4 auto-generated-by: OBO-Edit 2.3.1
5 subsetdef: biosapiens "biosapiens protein feature ontology"
6 subsetdef: DBVAR "database of genomic structural variation"
7 subsetdef: SOFA "SO feature annotation"
8 synonymtypedef: aa1 "amino acid 1 letter code"
9 synonymtypedef: aa3 "amino acid 3 letter code"
10 synonymtypedef: AAMOD "amino acid modification"
11 synonymtypedef: BS "biosapiens"
12 synonymtypedef: dbsnp "dbsnp variant terms"
13 synonymtypedef: dbvar "DBVAR"
14 synonymtypedef: ebi_variants "ensembl variant terms"
15 synonymtypedef: RNAMOD "RNA modification" EXACT
16 synonymtypedef: VAR "variant annotation term"
17 default-namespace: sequence
18 remark: autogenerated-by: DAG-Edit version 1.417\nsaved-by: eilbeck\ndate: Tue May 11 15:18:44 PDT 2004\nversion: $Revision: 1.45 $
23 name: Sequence_Ontology
30 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]
32 synonym: "sequence" EXACT []
33 is_a: SO:0000110 ! sequence_feature
34 disjoint_from: SO:0000699 ! junction
38 name: sequence_secondary_structure
39 def: "A folded sequence." [SO:ke]
40 synonym: "sequence secondary structure" EXACT []
41 is_a: SO:0001411 ! biological_region
46 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]
47 synonym: "G quartet" EXACT []
48 synonym: "G tetrad" EXACT []
49 synonym: "G-quadruplex" EXACT []
50 synonym: "G-quartet" EXACT []
51 synonym: "G-tetrad" EXACT []
52 synonym: "G_quadruplex" EXACT []
53 synonym: "guanine tetrad" EXACT []
54 xref: http://en.wikipedia.org/wiki/G-quadruplex "wiki"
55 is_a: SO:0000002 ! sequence_secondary_structure
59 name: interior_coding_exon
61 synonym: "interior coding exon" EXACT []
62 is_a: SO:0000195 ! coding_exon
67 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]
69 synonym: "satellite DNA" EXACT []
70 xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki"
71 is_a: SO:0000705 ! tandem_repeat
76 def: "A region amplified by a PCR reaction." [SO:ke]
77 comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
79 synonym: "amplicon" RELATED []
80 synonym: "PCR product" EXACT []
81 xref: http://en.wikipedia.org/wiki/RAPD "wiki"
82 is_a: SO:0000695 ! reagent
87 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]
89 synonym: "mate pair" EXACT []
90 synonym: "read-pair" EXACT []
91 is_a: SO:0000150 ! read
92 relationship: part_of SO:0000149 ! contig
93 relationship: part_of SO:0001790 ! paired_end_fragment
97 name: gene_sensu_your_favorite_organism
108 synonym: "protein-coding" EXACT []
109 is_a: SO:0000401 ! gene_attribute
113 name: non_protein_coding
114 synonym: "non protein-coding" EXACT []
115 is_a: SO:0000401 ! gene_attribute
119 name: scRNA_primary_transcript
120 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]
121 synonym: "scRNA primary transcript" EXACT []
122 synonym: "scRNA transcript" EXACT []
123 synonym: "small cytoplasmic RNA" RELATED []
124 synonym: "small cytoplasmic RNA transcript" EXACT []
125 synonym: "small_cytoplasmic_RNA" RELATED []
126 is_a: SO:0000483 ! nc_primary_transcript
131 def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke]
133 synonym: "small cytoplasmic RNA" EXACT []
134 is_a: SO:0000655 ! ncRNA
135 relationship: derives_from SO:0000012 ! scRNA_primary_transcript
140 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]
141 comment: Binds TAF1, TAF2.
142 synonym: "DMp2" RELATED []
143 synonym: "initiator" EXACT []
144 synonym: "initiator motif" EXACT []
145 synonym: "INR motif" EXACT []
146 is_a: SO:0001660 ! core_promoter_element
147 relationship: part_of SO:0001669 ! RNApol_II_core_promoter
152 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]
153 comment: Binds TAF6, TAF9.
154 synonym: "CRWMGCGWKCGCTTS" NARROW []
155 synonym: "downstream core promoter element" EXACT []
156 synonym: "DPE motif" EXACT []
157 is_a: SO:0001660 ! core_promoter_element
158 relationship: part_of SO:0001669 ! RNApol_II_core_promoter
163 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]
164 comment: Binds TFIIB.
165 synonym: "B-recognition element" EXACT []
166 synonym: "BRE motif" EXACT []
167 synonym: "BREu" RELATED []
168 synonym: "BREu motif" EXACT []
169 synonym: "TFIIB recognition element" RELATED []
170 synonym: "transcription factor B-recognition element" EXACT []
171 is_a: SO:0001660 ! core_promoter_element
172 relationship: part_of SO:0001669 ! RNApol_II_core_promoter
177 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]
178 synonym: "proximal sequence element" EXACT []
179 synonym: "PSE motif" EXACT []
180 is_a: SO:0000713 ! DNA_motif
181 relationship: part_of SO:0000167 ! promoter
186 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]
187 synonym: "linkage group" EXACT []
188 xref: http://en.wikipedia.org/wiki/Linkage_group "wiki"
189 is_a: SO:0001411 ! biological_region
193 name: RNA_internal_loop
194 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]
195 synonym: "RNA internal loop" EXACT []
196 is_a: SO:0000715 ! RNA_motif
200 name: asymmetric_RNA_internal_loop
201 def: "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]
202 synonym: "asymmetric RNA internal loop" EXACT []
203 is_a: SO:0000020 ! RNA_internal_loop
207 name: A_minor_RNA_motif
208 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]
209 synonym: "A minor RNA motif" EXACT []
210 is_a: SO:0000715 ! RNA_motif
214 name: K_turn_RNA_motif
215 def: "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]
216 synonym: "K turn RNA motif" EXACT []
217 synonym: "K-turn" EXACT []
218 synonym: "kink turn" EXACT []
219 synonym: "kink-turn motif" EXACT []
220 xref: http://en.wikipedia.org/wiki/K-turn "wiki"
221 is_a: SO:0000021 ! asymmetric_RNA_internal_loop
225 name: sarcin_like_RNA_motif
226 def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]
227 synonym: "sarcin like RNA motif" EXACT []
228 synonym: "sarcin/ricin domain" EXACT []
229 synonym: "sarcin/ricin loop" EXACT []
230 synonym: "sarcin/ricin RNA domain" EXACT []
231 is_a: SO:0000021 ! asymmetric_RNA_internal_loop
235 name: symmetric_RNA_internal_loop
236 def: "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]
237 synonym: "A-minor RNA motif" EXACT []
238 is_a: SO:0000020 ! RNA_internal_loop
242 name: RNA_junction_loop
243 synonym: "RNA junction loop" EXACT []
244 is_a: SO:0000715 ! RNA_motif
249 synonym: "hook turn" RELATED []
250 synonym: "hook-turn motif" EXACT []
251 synonym: "RNA hook turn" EXACT []
252 is_a: SO:0000026 ! RNA_junction_loop
257 synonym: "base pair" EXACT []
258 xref: http://en.wikipedia.org/wiki/Base_pair "wiki"
259 is_a: SO:0000002 ! sequence_secondary_structure
264 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]
265 synonym: "canonical base pair" EXACT []
266 synonym: "Watson Crick base pair" EXACT []
267 synonym: "Watson-Crick base pair" RELATED []
