "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]
+synonym: "laevosynaptic chromosome" EXACT []
+is_a: SO:1000136 ! autosynaptic_chromosome
+
+[Term]
+id: SO:1000144
+name: free_duplication
+def: "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]
+synonym: "free duplication" EXACT []
+is_a: SO:1000037 ! chromosomal_duplication
+
+[Term]
+id: SO:1000145
+name: free_ring_duplication
+def: "A ring chromosome which is a copy of another chromosome." [SO:ke]
+synonym: "(Drosophila)R" RELATED []
+synonym: "free ring duplication" EXACT []
+is_a: SO:1000045 ! ring_chromosome
+is_a: SO:1000144 ! free_duplication
+relationship: has_quality SO:0001516 ! free
+
+[Term]
+id: SO:1000147
+name: deficient_translocation
+def: "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]
+synonym: "(Drosophila)Df" RELATED []
+synonym: "(Drosophila)DfT" RELATED []
+synonym: "deficient translocation" EXACT []
+is_a: SO:1000029 ! chromosomal_deletion
+is_a: SO:1000044 ! chromosomal_translocation
+relationship: has_part SO:0000159 ! deletion
+
+[Term]
+id: SO:1000148
+name: inversion_cum_translocation
+def: "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]
+synonym: "(Drosophila)InT" RELATED []
+synonym: "(Drosophila)T" RELATED []
+synonym: "inversion cum translocation" EXACT []
+is_a: SO:1000030 ! chromosomal_inversion
+is_a: SO:1000044 ! chromosomal_translocation
+relationship: has_part SO:1000036 ! inversion
+
+[Term]
+id: SO:1000149
+name: bipartite_duplication
+def: "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]
+synonym: "(Drosophila)bDp" RELATED []
+synonym: "bipartite duplication" EXACT []
+is_a: SO:1000031 ! interchromosomal_mutation
+is_a: SO:1000038 ! intrachromosomal_duplication
+
+[Term]
+id: SO:1000150
+name: cyclic_translocation
+def: "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]
+synonym: "cyclic translocation" EXACT []
+is_a: SO:0002060 ! interchomosomal_translocation
+
+[Term]
+id: SO:1000151
+name: bipartite_inversion
+def: "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]
+synonym: "(Drosophila)bIn" RELATED []
+synonym: "bipartite inversion" EXACT []
+is_a: SO:1000030 ! chromosomal_inversion
+
+[Term]
+id: SO:1000152
+name: uninverted_insertional_duplication
+def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
+synonym: "(Drosophila)eDp" RELATED []
+synonym: "uninverted insertional duplication" EXACT []
+is_a: SO:1000154 ! insertional_duplication
+
+[Term]
+id: SO:1000153
+name: inverted_insertional_duplication
+def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]
+synonym: "(Drosophila)iDp" RELATED []
+synonym: "inverted insertional duplication" EXACT []
+is_a: SO:1000154 ! insertional_duplication
+
+[Term]
+id: SO:1000154
+name: insertional_duplication
+def: "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]
+synonym: "(Drosophila)Dpp" RELATED []
+synonym: "insertional duplication" EXACT []
+is_a: SO:1000037 ! chromosomal_duplication
+
+[Term]
+id: SO:1000155
+name: interchromosomal_transposition
+def: "A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]
+synonym: "(Drosophila)Tp" RELATED []
+synonym: "interchromosomal transposition" EXACT []
+is_a: SO:0000453 ! chromosomal_transposition
+is_a: SO:1000031 ! interchromosomal_mutation
+
+[Term]
+id: SO:1000156
+name: inverted_interchromosomal_transposition
+def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]
+synonym: "(Drosophila)iTp" RELATED []
+synonym: "inverted interchromosomal transposition" EXACT []
+is_a: SO:1000155 ! interchromosomal_transposition
+
+[Term]
+id: SO:1000157
+name: uninverted_interchromosomal_transposition
+def: "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
+synonym: "(Drosophila)eTp" RELATED []
+synonym: "uninverted interchromosomal transposition" EXACT []
+is_a: SO:1000155 ! interchromosomal_transposition
+
+[Term]
+id: SO:1000158
+name: inverted_intrachromosomal_transposition
+def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]
+synonym: "(Drosophila)iTp" RELATED []
+synonym: "inverted intrachromosomal transposition" EXACT []
+is_a: SO:1000148 ! inversion_cum_translocation
+relationship: has_part SO:1000036 ! inversion
+
+[Term]
+id: SO:1000159
+name: uninverted_intrachromosomal_transposition
+def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
+synonym: "(Drosophila)eTp" RELATED []
+synonym: "uninverted intrachromosomal transposition" EXACT []
+is_a: SO:1000041 ! intrachromosomal_transposition
+relationship: has_part SO:0001514 ! direct
+
+[Term]
+id: SO:1000160
+name: unoriented_insertional_duplication
+def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
+comment: Flag - unknown in the definition.