268 synonym: "Watson-Crick pair" EXACT []
269 synonym: "WC base pair" EXACT []
270 is_a: SO:0000028 ! base_pair
274 name: sugar_edge_base_pair
275 def: "A type of non-canonical base-pairing." [PMID:12177293]
276 synonym: "sugar edge base pair" EXACT []
277 is_a: SO:0000028 ! base_pair
282 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]
283 xref: http://en.wikipedia.org/wiki/Aptamer "wiki"
284 is_a: SO:0000696 ! oligo
289 def: "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]
290 synonym: "DNA aptamer" EXACT []
291 is_a: SO:0000031 ! aptamer
296 def: "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]
297 synonym: "RNA aptamer" EXACT []
298 is_a: SO:0000031 ! aptamer
302 name: morpholino_oligo
303 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/]
304 synonym: "morphant" BROAD []
305 synonym: "morpholino" EXACT []
306 synonym: "morpholino oligo" EXACT []
307 is_a: SO:0001247 ! synthetic_oligo
308 relationship: has_quality SO:0001183 ! morpholino_backbone
313 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]
314 synonym: "riboswitch RNA" EXACT []
315 xref: http://en.wikipedia.org/wiki/Riboswitch "wiki"
316 is_a: SO:0000836 ! mRNA_region
317 relationship: part_of SO:0000234 ! mRNA
321 name: matrix_attachment_site
322 def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]
323 synonym: "MAR" EXACT []
324 synonym: "matrix association region" EXACT []
325 synonym: "matrix attachment region" EXACT []
326 synonym: "matrix attachment site" EXACT []
327 synonym: "nuclear matrix association region" EXACT []
328 synonym: "nuclear matrix attachment site" EXACT []
329 synonym: "S/MAR" EXACT []
330 synonym: "S/MAR element" RELATED []
331 synonym: "scaffold attachment site" EXACT []
332 synonym: "scaffold matrix attachment region" EXACT []
333 synonym: "SMAR" EXACT []
334 xref: http://en.wikipedia.org/wiki/Matrix_attachment_site "wiki"
335 is_a: SO:0000626 ! chromosomal_regulatory_element
339 name: locus_control_region
340 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]
341 synonym: "LCR" EXACT []
342 synonym: "locus control element" RELATED []
343 synonym: "locus control region" EXACT []
344 xref: http://en.wikipedia.org/wiki/Locus_control_region "wiki"
345 is_a: SO:0000727 ! CRM
350 def: "A collection of match parts." [SO:ke]
357 def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke]
359 synonym: "match part" EXACT []
360 is_a: SO:0001410 ! experimental_feature
361 relationship: part_of SO:0000343 ! match
366 def: "A clone of a DNA region of a genome." [SO:ma]
367 synonym: "genomic clone" EXACT []
368 is_a: SO:0000151 ! clone
369 relationship: has_quality SO:0000991 ! genomic_DNA
373 name: sequence_operation
374 def: "An operation that can be applied to a sequence, that results in a change." [SO:ke]
375 synonym: "sequence operation" EXACT []
380 name: pseudogene_attribute
381 def: "An attribute of a pseudogene (SO:0000336)." [SO:ma]
382 synonym: "pseudogene attribute" EXACT []
387 name: processed_pseudogene
388 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]
389 comment: Please not the synonym R psi M uses the spelled out form of the greek letter.
390 synonym: "processed pseudogene" EXACT []
391 synonym: "pseudogene by reverse transcription" RELATED []
392 synonym: "R psi G" RELATED []
393 synonym: "retropseudogene" EXACT []
394 is_a: SO:0000336 ! pseudogene
398 name: pseudogene_by_unequal_crossing_over
399 def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke]
400 synonym: "pseudogene by unequal crossing over" EXACT []
401 is_a: SO:0001760 ! non_processed_pseudogene
406 def: "To remove a subsection of sequence." [SO:ke]
412 def: "To insert a subsection of sequence." [SO:ke]
418 def: "To invert a subsection of sequence." [SO:ke]
424 def: "To substitute a subsection of sequence for another." [SO:ke]
430 def: "To translocate a subsection of sequence." [SO:ke]
436 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]
443 def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]
444 xref: http://en.wikipedia.org/wiki/Hybridization_probe "wiki"
445 is_a: SO:0000696 ! oligo
449 name: assortment_derived_deficiency
450 synonym: "assortment-derived_deficiency" RELATED []
455 name: sequence_variant_affecting_regulatory_region
456 def: "A sequence_variant_effect which changes the regulatory region of a gene." [SO:ke]
457 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
458 synonym: "mutation affecting regulatory region" RELATED []
459 synonym: "sequence variant affecting regulatory region" EXACT []
461 replaced_by: SO:0001556
466 def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
467 xref: http://en.wikipedia.org/wiki/Aneuploid "wiki"
468 is_a: SO:1000182 ! chromosome_number_variation
473 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]
474 xref: http://en.wikipedia.org/wiki/Hyperploid "wiki"
475 is_a: SO:0000054 ! aneuploid
480 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]
481 xref: http://en.wikipedia.org/wiki/Hypoploid "wiki"
482 is_a: SO:0000054 ! aneuploid
487 def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]
489 synonym: "operator segment" EXACT []
490 xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki"
491 is_a: SO:0000752 ! gene_group_regulatory_region
495 name: assortment_derived_aneuploid
496 synonym: "assortment-derived_aneuploid" RELATED []
501 name: nuclease_binding_site
502 def: "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]
504 synonym: "nuclease binding site" EXACT []
505 is_a: SO:0001654 ! nucleotide_to_protein_binding_site
509 name: compound_chromosome_arm
510 comment: FLAG - this term is should probably be a part of rather than an is_a.
511 synonym: "compound chromosome arm" EXACT []
512 is_a: SO:1000042 ! compound_chromosome
516 name: restriction_enzyme_binding_site
517 def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]
518 comment: A region of a molecule that binds to a restriction enzyme.
519 synonym: "restriction endonuclease binding site" EXACT []
520 synonym: "restriction enzyme binding site" EXACT []
521 is_a: SO:0000059 ! nuclease_binding_site
525 name: deficient_intrachromosomal_transposition
526 def: "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]
527 synonym: "deficient intrachromosomal transposition" EXACT []
528 is_a: SO:1000029 ! chromosomal_deletion
529 is_a: SO:1000041 ! intrachromosomal_transposition
530 relationship: has_part SO:0000159 ! deletion
534 name: deficient_interchromosomal_transposition
535 def: "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]
536 synonym: "deficient interchromosomal transposition" EXACT []
537 is_a: SO:1000155 ! interchromosomal_transposition
541 name: gene_by_transcript_attribute
542 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.
547 name: free_chromosome_arm
548 def: "A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]
549 synonym: "free chromosome arm" EXACT []
550 is_a: SO:1000183 ! chromosome_structure_variation
554 name: gene_by_polyadenylation_attribute
559 name: gene_to_gene_feature
560 synonym: "gene to gene feature" EXACT []
561 is_a: SO:0000401 ! gene_attribute
566 def: "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]
567 is_a: SO:0000067 ! gene_to_gene_feature
572 def: "An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]
573 synonym: "inside intron" EXACT []
574 is_a: SO:0000068 ! overlapping
578 name: inside_intron_antiparallel
579 def: "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]
580 synonym: "inside intron antiparallel" EXACT []
581 is_a: SO:0000069 ! inside_intron
585 name: inside_intron_parallel
586 def: "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]
587 synonym: "inside intron parallel" EXACT []
588 is_a: SO:0000069 ! inside_intron
592 name: end_overlapping_gene
597 name: five_prime_three_prime_overlap
598 def: "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]
599 synonym: "five prime-three prime overlap" EXACT []
600 is_a: SO:0000068 ! overlapping
604 name: five_prime_five_prime_overlap
605 def: "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]
606 synonym: "five prime-five prime overlap" EXACT []
607 is_a: SO:0000068 ! overlapping
611 name: three_prime_three_prime_overlap
612 def: "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]
613 synonym: "three prime-three prime overlap" EXACT []
614 is_a: SO:0000068 ! overlapping
618 name: three_prime_five_prime_overlap
619 def: "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]
620 synonym: "5' 3' overlap" EXACT []
621 synonym: "three prime five prime overlap" EXACT []
622 is_a: SO:0000068 ! overlapping
627 def: "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]
628 xref: http://en.wikipedia.org/wiki/Antisense "wiki"
629 is_a: SO:0000068 ! overlapping
633 name: polycistronic_transcript
634 def: "A transcript that is polycistronic." [SO:xp]
635 synonym: "polycistronic transcript" EXACT []
636 is_a: SO:0000673 ! transcript
637 relationship: has_quality SO:0000880 ! polycistronic
641 name: dicistronic_transcript
642 def: "A transcript that is dicistronic." [SO:ke]
643 synonym: "dicistronic transcript" EXACT []
644 is_a: SO:0000078 ! polycistronic_transcript
645 relationship: has_quality SO:0000879 ! dicistronic
650 synonym: "operon member" EXACT []
651 is_a: SO:0000081 ! gene_array_member
655 name: gene_array_member
656 synonym: "gene array member" EXACT []
657 is_a: SO:0000401 ! gene_attribute
661 name: processed_transcript_attribute
666 name: macronuclear_sequence
667 synonym: "macronuclear sequence" EXACT []
668 is_a: SO:0000736 ! organelle_sequence
672 name: micronuclear_sequence
673 synonym: "micronuclear sequence" EXACT []
674 is_a: SO:0000736 ! organelle_sequence
678 name: gene_by_genome_location
683 name: gene_by_organelle_of_genome
689 def: "A gene from nuclear sequence." [SO:xp]
690 synonym: "nuclear gene" EXACT []
691 xref: http://en.wikipedia.org/wiki/Nuclear_gene "wiki"
692 is_a: SO:0000704 ! gene
693 relationship: has_origin SO:0000738 ! nuclear_sequence
698 def: "A gene located in mitochondrial sequence." [SO:xp]
699 synonym: "mitochondrial gene" EXACT []
700 synonym: "mt gene" EXACT []
701 xref: http://en.wikipedia.org/wiki/Mitochondrial_gene "wiki"
702 is_a: SO:0000704 ! gene
703 relationship: has_origin SO:0000737 ! mitochondrial_sequence
707 name: kinetoplast_gene
708 def: "A gene located in kinetoplast sequence." [SO:xp]
709 synonym: "kinetoplast gene" EXACT []
710 is_a: SO:0000088 ! mt_gene
711 relationship: has_origin SO:0000741 ! kinetoplast
716 def: "A gene from plastid sequence." [SO:xp]
717 synonym: "plastid gene" EXACT []
718 is_a: SO:0000704 ! gene
719 relationship: has_origin SO:0000740 ! plastid_sequence
723 name: apicoplast_gene
724 def: "A gene from apicoplast sequence." [SO:xp]
725 synonym: "apicoplast gene" EXACT []
726 is_a: SO:0000090 ! plastid_gene
727 relationship: has_origin SO:0000743 ! apicoplast_sequence
732 def: "A gene from chloroplast sequence." [SO:xp]
733 synonym: "chloroplast gene" EXACT []
734 synonym: "ct gene" EXACT []
735 is_a: SO:0000090 ! plastid_gene
736 relationship: has_origin SO:0000745 ! chloroplast_sequence
740 name: chromoplast_gene
741 def: "A gene from chromoplast_sequence." [SO:xp]
742 synonym: "chromoplast gene" EXACT []
743 is_a: SO:0000090 ! plastid_gene
744 relationship: has_origin SO:0000744 ! chromoplast_sequence
749 def: "A gene from cyanelle sequence." [SO:xp]
750 synonym: "cyanelle gene" EXACT []
751 is_a: SO:0000090 ! plastid_gene
752 relationship: has_origin SO:0000746 ! cyanelle_sequence
756 name: leucoplast_gene
757 def: "A plastid gene from leucoplast sequence." [SO:xp]
758 synonym: "leucoplast gene" EXACT []
759 is_a: SO:0000090 ! plastid_gene
760 relationship: has_origin SO:0000747 ! leucoplast_sequence
764 name: proplastid_gene
765 def: "A gene from proplastid sequence." [SO:ke]
766 synonym: "proplastid gene" EXACT []
767 is_a: SO:0000090 ! plastid_gene
768 relationship: has_origin SO:0000748 ! proplastid_sequence
772 name: nucleomorph_gene
773 def: "A gene from nucleomorph sequence." [SO:xp]
774 synonym: "nucleomorph gene" EXACT []
775 is_a: SO:0000704 ! gene
776 relationship: has_origin SO:0000739 ! nucleomorphic_sequence
781 def: "A gene from plasmid sequence." [SO:xp]
782 synonym: "plasmid gene" EXACT []
783 is_a: SO:0000704 ! gene
784 relationship: has_origin SO:0000749 ! plasmid_location
789 def: "A gene from proviral sequence." [SO:xp]
790 synonym: "proviral gene" EXACT []
791 is_a: SO:0000704 ! gene
792 relationship: has_origin SO:0000751 ! proviral_location
796 name: endogenous_retroviral_gene
797 def: "A proviral gene with origin endogenous retrovirus." [SO:xp]
798 synonym: "endogenous retroviral gene" EXACT []
799 is_a: SO:0000099 ! proviral_gene
800 relationship: has_origin SO:0000903 ! endogenous_retroviral_sequence
804 name: transposable_element
805 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]
807 synonym: "transposable element" EXACT []
808 synonym: "transposon" EXACT []
809 xref: http://en.wikipedia.org/wiki/Transposable_element "wiki"
810 is_a: SO:0001039 ! integrated_mobile_genetic_element
814 name: expressed_sequence_match
815 def: "A match to an EST or cDNA sequence." [SO:ke]
817 synonym: "expressed sequence match" EXACT []
818 is_a: SO:0000347 ! nucleotide_match
822 name: clone_insert_end
823 def: "The end of the clone insert." [SO:ke]
825 synonym: "clone insert end" EXACT []
826 is_a: SO:0000699 ! junction
827 relationship: part_of SO:0000753 ! clone_insert
833 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]
834 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.