+synonym: "(Drosophila)uDp" RELATED []
+synonym: "unoriented insertional duplication" EXACT []
+is_a: SO:1000154 ! insertional_duplication
+
+[Term]
+id: SO:1000161
+name: unoriented_interchromosomal_transposition
+def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
+comment: FLAG - term describes an unknown.
+synonym: "(Drosophila)uTp" RELATED []
+synonym: "unorientated interchromosomal transposition" EXACT []
+is_a: SO:1000155 ! interchromosomal_transposition
+
+[Term]
+id: SO:1000162
+name: unoriented_intrachromosomal_transposition
+def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
+comment: FLAG - definition describes an unknown.
+synonym: "(Drosophila)uTp" RELATED []
+synonym: "unorientated intrachromosomal transposition" EXACT []
+is_a: SO:1000041 ! intrachromosomal_transposition
+
+[Term]
+id: SO:1000170
+name: uncharacterized_chromosomal_mutation
+synonym: "uncharacterized chromosomal mutation" EXACT []
+is_a: SO:1000183 ! chromosome_structure_variation
+
+[Term]
+id: SO:1000171
+name: deficient_inversion
+def: "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]
+synonym: "(Drosophila)Df" RELATED []
+synonym: "(Drosophila)DfIn" RELATED []
+synonym: "deficient inversion" EXACT []
+is_a: SO:1000029 ! chromosomal_deletion
+is_a: SO:1000030 ! chromosomal_inversion
+relationship: has_part SO:0000159 ! deletion
+relationship: has_part SO:1000036 ! inversion
+
+[Term]
+id: SO:1000173
+name: tandem_duplication
+def: "A duplication consisting of 2 identical adjacent regions." [SO:ke]
+subset: DBVAR
+synonym: "erverted" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
+synonym: "tandem duplication" EXACT []
+is_a: SO:1000035 ! duplication
+
+[Term]
+id: SO:1000175
+name: partially_characterized_chromosomal_mutation
+synonym: "partially characterized chromosomal mutation" EXACT []
+is_a: SO:1000170 ! uncharacterized_chromosomal_mutation
+
+[Term]
+id: SO:1000180
+name: sequence_variant_affecting_gene_structure
+def: "A sequence_variant_effect that changes the gene structure." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation affecting gene structure" RELATED []
+synonym: "sequence variant affecting gene structure" EXACT []
+is_obsolete: true
+replaced_by: SO:0001564
+
+[Term]
+id: SO:1000181
+name: sequence_variant_causing_gene_fusion
+def: "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causing gene fusion" RELATED []
+synonym: "sequence variant causing gene fusion" EXACT []
+is_obsolete: true
+replaced_by: SO:0001565
+
+[Term]
+id: SO:1000182
+name: chromosome_number_variation
+def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
+synonym: "chromosome number variation" EXACT []
+is_a: SO:0000240 ! chromosome_variation
+
+[Term]
+id: SO:1000183
+name: chromosome_structure_variation
+synonym: "chromosome structure variation" EXACT []
+is_a: SO:0000240 ! chromosome_variation
+
+[Term]
+id: SO:1000184
+name: sequence_variant_causes_exon_loss
+def: "A sequence variant affecting splicing and causes an exon loss." [SO:ke]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causes exon loss" RELATED []
+synonym: "sequence variant causes exon loss" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000185
+name: sequence_variant_causes_intron_gain
+def: "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "mutation causes intron gain" RELATED []
+synonym: "sequence variant causes intron gain" EXACT []
+is_obsolete: true
+
+[Term]
+id: SO:1000186
+name: sequence_variant_causing_cryptic_splice_donor_activation
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "sequence variant causing cryptic splice donor activation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001571
+
+[Term]
+id: SO:1001186
+name: sequence_variant_causing_cryptic_splice_acceptor_activation
+comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