836 synonym: "protein" EXACT []
837 xref: http://en.wikipedia.org/wiki/Polypeptide "wiki"
838 is_a: SO:0001411 ! biological_region
839 relationship: derives_from SO:0000316 ! CDS
844 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]
845 synonym: "chromosome arm" EXACT []
846 is_a: SO:0000830 ! chromosome_part
850 name: non_capped_primary_transcript
855 name: sequencing_primer
856 synonym: "sequencing primer" EXACT []
857 is_a: SO:0000112 ! primer
861 name: mRNA_with_frameshift
862 def: "An mRNA with a frameshift." [SO:xp]
863 synonym: "frameshifted mRNA" EXACT []
864 synonym: "mRNA with frameshift" EXACT []
865 is_a: SO:0000234 ! mRNA
866 relationship: has_quality SO:0000865 ! frameshift
870 name: sequence_variant_obs
871 def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
873 synonym: "mutation" RELATED []
878 name: sequence_feature
879 def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]
881 synonym: "located sequence feature" RELATED []
882 synonym: "located_sequence_feature" EXACT []
883 synonym: "sequence feature" EXACT []
884 disjoint_from: SO:0000400 ! sequence_attribute
888 name: transposable_element_gene
889 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]
890 synonym: "transposable element gene" EXACT []
891 is_a: SO:0000704 ! gene
892 relationship: part_of SO:0000101 ! transposable_element
897 def: "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]
899 synonym: "DNA primer" EXACT []
900 synonym: "primer oligonucleotide" EXACT []
901 synonym: "primer polynucleotide" EXACT []
902 synonym: "primer sequence" EXACT []
903 xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki"
904 is_a: SO:0000441 ! ss_oligo
908 name: proviral_region
909 def: "A viral sequence which has integrated into a host genome." [SO:ke]
911 synonym: "proviral region" EXACT []
912 synonym: "proviral sequence" RELATED []
913 is_a: SO:0001039 ! integrated_mobile_genetic_element
917 name: methylated_cytosine
918 def: "A methylated deoxy-cytosine." [SO:ke]
920 synonym: "methylated C" EXACT []
921 synonym: "methylated cytosine" EXACT []
922 synonym: "methylated cytosine base" EXACT []
923 synonym: "methylated cytosine residue" EXACT []
924 synonym: "methylated_C" EXACT []
925 is_a: SO:0000306 ! methylated_DNA_base_feature
926 is_a: SO:0001963 ! modified_cytosine
930 name: transcript_feature
936 def: "An attribute describing a sequence that is modified by editing." [SO:ke]
937 is_a: SO:0000237 ! transcript_attribute
941 name: transcript_with_readthrough_stop_codon
946 name: transcript_with_translational_frameshift
947 def: "A transcript with a translational frameshift." [SO:xp]
948 synonym: "transcript with translational frameshift" EXACT []
949 is_a: SO:0000673 ! transcript
950 relationship: has_quality SO:0000887 ! translationally_frameshifted
955 def: "An attribute to describe a sequence that is regulated." [SO:ke]
956 is_a: SO:0000401 ! gene_attribute
960 name: protein_coding_primary_transcript
961 def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]
962 comment: May contain introns.
964 synonym: "pre mRNA" RELATED []
965 synonym: "protein coding primary transcript" EXACT []
966 is_a: SO:0000185 ! primary_transcript
971 def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
972 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
973 synonym: "DNA forward primer" EXACT []
974 synonym: "forward DNA primer" EXACT []
975 synonym: "forward primer" EXACT []
976 synonym: "forward primer oligo" EXACT []
977 synonym: "forward primer oligonucleotide" EXACT []
978 synonym: "forward primer polynucleotide" EXACT []
979 synonym: "forward primer sequence" EXACT []
980 is_a: SO:0000112 ! primer
981 relationship: has_quality SO:0001030 ! forward
985 name: RNA_sequence_secondary_structure
986 def: "A folded RNA sequence." [SO:ke]
987 synonym: "RNA sequence secondary structure" EXACT []
988 is_a: SO:0000002 ! sequence_secondary_structure
992 name: transcriptionally_regulated
993 def: "An attribute describing a gene that is regulated at transcription." [SO:ma]
994 comment: By:<protein_id>.
995 synonym: "transcriptionally regulated" EXACT []
996 is_a: SO:0000119 ! regulated
1000 name: transcriptionally_constitutive
1001 def: "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]
1002 synonym: "transcriptionally constitutive" EXACT []
1003 is_a: SO:0000123 ! transcriptionally_regulated
1007 name: transcriptionally_induced
1008 def: "An inducer molecule is required for transcription to occur." [SO:ke]
1009 synonym: "transcriptionally induced" EXACT []
1010 is_a: SO:0000123 ! transcriptionally_regulated
1014 name: transcriptionally_repressed
1015 def: "A repressor molecule is required for transcription to stop." [SO:ke]
1016 synonym: "transcriptionally repressed" EXACT []
1017 is_a: SO:0000123 ! transcriptionally_regulated
1022 def: "A gene that is silenced." [SO:xp]
1023 synonym: "silenced gene" EXACT []
1024 is_a: SO:0000704 ! gene
1025 relationship: has_quality SO:0000893 ! silenced
1029 name: gene_silenced_by_DNA_modification
1030 def: "A gene that is silenced by DNA modification." [SO:xp]
1031 synonym: "gene silenced by DNA modification" EXACT []
1032 is_a: SO:0000127 ! silenced_gene
1033 relationship: has_quality SO:0000894 ! silenced_by_DNA_modification
1037 name: gene_silenced_by_DNA_methylation
1038 def: "A gene that is silenced by DNA methylation." [SO:xp]
1039 synonym: "gene silenced by DNA methylation" EXACT []
1040 synonym: "methylation-silenced gene" EXACT []
1041 is_a: SO:0000128 ! gene_silenced_by_DNA_modification
1042 relationship: has_quality SO:0000895 ! silenced_by_DNA_methylation
1046 name: post_translationally_regulated
1047 def: "An attribute describing a gene that is regulated after it has been translated." [SO:ke]
1048 synonym: "post translationally regulated" EXACT []
1049 synonym: "post-translationally regulated" EXACT []
1050 is_a: SO:0000119 ! regulated
1054 name: translationally_regulated
1055 def: "An attribute describing a gene that is regulated as it is translated." [SO:ke]
1056 synonym: "translationally regulated" EXACT []
1057 is_a: SO:0000119 ! regulated
1061 name: reverse_primer
1062 def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
1063 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
1064 synonym: "DNA reverse primer" EXACT []
1065 synonym: "reverse DNA primer" EXACT []
1066 synonym: "reverse primer" EXACT []
1067 synonym: "reverse primer oligo" EXACT []
1068 synonym: "reverse primer oligonucleotide" EXACT []
1069 synonym: "reverse primer sequence" EXACT []
1070 is_a: SO:0000112 ! primer
1071 relationship: has_quality SO:0001031 ! reverse
1075 name: epigenetically_modified
1076 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]
1077 synonym: "epigenetically modified" EXACT []
1078 is_a: SO:0000401 ! gene_attribute
1082 name: genomically_imprinted
1083 def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]
1084 synonym: "genomically imprinted" EXACT []
1085 synonym: "imprinted" BROAD []
1086 xref: http:http://en.wikipedia.org/wiki/Genomic_imprinting "wiki"
1087 is_a: SO:0000119 ! regulated
1088 is_a: SO:0000133 ! epigenetically_modified
1092 name: maternally_imprinted
1093 def: "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]
1094 synonym: "maternally imprinted" EXACT []
1095 is_a: SO:0000134 ! genomically_imprinted
1099 name: paternally_imprinted
1100 def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]
1101 synonym: "paternally imprinted" EXACT []
1102 is_a: SO:0000134 ! genomically_imprinted
1106 name: allelically_excluded
1107 def: "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]
1108 comment: Examples are x-inactivation and immunoglobulin formation.
1109 synonym: "allelically excluded" EXACT []
1110 is_a: SO:0000133 ! epigenetically_modified
1114 name: gene_rearranged_at_DNA_level
1115 def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp]
1116 synonym: "gene rearranged at DNA level" EXACT []
1117 is_a: SO:0000898 ! epigenetically_modified_gene
1118 relationship: has_quality SO:0000904 ! rearranged_at_DNA_level
1122 name: ribosome_entry_site
1123 def: "Region in mRNA where ribosome assembles." [SO:ke]
1125 synonym: "ribosome entry site" EXACT []
1126 is_a: SO:0000836 ! mRNA_region
1127 relationship: part_of SO:0000204 ! five_prime_UTR
1132 def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]
1134 synonym: "attenuator sequence" EXACT []
1135 xref: http://en.wikipedia.org/wiki/Attenuator "wiki"
1136 is_a: SO:0001680 ! translation_regulatory_region
1137 relationship: part_of SO:0000234 ! mRNA
1142 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]
1144 synonym: "terminator sequence" EXACT []
1145 xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki"
1146 is_a: SO:0001679 ! transcription_regulatory_region
1147 relationship: part_of SO:0000673 ! transcript
1151 name: DNA_sequence_secondary_structure
1152 def: "A folded DNA sequence." [SO:ke]
1153 synonym: "DNA sequence secondary structure" EXACT []
1154 is_a: SO:0000002 ! sequence_secondary_structure
1158 name: assembly_component
1159 def: "A region of known length which may be used to manufacture a longer region." [SO:ke]
1161 synonym: "assembly component" EXACT []
1162 is_a: SO:0001410 ! experimental_feature
1166 name: primary_transcript_attribute
1172 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]
1173 synonym: "recoded codon" EXACT []
1174 is_a: SO:0000360 ! codon
1179 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]
1180 is_a: SO:0000237 ! transcript_attribute
1185 def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]
1186 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
1188 xref: http://en.wikipedia.org/wiki/Exon "wiki"
1189 is_a: SO:0000833 ! transcript_region
1194 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]
1196 synonym: "scaffold" RELATED []
1197 is_a: SO:0001876 ! partial_genomic_sequence_assembly
1198 relationship: part_of SO:0000719 ! ultracontig
1203 def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]
1205 xref: http://en.wikipedia.org/wiki/Contig "wiki"
1206 is_a: SO:0000143 ! assembly_component
1207 is_a: SO:0000353 ! sequence_assembly
1208 relationship: part_of SO:0000148 ! supercontig
1213 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]
1215 is_a: SO:0000143 ! assembly_component
1216 relationship: part_of SO:0000149 ! contig
1221 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]
1223 xref: http:http://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
1224 is_a: SO:0000695 ! reagent
1229 def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]
1230 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
1231 synonym: "yeast artificial chromosome" EXACT []
1232 is_a: SO:0000440 ! vector_replicon
1237 def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]
1238 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
1239 synonym: "bacterial artificial chromosome" EXACT []
1240 is_a: SO:0000440 ! vector_replicon
1245 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]
1246 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.
1247 synonym: "P1" EXACT []
1248 synonym: "P1 artificial chromosome" EXACT []
1249 xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome "wiki"
1250 is_a: SO:0000440 ! vector_replicon
1255 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]
1256 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
1257 synonym: "plasmid sequence" EXACT []
1258 is_a: SO:0001235 ! replicon
1263 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]
1264 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.
1265 synonym: "cosmid vector" EXACT []
1266 xref: http://en.wikipedia.org/wiki/Cosmid "wiki"
1267 is_a: SO:0000440 ! vector_replicon
1272 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]
1273 synonym: "phagemid vector" RELATED []
1274 xref: http://en.wikipedia.org/wiki/Phagemid "wiki"
1275 is_a: SO:0000440 ! vector_replicon
1280 def: "A cloning vector that utilizes the E. coli F factor." [SO:ma]
1281 comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
1282 synonym: "fosmid vector" RELATED []
1283 xref: http://en.wikipedia.org/wiki/Fosmid "wiki"
1284 is_a: SO:0000440 ! vector_replicon
1290 def: "The point at which one or more contiguous nucleotides were excised." [SO:ke]
1292 synonym: "deleted_sequence" EXACT []
1293 synonym: "nucleotide deletion" EXACT []
1294 synonym: "nucleotide_deletion" EXACT []
1295 xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki"
1296 xref: loinc:LA6692-3 "Deletion"
1297 is_a: SO:0001059 ! sequence_alteration
1298 is_a: SO:0001411 ! biological_region
1303 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]
1308 name: methylated_adenine
1309 def: "A modified base in which adenine has been methylated." [SO:ke]
1311 synonym: "methylated A" EXACT []
1312 synonym: "methylated adenine" EXACT []
1313 synonym: "methylated adenine base" EXACT []
1314 synonym: "methylated adenine residue" EXACT []
1315 synonym: "methylated_A" EXACT []
1316 is_a: SO:0000306 ! methylated_DNA_base_feature
1317 is_a: SO:0001962 ! modified_adenine
1322 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]
1323 comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery.
1325 synonym: "splice site" EXACT []
1326 xref: http://en.wikipedia.org/wiki/Splice_site "wiki"
1327 is_a: SO:0000835 ! primary_transcript_region
1331 name: five_prime_cis_splice_site
1332 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]
1334 synonym: "5' splice site" EXACT []
1335 synonym: "donor" RELATED []
1336 synonym: "donor splice site" EXACT []
1337 synonym: "five prime splice site" EXACT []
1338 synonym: "splice donor site" EXACT []
1339 is_a: SO:0001419 ! cis_splice_site
1343 name: three_prime_cis_splice_site
1344 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]
1346 synonym: "3' splice site" RELATED []
1347 synonym: "acceptor" RELATED []
1348 synonym: "acceptor splice site" EXACT []
1349 synonym: "splice acceptor site" EXACT []
1350 synonym: "three prime splice site" EXACT []
1351 is_a: SO:0001419 ! cis_splice_site
1356 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]
1357 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.
1359 xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki"
1360 is_a: SO:0000727 ! CRM
1364 name: enhancer_bound_by_factor
1365 def: "An enhancer bound by a factor." [SO:xp]
1366 synonym: "enhancer bound by factor" EXACT []
1367 is_a: SO:0000165 ! enhancer
1368 relationship: has_quality SO:0000277 ! bound_by_factor
1373 def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]
1374 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.