+synonym: "sequence variant causing cryptic splice acceptor activation" EXACT []
+is_obsolete: true
+replaced_by: SO:0001570
+
+[Term]
+id: SO:1001187
+name: alternatively_spliced_transcript
+def: "A transcript that is alternatively spliced." [SO:xp]
+synonym: "alternatively spliced transcript" EXACT []
+is_a: SO:0000673 ! transcript
+relationship: has_quality SO:0000877 ! alternatively_spliced
+
+[Term]
+id: SO:1001188
+name: encodes_1_polypeptide
+def: "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]
+synonym: "encodes 1 polypeptide" EXACT []
+is_a: SO:0000463 ! encodes_alternately_spliced_transcripts
+
+[Term]
+id: SO:1001189
+name: encodes_greater_than_1_polypeptide
+def: "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]
+synonym: "encodes greater than 1 polypeptide" EXACT []
+is_a: SO:0000463 ! encodes_alternately_spliced_transcripts
+
+[Term]
+id: SO:1001190
+name: encodes_different_polypeptides_different_stop
+def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]
+synonym: "encodes different polypeptides different stop" EXACT []
+is_a: SO:1001195 ! encodes_overlapping_peptides
+
+[Term]
+id: SO:1001191
+name: encodes_overlapping_peptides_different_start
+def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]
+synonym: "encodes overlapping peptides different start" EXACT []
+is_a: SO:1001195 ! encodes_overlapping_peptides
+
+[Term]
+id: SO:1001192
+name: encodes_disjoint_polypeptides
+def: "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]
+synonym: "encodes disjoint polypeptides" EXACT []
+is_a: SO:1001189 ! encodes_greater_than_1_polypeptide
+
+[Term]
+id: SO:1001193
+name: encodes_overlapping_polypeptides_different_start_and_stop
+def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]
+synonym: "encodes overlapping polypeptides different start and stop" EXACT []
+is_a: SO:1001195 ! encodes_overlapping_peptides
+
+[Term]
+id: SO:1001194
+name: alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
+is_obsolete: true
+
+[Term]
+id: SO:1001195
+name: encodes_overlapping_peptides
+def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]
+synonym: "encodes overlapping peptides" EXACT []
+is_a: SO:1001189 ! encodes_greater_than_1_polypeptide
+
+[Term]
+id: SO:1001196
+name: cryptogene
+def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]
+is_a: SO:0000654 ! maxicircle_gene
+is_a: SO:0001431 ! cryptic_gene
+relationship: has_quality SO:0000976 ! cryptic
+
+[Term]
+id: SO:1001197
+name: dicistronic_primary_transcript
+def: "A primary transcript that has the quality dicistronic." [SO:xp]
+synonym: "dicistronic primary transcript" EXACT []
+is_a: SO:0000079 ! dicistronic_transcript
+is_a: SO:0000631 ! polycistronic_primary_transcript
+relationship: has_quality SO:0000879 ! dicistronic
+
+[Term]
+id: SO:1001217
+name: member_of_regulon
+synonym: "member of regulon" EXACT []
+is_a: SO:0000081 ! gene_array_member
+
+[Term]
+id: SO:1001244
+name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
+synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED []
+is_obsolete: true
+
+[Term]
+id: SO:1001246
+name: CDS_independently_known
+def: "A CDS with the evidence status of being independently known." [SO:xp]
+synonym: "CDS independently known" EXACT []
+is_a: SO:0000316 ! CDS
+relationship: has_quality SO:0000906 ! independently_known
+
+[Term]
+id: SO:1001247
+name: orphan_CDS
+def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]
+synonym: "orphan CDS" EXACT []
+is_a: SO:1001254 ! CDS_predicted
+relationship: has_origin SO:0000910 ! orphan
+
+[Term]
+id: SO:1001249
+name: CDS_supported_by_domain_match_data
+def: "A CDS that is supported by domain similarity." [SO:xp]
+synonym: "CDS supported by domain match data" EXACT []
+is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