1376 synonym: "promoter sequence" EXACT []
1377 xref: http://en.wikipedia.org/wiki/Promoter "wiki"
1378 is_a: SO:0001055 ! transcriptional_cis_regulatory_region
1382 name: restriction_enzyme_cut_site
1383 def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma]
1388 name: RNApol_I_promoter
1389 def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]
1390 synonym: "pol I promoter" EXACT []
1391 synonym: "polymerase I promoter" EXACT []
1392 synonym: "RNA polymerase A promoter" EXACT []
1393 synonym: "RNApol I promoter" EXACT []
1394 is_a: SO:0001203 ! RNA_polymerase_promoter
1398 name: RNApol_II_promoter
1399 def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]
1400 synonym: "pol II promoter" RELATED []
1401 synonym: "polymerase II promoter" EXACT []
1402 synonym: "RNA polymerase B promoter" EXACT []
1403 synonym: "RNApol II promoter" EXACT []
1404 is_a: SO:0001203 ! RNA_polymerase_promoter
1408 name: RNApol_III_promoter
1409 def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]
1410 synonym: "pol III promoter" EXACT []
1411 synonym: "polymerase III promoter" EXACT []
1412 synonym: "RNA polymerase C promoter" EXACT []
1413 synonym: "RNApol III promoter" EXACT []
1414 is_a: SO:0001203 ! RNA_polymerase_promoter
1419 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]
1420 synonym: "CAAT box" EXACT []
1421 synonym: "CAAT signal" EXACT []
1422 synonym: "CAAT-box" EXACT []
1423 xref: http://en.wikipedia.org/wiki/CAAT_box "wiki"
1424 is_a: SO:0000713 ! DNA_motif
1425 relationship: part_of SO:0000170 ! RNApol_II_promoter
1429 name: GC_rich_promoter_region
1430 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]
1431 synonym: "GC rich promoter region" EXACT []
1432 synonym: "GC-rich region" EXACT []
1433 is_a: SO:0001659 ! promoter_element
1434 relationship: part_of SO:0000170 ! RNApol_II_promoter
1439 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]
1441 synonym: "Goldstein-Hogness box" EXACT []
1442 synonym: "TATA box" EXACT []
1443 xref: http://en.wikipedia.org/wiki/TATA_box "wiki"
1444 is_a: SO:0001660 ! core_promoter_element
1448 name: minus_10_signal
1449 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]
1450 synonym: "-10 signal" EXACT []
1451 synonym: "minus 10 signal" EXACT []
1452 synonym: "Pribnow box" EXACT []
1453 synonym: "Pribnow Schaller box" EXACT []
1454 synonym: "Pribnow-Schaller box" EXACT []
1455 xref: http://en.wikipedia.org/wiki/Pribnow_box "wiki"
1456 is_a: SO:0000713 ! DNA_motif
1457 relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70
1458 relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf
1462 name: minus_35_signal
1463 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]
1464 synonym: "-35 signal" EXACT []
1465 synonym: "minus 35 signal" EXACT []
1466 is_a: SO:0000713 ! DNA_motif
1467 relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70
1468 relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf
1472 name: cross_genome_match
1473 def: "A nucleotide match against a sequence from another organism." [SO:ma]
1475 synonym: "cross genome match" EXACT []
1476 is_a: SO:0000347 ! nucleotide_match
1481 def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
1482 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
1484 xref: http://en.wikipedia.org/wiki/Operon "wiki"
1485 is_a: SO:0005855 ! gene_group
1489 name: clone_insert_start
1490 def: "The start of the clone insert." [SO:ke]
1492 synonym: "clone insert start" EXACT []
1493 is_a: SO:0000699 ! junction
1494 relationship: part_of SO:0000753 ! clone_insert
1498 name: retrotransposon
1499 def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]
1500 synonym: "class I" RELATED []
1501 synonym: "class I transposon" EXACT []
1502 synonym: "retrotransposon element" EXACT []
1503 xref: http://en.wikipedia.org/wiki/Retrotransposon "wiki"
1504 is_a: SO:0000101 ! transposable_element
1508 name: translated_nucleotide_match
1509 def: "A match against a translated sequence." [SO:ke]
1511 synonym: "translated nucleotide match" EXACT []
1512 is_a: SO:0000347 ! nucleotide_match
1516 name: DNA_transposon
1517 def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]
1518 synonym: "class II" RELATED []
1519 synonym: "class II transposon" EXACT []
1520 synonym: "DNA transposon" EXACT []
1521 is_a: SO:0000101 ! transposable_element
1525 name: non_transcribed_region
1526 def: "A region of the gene which is not transcribed." [SO:ke]
1528 synonym: "non transcribed region" EXACT []
1529 synonym: "non-transcribed sequence" EXACT []
1530 synonym: "nontranscribed region" EXACT []
1531 synonym: "nontranscribed sequence" EXACT []
1532 is_a: SO:0000842 ! gene_component_region
1537 def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]
1538 comment: May have either GT-AG or AT-AG 5' and 3' boundaries.
1539 synonym: "U2 intron" EXACT []
1540 is_a: SO:0000662 ! spliceosomal_intron
1544 name: primary_transcript
1545 def: "A transcript that in its initial state requires modification to be functional." [SO:ma]
1547 synonym: "precursor RNA" EXACT []
1548 synonym: "primary transcript" EXACT []
1549 xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki"
1550 is_a: SO:0000673 ! transcript
1554 name: LTR_retrotransposon
1555 def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke]
1556 synonym: "long terminal repeat retrotransposon" EXACT []
1557 synonym: "LTR retrotransposon" EXACT []
1558 is_a: SO:0000180 ! retrotransposon
1563 def: "A group of characterized repeat sequences." [SO:ke]
1570 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]
1571 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
1573 xref: http://en.wikipedia.org/wiki/Intron "wiki"
1574 is_a: SO:0000835 ! primary_transcript_region
1578 name: non_LTR_retrotransposon
1579 def: "A retrotransposon without long terminal repeat sequences." [SO:ke]
1580 synonym: "non LTR retrotransposon" EXACT []
1581 is_a: SO:0000180 ! retrotransposon
1585 name: five_prime_intron
1586 synonym: "5' intron" EXACT []
1587 synonym: "5' intron sequence" EXACT []
1588 synonym: "five prime intron" EXACT []
1589 is_a: SO:0000188 ! intron
1593 name: interior_intron
1594 synonym: "interior intron" EXACT []
1595 is_a: SO:0000188 ! intron
1599 name: three_prime_intron
1600 synonym: "3' intron" EXACT []
1601 synonym: "3' intron sequence" RELATED []
1602 synonym: "three prime intron" EXACT []
1603 is_a: SO:0000188 ! intron
1608 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]
1610 synonym: "restriction fragment length polymorphism" EXACT []
1611 synonym: "RFLP" EXACT []
1612 synonym: "RFLP fragment" EXACT []
1613 xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki"
1614 is_a: SO:0000412 ! restriction_fragment
1619 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]
1620 synonym: "LINE" EXACT []
1621 synonym: "LINE element" EXACT []
1622 synonym: "Long interspersed element" EXACT []
1623 synonym: "Long interspersed nuclear element" EXACT []
1624 is_a: SO:0000189 ! non_LTR_retrotransposon
1629 def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]
1631 synonym: "coding exon" EXACT []
1632 is_a: SO:0000147 ! exon
1636 name: five_prime_coding_exon_coding_region
1637 def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]
1639 synonym: "five prime exon coding region" EXACT []
1640 is_a: SO:0001215 ! coding_region_of_exon
1641 relationship: part_of SO:0000200 ! five_prime_coding_exon
1645 name: three_prime_coding_exon_coding_region
1646 def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]
1648 synonym: "three prime exon coding region" EXACT []
1649 is_a: SO:0001215 ! coding_region_of_exon
1650 relationship: part_of SO:0000202 ! three_prime_coding_exon
1654 name: noncoding_exon
1655 def: "An exon that does not contain any codons." [SO:ke]
1657 synonym: "noncoding exon" EXACT []
1658 is_a: SO:0000147 ! exon
1663 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]
1665 synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/]
1666 synonym: "translocated sequence" EXACT []
1667 is_a: SO:0001785 ! structural_alteration
1671 name: five_prime_coding_exon
1672 def: "The 5' most coding exon." [SO:ke]
1674 synonym: "5' coding exon" EXACT []