+relationship: has_quality SO:0000908 ! supported_by_domain_match
+
+[Term]
+id: SO:1001251
+name: CDS_supported_by_sequence_similarity_data
+def: "A CDS that is supported by sequence similarity data." [SO:xp]
+synonym: "CDS supported by sequence similarity data" EXACT []
+is_a: SO:1001254 ! CDS_predicted
+relationship: has_quality SO:0000907 ! supported_by_sequence_similarity
+
+[Term]
+id: SO:1001254
+name: CDS_predicted
+def: "A CDS that is predicted." [SO:ke]
+synonym: "CDS predicted" EXACT []
+is_a: SO:0000316 ! CDS
+relationship: has_quality SO:0000732 ! predicted
+
+[Term]
+id: SO:1001255
+name: status_of_coding_sequence
+is_obsolete: true
+
+[Term]
+id: SO:1001259
+name: CDS_supported_by_EST_or_cDNA_data
+def: "A CDS that is supported by similarity to EST or cDNA data." [SO:xp]
+synonym: "CDS supported by EST or cDNA data" EXACT []
+is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
+relationship: has_quality SO:0000909 ! supported_by_EST_or_cDNA
+
+[Term]
+id: SO:1001260
+name: internal_Shine_Dalgarno_sequence
+def: "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]
+synonym: "internal Shine Dalgarno sequence" EXACT []
+synonym: "internal Shine-Dalgarno sequence" EXACT []
+is_a: SO:0000243 ! internal_ribosome_entry_site
+is_a: SO:1001268 ! recoding_stimulatory_region
+
+[Term]
+id: SO:1001261
+name: recoded_mRNA
+def: "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
+synonym: "recoded mRNA" EXACT []
+is_a: SO:0000234 ! mRNA
+relationship: has_quality SO:0000881 ! recoded
+
+[Term]
+id: SO:1001262
+name: minus_1_translationally_frameshifted
+def: "An attribute describing a translational frameshift of -1." [SO:ke]
+synonym: "minus 1 translationally frameshifted" EXACT []
+is_a: SO:0000887 ! translationally_frameshifted
+
+[Term]
+id: SO:1001263
+name: plus_1_translationally_frameshifted
+def: "An attribute describing a translational frameshift of +1." [SO:ke]
+synonym: "plus 1 translationally frameshifted" EXACT []
+is_a: SO:0000887 ! translationally_frameshifted
+
+[Term]
+id: SO:1001264
+name: mRNA_recoded_by_translational_bypass
+def: "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
+synonym: "mRNA recoded by translational bypass" EXACT []
+is_a: SO:1001261 ! recoded_mRNA
+relationship: has_quality SO:0000886 ! recoded_by_translational_bypass
+
+[Term]
+id: SO:1001265
+name: mRNA_recoded_by_codon_redefinition
+def: "A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]
+synonym: "mRNA recoded by codon redefinition" EXACT []
+is_a: SO:1001261 ! recoded_mRNA
+relationship: has_quality SO:0000882 ! codon_redefined
+
+[Term]
+id: SO:1001266
+name: stop_codon_redefinition_as_selenocysteine
+is_obsolete: true
+
+[Term]
+id: SO:1001267
+name: stop_codon_readthrough
+is_obsolete: true
+
+[Term]
+id: SO:1001268
+name: recoding_stimulatory_region
+def: "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]
+synonym: "recoding stimulatory region" EXACT []
+synonym: "recoding stimulatory signal" EXACT []
+is_a: SO:0000836 ! mRNA_region
+
+[Term]
+id: SO:1001269
+name: four_bp_start_codon
+def: "A non-canonical start codon with 4 base pairs." [SO:ke]
+synonym: "4bp start codon" EXACT []
+synonym: "four bp start codon" EXACT []
+is_a: SO:0000680 ! non_canonical_start_codon
+
+[Term]
+id: SO:1001270
+name: stop_codon_redefinition_as_pyrrolysine
+is_obsolete: true
+
+[Term]
+id: SO:1001271
+name: archaeal_intron
+def: "An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]
+comment: Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
+synonym: "archaeal intron" EXACT []
+is_a: SO:0001216 ! endonuclease_spliced_intron
+
+[Term]
+id: SO:1001272
+name: tRNA_intron
+def: "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]
+comment: Could be a cross product with Gene ontology, GO:0006388.
+synonym: "pre-tRNA intron" EXACT []
+synonym: "tRNA intron" EXACT []
+is_a: SO:0001216 ! endonuclease_spliced_intron
+
+[Term]
+id: SO:1001273
+name: CTG_start_codon
+def: "A non-canonical start codon of sequence CTG." [SO:ke]
+synonym: "CTG start codon" EXACT []
+is_a: SO:0000680 ! non_canonical_start_codon
+
+[Term]
+id: SO:1001274
+name: SECIS_element
+def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]
+synonym: "SECIS element" EXACT []
+xref: http://en.wikipedia.org/wiki/SECIS_element "wiki"
+is_a: SO:1001268 ! recoding_stimulatory_region
+
+[Term]
+id: SO:1001275
+name: retron
+def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]
+is_a: SO:0001411 ! biological_region
+
+[Term]
+id: SO:1001277
+name: three_prime_recoding_site
+def: "The recoding stimulatory signal located downstream of the recoding site." [SO:ke]
+synonym: "three prime recoding site" EXACT []
+is_a: SO:1001268 ! recoding_stimulatory_region
+
+[Term]
+id: SO:1001279
+name: three_prime_stem_loop_structure
+def: "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]
+synonym: "three prime stem loop structure" EXACT []
+is_a: SO:1001277 ! three_prime_recoding_site
+
+[Term]
+id: SO:1001280
+name: five_prime_recoding_site
+def: "The recoding stimulatory signal located upstream of the recoding site." [SO:ke]
+synonym: "five prime recoding site" EXACT []
+is_a: SO:1001268 ! recoding_stimulatory_region
+
+[Term]
+id: SO:1001281
+name: flanking_three_prime_quadruplet_recoding_signal
+def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]
+synonym: "flanking three prime quadruplet recoding signal" EXACT []
+is_a: SO:1001277 ! three_prime_recoding_site
+
+[Term]
+id: SO:1001282
+name: UAG_stop_codon_signal
+def: "A stop codon signal for a UAG stop codon redefinition." [SO:ke]
+synonym: "UAG stop codon signal" EXACT []
+is_a: SO:1001288 ! stop_codon_signal
+
+[Term]
+id: SO:1001283
+name: UAA_stop_codon_signal
+def: "A stop codon signal for a UAA stop codon redefinition." [SO:ke]
+synonym: "UAA stop codon signal" EXACT []
+is_a: SO:1001288 ! stop_codon_signal
+
+[Term]
+id: SO:1001284
+name: regulon
+def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]
+subset: SOFA
+xref: http://en.wikipedia.org/wiki/Regulon "wiki"
+is_a: SO:0005855 ! gene_group
+
+[Term]
+id: SO:1001285
+name: UGA_stop_codon_signal
+def: "A stop codon signal for a UGA stop codon redefinition." [SO:ke]
+synonym: "UGA stop codon signal" EXACT []
+is_a: SO:1001288 ! stop_codon_signal
+
+[Term]
+id: SO:1001286
+name: three_prime_repeat_recoding_signal
+def: "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]
+synonym: "three prime repeat recoding signal" EXACT []
+is_a: SO:1001277 ! three_prime_recoding_site
+
+[Term]
+id: SO:1001287
+name: distant_three_prime_recoding_signal
+def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]
+synonym: "distant three prime recoding signal" EXACT []
+is_a: SO:1001277 ! three_prime_recoding_site
+
+[Term]
+id: SO:1001288
+name: stop_codon_signal
+def: "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]
+comment: This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.
+synonym: "stop codon signal" EXACT []
+is_a: SO:1001268 ! recoding_stimulatory_region
+
+[Term]
+id: SO:2000061
+name: databank_entry
+def: "The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]
+subset: SOFA
+synonym: "accession" RELATED []
+synonym: "databank entry" EXACT []
+is_a: SO:0000695 ! reagent
+
+[Term]
+id: SO:3000000
+name: gene_segment
+def: "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]
+comment: Requested by tracker 2021594, July 2008, by Alex.