1675 synonym: "five prime coding exon" EXACT []
1676 is_a: SO:0000195 ! coding_exon
1681 def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]
1682 synonym: "interior exon" EXACT []
1683 is_a: SO:0000147 ! exon
1687 name: three_prime_coding_exon
1688 def: "The coding exon that is most 3-prime on a given transcript." [SO:ma]
1689 synonym: "3' coding exon" RELATED []
1690 synonym: "three prime coding exon" EXACT []
1691 is_a: SO:0000195 ! coding_exon
1696 def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]
1698 synonym: "untranslated region" EXACT []
1699 is_a: SO:0000836 ! mRNA_region
1703 name: five_prime_UTR
1704 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]
1706 synonym: "5' UTR" EXACT []
1707 synonym: "five prime UTR" EXACT []
1708 synonym: "five_prime_untranslated_region" EXACT []
1709 xref: http://en.wikipedia.org/wiki/5'_UTR "wiki"
1710 is_a: SO:0000203 ! UTR
1714 name: three_prime_UTR
1715 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]
1717 synonym: "three prime untranslated region" EXACT []
1718 synonym: "three prime UTR" EXACT []
1719 xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki"
1720 is_a: SO:0000203 ! UTR
1725 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]
1726 synonym: "Short interspersed element" EXACT []
1727 synonym: "Short interspersed nuclear element" EXACT []
1728 synonym: "SINE element" EXACT []
1729 xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element "wiki"
1730 is_a: SO:0000189 ! non_LTR_retrotransposon
1734 name: simple_sequence_length_variation
1735 synonym: "simple sequence length polymorphism" RELATED []
1736 synonym: "simple sequence length variation" EXACT []
1737 synonym: "SSLP" RELATED []
1738 is_a: SO:0000248 ! sequence_length_variation
1742 name: terminal_inverted_repeat_element
1743 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]
1744 synonym: "terminal inverted repeat element" EXACT []
1745 synonym: "TIR element" EXACT []
1746 is_a: SO:0000182 ! DNA_transposon
1750 name: rRNA_primary_transcript
1751 def: "A primary transcript encoding a ribosomal RNA." [SO:ke]
1753 synonym: "ribosomal RNA primary transcript" EXACT []
1754 synonym: "rRNA primary transcript" EXACT []
1755 is_a: SO:0000483 ! nc_primary_transcript
1759 name: tRNA_primary_transcript
1760 def: "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]
1761 synonym: "tRNA primary transcript" EXACT []
1762 is_a: SO:0000483 ! nc_primary_transcript
1766 name: alanine_tRNA_primary_transcript
1767 def: "A primary transcript encoding alanyl tRNA." [SO:ke]
1768 synonym: "alanine tRNA primary transcript" EXACT []
1769 is_a: SO:0000210 ! tRNA_primary_transcript
1773 name: arginine_tRNA_primary_transcript
1774 def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]
1775 synonym: "arginine tRNA primary transcript" EXACT []
1776 is_a: SO:0000210 ! tRNA_primary_transcript
1780 name: asparagine_tRNA_primary_transcript
1781 def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]
1782 synonym: "asparagine tRNA primary transcript" EXACT []
1783 is_a: SO:0000210 ! tRNA_primary_transcript
1787 name: aspartic_acid_tRNA_primary_transcript
1788 def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]
1789 synonym: "aspartic acid tRNA primary transcript" EXACT []
1790 is_a: SO:0000210 ! tRNA_primary_transcript
1794 name: cysteine_tRNA_primary_transcript
1795 def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]
1796 synonym: "cysteine tRNA primary transcript" EXACT []
1797 is_a: SO:0000210 ! tRNA_primary_transcript
1801 name: glutamic_acid_tRNA_primary_transcript
1802 def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]
1803 synonym: "glutamic acid tRNA primary transcript" EXACT []
1804 is_a: SO:0000210 ! tRNA_primary_transcript
1808 name: glutamine_tRNA_primary_transcript
1809 def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]
1810 synonym: "glutamine tRNA primary transcript" EXACT []
1811 is_a: SO:0000210 ! tRNA_primary_transcript
1815 name: glycine_tRNA_primary_transcript
1816 def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]
1817 synonym: "glycine tRNA primary transcript" EXACT []
1818 is_a: SO:0000210 ! tRNA_primary_transcript
1822 name: histidine_tRNA_primary_transcript
1823 def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]
1824 synonym: "histidine tRNA primary transcript" EXACT []
1825 is_a: SO:0000210 ! tRNA_primary_transcript
1829 name: isoleucine_tRNA_primary_transcript
1830 def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]
1831 synonym: "isoleucine tRNA primary transcript" EXACT []
1832 is_a: SO:0000210 ! tRNA_primary_transcript
1836 name: leucine_tRNA_primary_transcript
1837 def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]
1838 synonym: "leucine tRNA primary transcript" EXACT []
1839 is_a: SO:0000210 ! tRNA_primary_transcript
1843 name: lysine_tRNA_primary_transcript
1844 def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]
1845 synonym: "lysine tRNA primary transcript" EXACT []
1846 is_a: SO:0000210 ! tRNA_primary_transcript
1850 name: methionine_tRNA_primary_transcript
1851 def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]
1852 synonym: "methionine tRNA primary transcript" EXACT []
1853 is_a: SO:0000210 ! tRNA_primary_transcript
1857 name: phenylalanine_tRNA_primary_transcript
1858 def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]
1859 synonym: "phenylalanine tRNA primary transcript" EXACT []
1860 is_a: SO:0000210 ! tRNA_primary_transcript
1864 name: proline_tRNA_primary_transcript
1865 def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]
1866 synonym: "proline tRNA primary transcript" EXACT []
1867 is_a: SO:0000210 ! tRNA_primary_transcript
1871 name: serine_tRNA_primary_transcript
1872 def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
1873 synonym: "serine tRNA primary transcript" EXACT []
1874 is_a: SO:0000210 ! tRNA_primary_transcript
1878 name: threonine_tRNA_primary_transcript
1879 def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]
1880 synonym: "threonine tRNA primary transcript" EXACT []
1881 is_a: SO:0000210 ! tRNA_primary_transcript
1885 name: tryptophan_tRNA_primary_transcript
1886 def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]
1887 synonym: "tryptophan tRNA primary transcript" EXACT []
1888 is_a: SO:0000210 ! tRNA_primary_transcript
1892 name: tyrosine_tRNA_primary_transcript
1893 def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]
1894 synonym: "tyrosine tRNA primary transcript" EXACT []
1895 is_a: SO:0000210 ! tRNA_primary_transcript
1899 name: valine_tRNA_primary_transcript
1900 def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]
1901 synonym: "valine tRNA primary transcript" EXACT []
1902 is_a: SO:0000210 ! tRNA_primary_transcript
1906 name: snRNA_primary_transcript
1907 def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]
1908 synonym: "snRNA primary transcript" EXACT []
1909 is_a: SO:0000483 ! nc_primary_transcript
1913 name: snoRNA_primary_transcript
1914 def: "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]
1915 synonym: "snoRNA primary transcript" EXACT []
1916 is_a: SO:0000483 ! nc_primary_transcript
1920 name: mature_transcript
1921 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]
1922 comment: A processed transcript cannot contain introns.
1924 synonym: "mature transcript" EXACT []
1925 xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki"
1926 is_a: SO:0000673 ! transcript
1927 relationship: derives_from SO:0000185 ! primary_transcript
1932 def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]
1933 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.
1935 synonym: "messenger RNA" EXACT []
1936 xref: http://en.wikipedia.org/wiki/MRNA "wiki"
1937 is_a: SO:0000233 ! mature_transcript
1941 name: TF_binding_site
1942 def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]
1944 synonym: "TF binding site" EXACT []
1945 synonym: "transcription factor binding site" EXACT []
1946 is_a: SO:0001654 ! nucleotide_to_protein_binding_site
1947 is_a: SO:0001679 ! transcription_regulatory_region
1952 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]
1953 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.