+synonym: "gene segment" EXACT []
+is_a: SO:0000842 ! gene_component_region
+
+[Typedef]
+id: adjacent_to
+name: adjacent_to
+def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." [PMID:20226267, SO:ke]
+subset: SOFA
+
+[Typedef]
+id: associated_with
+name: associated_with
+comment: This relationship is vague and up for discussion.
+
+[Typedef]
+id: complete_evidence_for_feature
+name: complete_evidence_for_feature
+def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke]
+comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
+is_transitive: true
+is_a: evidence_for_feature ! evidence_for_feature
+
+[Typedef]
+id: connects_on
+name: connects_on
+def: "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." [PMID:20226267]
+comment: Example: A splice_junction connects_on exon, exon, mature_transcript.
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:38:51Z
+
+[Typedef]
+id: contained_by
+name: contained_by
+def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267]
+comment: The inverse is contains. Example: intein contained_by immature_peptide_region.
+is_transitive: true
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:26:16Z
+
+[Typedef]
+id: contains
+name: contains
+def: "The inverse of contained_by." [PMID:20226267]
+comment: Example: pre_miRNA contains miRNA_loop.
+is_transitive: true
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:32:15Z
+
+[Typedef]
+id: derives_from
+name: derives_from
+subset: SOFA
+is_transitive: true
+
+[Typedef]
+id: disconnected_from
+name: disconnected_from
+def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267]
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:42:10Z
+
+[Typedef]
+id: edited_from
+name: edited_from
+created_by: kareneilbeck
+creation_date: 2009-08-19T02:19:45Z
+
+[Typedef]
+id: edited_to
+name: edited_to
+created_by: kareneilbeck
+creation_date: 2009-08-19T02:19:11Z
+
+[Typedef]
+id: evidence_for_feature
+name: evidence_for_feature
+def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke]
+comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
+is_transitive: true
+
+[Typedef]
+id: exemplar_of
+name: exemplar_of
+def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke]
+comment: Tracker id: 2594157.
+
+[Typedef]
+id: finished_by
+name: finished_by
+def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267]
+comment: Example CDS finished_by stop_codon.
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:45:45Z
+
+[Typedef]
+id: finishes
+name: finishes
+def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267]
+comment: Example: stop_codon finishes CDS.
+created_by: kareneilbeck
+creation_date: 2010-10-14T02:17:53Z
+
+[Typedef]
+id: gained
+name: gained
+def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke]
+comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence.
+created_by: kareneilbeck
+creation_date: 2011-06-28T12:51:10Z
+
+[Typedef]
+id: genome_of
+name: genome_of
+
+[Typedef]
+id: guided_by
+name: guided_by
+created_by: kareneilbeck
+creation_date: 2009-08-19T02:27:04Z
+
+[Typedef]
+id: guides
+name: guides
+created_by: kareneilbeck
+creation_date: 2009-08-19T02:27:24Z
+
+[Typedef]
+id: has_integral_part
+name: has_integral_part
+def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: mRNA has_integral_part CDS.
+is_a: has_part ! has_part
+created_by: kareneilbeck
+creation_date: 2009-08-19T12:01:46Z
+
+[Typedef]
+id: has_origin
+name: has_origin
+
+[Typedef]
+id: has_part
+name: has_part
+def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: operon has_part gene.
+
+[Typedef]
+id: has_quality
+name: has_quality
+comment: The relationship between a feature and an attribute.
+
+[Typedef]
+id: homologous_to
+name: homologous_to
+subset: SOFA
+is_symmetric: true
+is_a: similar_to ! similar_to
+
+[Typedef]
+id: integral_part_of
+name: integral_part_of
+def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: exon integral_part_of transcript.
+is_a: part_of ! part_of
+created_by: kareneilbeck
+creation_date: 2009-08-19T12:03:28Z
+
+[Typedef]
+id: is_consecutive_sequence_of
+name: is_consecutive_sequence_of
+def: "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." [PMID:20226267]
+comment: Example: region is consecutive_sequence of base.
+created_by: kareneilbeck
+creation_date: 2010-10-14T02:19:48Z
+
+[Typedef]
+id: lost
+name: lost
+def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke]
+comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence.
+created_by: kareneilbeck
+creation_date: 2011-06-28T12:53:16Z
+
+[Typedef]
+id: maximally_overlaps
+name: maximally_overlaps
+def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267]
+comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:34:48Z
+
+[Typedef]
+id: member_of
+name: member_of
+comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
+subset: SOFA
+is_transitive: true
+is_a: part_of ! part_of
+
+[Typedef]
+id: non_functional_homolog_of
+name: non_functional_homolog_of
+def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
+subset: SOFA
+is_a: homologous_to ! homologous_to
+
+[Typedef]
+id: orthologous_to
+name: orthologous_to
+subset: SOFA
+is_symmetric: true
+is_a: homologous_to ! homologous_to
+
+[Typedef]
+id: overlaps
+name: overlaps
+def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267]
+comment: Example: coding_exon overlaps CDS.
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:33:15Z
+
+[Typedef]
+id: paralogous_to
+name: paralogous_to
+subset: SOFA
+is_symmetric: true
+is_a: homologous_to ! homologous_to
+
+[Typedef]
+id: part_of
+name: part_of
+def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: amino_acid part_of polypeptide.
+subset: SOFA
+is_transitive: true
+
+[Typedef]
+id: partial_evidence_for_feature
+name: partial_evidence_for_feature
+def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke]
+is_a: evidence_for_feature ! evidence_for_feature
+
+[Typedef]
+id: position_of
+name: position_of
+
+[Typedef]
+id: processed_from
+name: processed_from
+def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: miRNA processed_from miRNA_primary_transcript.
+created_by: kareneilbeck
+creation_date: 2009-08-19T12:14:00Z
+
+[Typedef]
+id: processed_into
+name: processed_into
+def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: miRNA_primary_transcript processed into miRNA.
+created_by: kareneilbeck
+creation_date: 2009-08-19T12:15:02Z
+
+[Typedef]
+id: recombined_from
+name: recombined_from
+created_by: kareneilbeck
+creation_date: 2009-08-19T02:21:03Z
+
+[Typedef]
+id: recombined_to
+name: recombined_to
+created_by: kareneilbeck
+creation_date: 2009-08-19T02:20:07Z
+
+[Typedef]
+id: sequence_of
+name: sequence_of
+
+[Typedef]
+id: similar_to
+name: similar_to
+subset: SOFA
+is_symmetric: true
+
+[Typedef]
+id: started_by
+name: started_by
+def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267]
+comment: Example: CDS started_by start_codon.
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:43:55Z
+
+[Typedef]
+id: starts
+name: starts
+def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267]
+comment: Example: start_codon starts CDS.
+created_by: kareneilbeck
+creation_date: 2010-10-14T01:47:53Z
+
+[Typedef]
+id: trans_spliced_from
+name: trans_spliced_from
+created_by: kareneilbeck
+creation_date: 2009-08-19T02:22:14Z
+
+[Typedef]
+id: trans_spliced_to
+name: trans_spliced_to
+created_by: kareneilbeck
+creation_date: 2009-08-19T02:22:00Z
+
+[Typedef]
+id: transcribed_from
+name: transcribed_from
+def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: primary_transcript transcribed_from gene.
+created_by: kareneilbeck
+creation_date: 2009-08-19T12:05:39Z
+
+[Typedef]
+id: transcribed_to
+name: transcribed_to
+def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: gene transcribed_to primary_transcript.
+created_by: kareneilbeck
+creation_date: 2009-08-19T12:08:24Z
+
+[Typedef]
+id: translates_to
+name: translates_to
+def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: codon translates_to amino_acid.
+created_by: kareneilbeck
+creation_date: 2009-08-19T12:11:53Z
+
+[Typedef]
+id: translation_of
+name: translation_of
+def: "X is translation of Y if Y is translated by ribosome to create X." [http://precedings.nature.com/documents/3495/version/1]
+comment: Example: Polypeptide translation_of CDS.
+created_by: kareneilbeck
+creation_date: 2009-08-19T12:09:59Z
+
+[Typedef]
+id: variant_of
+name: variant_of
+def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop]
+comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.
+
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