1955 synonym: "open reading frame" EXACT []
1956 is_a: SO:0000717 ! reading_frame
1960 name: transcript_attribute
1961 synonym: "transcript attribute" EXACT []
1962 is_a: SO:0000733 ! feature_attribute
1966 name: foldback_element
1967 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]
1968 synonym: "foldback element" EXACT []
1969 synonym: "long inverted repeat element" RELATED []
1970 synonym: "LVR element" RELATED []
1971 is_a: SO:0000182 ! DNA_transposon
1975 name: flanking_region
1976 def: "The sequences extending on either side of a specific region." [SO:ke]
1978 synonym: "flanking region" EXACT []
1979 is_a: SO:0001412 ! topologically_defined_region
1983 name: chromosome_variation
1984 synonym: "chromosome variation" EXACT []
1985 is_a: SO:0001507 ! variant_collection
1986 disjoint_from: SO:0000400 ! sequence_attribute
1987 relationship: part_of SO:0001524 ! chromosomally_aberrant_genome
1992 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]
1993 synonym: "internal UTR" EXACT []
1994 is_a: SO:0000203 ! UTR
1998 name: untranslated_region_polycistronic_mRNA
1999 def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]
2000 synonym: "untranslated region polycistronic mRNA" EXACT []
2001 is_a: SO:0000203 ! UTR
2005 name: internal_ribosome_entry_site
2006 def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]
2007 synonym: "internal ribosomal entry sequence" EXACT []
2008 synonym: "internal ribosomal entry site" EXACT []
2009 synonym: "internal ribosome entry sequence" RELATED []
2010 synonym: "internal ribosome entry site" EXACT []
2011 synonym: "IRES" EXACT []
2012 xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site "wiki"
2013 is_a: SO:0000139 ! ribosome_entry_site
2017 name: four_cutter_restriction_site
2018 synonym: "4-cutter_restriction_site" RELATED []
2019 synonym: "four-cutter_restriction_sit" RELATED []
2024 name: mRNA_by_polyadenylation_status
2029 name: polyadenylated
2030 def: "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]
2031 is_a: SO:0000863 ! mRNA_attribute
2035 name: mRNA_not_polyadenylated
2040 name: sequence_length_variation
2041 synonym: "sequence length variation" EXACT []
2042 is_a: SO:1000002 ! substitution
2046 name: six_cutter_restriction_site
2047 synonym: "6-cutter_restriction_site" RELATED []
2048 synonym: "six-cutter_restriction_site" RELATED []
2053 name: modified_RNA_base_feature
2054 def: "A post_transcriptionally modified base." [SO:ke]
2055 synonym: "modified RNA base feature" EXACT []
2056 is_a: SO:0001236 ! base
2060 name: eight_cutter_restriction_site
2061 synonym: "8-cutter_restriction_site" RELATED []
2062 synonym: "eight-cutter_restriction_site" RELATED []
2068 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]
2070 synonym: "ribosomal ribonucleic acid" EXACT []
2071 synonym: "ribosomal RNA" EXACT []
2072 xref: http://en.wikipedia.org/wiki/RRNA "wiki"
2073 is_a: SO:0000655 ! ncRNA
2074 relationship: derives_from SO:0000209 ! rRNA_primary_transcript
2079 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]
2080 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
2082 synonym: "transfer ribonucleic acid" RELATED []
2083 synonym: "transfer RNA" RELATED []
2084 xref: http://en.wikipedia.org/wiki/TRNA "wiki"
2085 is_a: SO:0000655 ! ncRNA
2086 relationship: derives_from SO:0000210 ! tRNA_primary_transcript
2091 def: "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]
2092 synonym: "alanyl tRNA" EXACT []
2093 synonym: "alanyl-transfer ribonucleic acid" EXACT []
2094 synonym: "alanyl-transfer RNA" EXACT []
2095 is_a: SO:0000253 ! tRNA
2096 relationship: derives_from SO:0000211 ! alanine_tRNA_primary_transcript
2100 name: rRNA_small_subunit_primary_transcript
2101 def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]
2102 synonym: "rRNA small subunit primary transcript" EXACT []
2103 is_a: SO:0000209 ! rRNA_primary_transcript
2107 name: asparaginyl_tRNA
2108 def: "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]
2109 synonym: "asparaginyl tRNA" EXACT []
2110 synonym: "asparaginyl-transfer ribonucleic acid" EXACT []
2111 synonym: "asparaginyl-transfer RNA" EXACT []
2112 is_a: SO:0000253 ! tRNA
2113 relationship: derives_from SO:0000213 ! asparagine_tRNA_primary_transcript
2118 def: "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]
2119 synonym: "aspartyl tRNA" EXACT []
2120 synonym: "aspartyl-transfer ribonucleic acid" EXACT []
2121 synonym: "aspartyl-transfer RNA" EXACT []
2122 is_a: SO:0000253 ! tRNA
2123 relationship: derives_from SO:0000214 ! aspartic_acid_tRNA_primary_transcript
2127 name: cysteinyl_tRNA
2128 def: "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]
2129 synonym: "cysteinyl tRNA" EXACT []
2130 synonym: "cysteinyl-transfer ribonucleic acid" EXACT []
2131 synonym: "cysteinyl-transfer RNA" EXACT []
2132 is_a: SO:0000253 ! tRNA
2133 relationship: derives_from SO:0000215 ! cysteine_tRNA_primary_transcript
2137 name: glutaminyl_tRNA
2138 def: "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]
2139 synonym: "glutaminyl tRNA" EXACT []
2140 synonym: "glutaminyl-transfer ribonucleic acid" EXACT []
2141 synonym: "glutaminyl-transfer RNA" EXACT []
2142 is_a: SO:0000253 ! tRNA
2143 relationship: derives_from SO:0000216 ! glutamic_acid_tRNA_primary_transcript
2148 def: "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]
2149 synonym: "glutamyl tRNA" EXACT []
2150 synonym: "glutamyl-transfer ribonucleic acid" EXACT []
2151 synonym: "glutamyl-transfer RNA" RELATED []
2152 is_a: SO:0000253 ! tRNA
2153 relationship: derives_from SO:0000217 ! glutamine_tRNA_primary_transcript
2158 def: "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]
2159 synonym: "glycyl tRNA" EXACT []
2160 synonym: "glycyl-transfer ribonucleic acid" RELATED []
2161 synonym: "glycyl-transfer RNA" RELATED []
2162 is_a: SO:0000253 ! tRNA
2163 relationship: derives_from SO:0000218 ! glycine_tRNA_primary_transcript
2168 def: "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]
2169 synonym: "histidyl tRNA" EXACT []
2170 synonym: "histidyl-transfer ribonucleic acid" EXACT []
2171 synonym: "histidyl-transfer RNA" EXACT []
2172 is_a: SO:0000253 ! tRNA
2173 relationship: derives_from SO:0000219 ! histidine_tRNA_primary_transcript
2177 name: isoleucyl_tRNA
2178 def: "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]
2179 synonym: "isoleucyl tRNA" EXACT []
2180 synonym: "isoleucyl-transfer ribonucleic acid" EXACT []
2181 synonym: "isoleucyl-transfer RNA" EXACT []
2182 is_a: SO:0000253 ! tRNA
2183 relationship: derives_from SO:0000220 ! isoleucine_tRNA_primary_transcript
2188 def: "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]
2189 synonym: "leucyl tRNA" EXACT []
2190 synonym: "leucyl-transfer ribonucleic acid" EXACT []
2191 synonym: "leucyl-transfer RNA" EXACT []
2192 is_a: SO:0000253 ! tRNA
2193 relationship: derives_from SO:0000221 ! leucine_tRNA_primary_transcript
2198 def: "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]
2199 synonym: "lysyl tRNA" EXACT []
2200 synonym: "lysyl-transfer ribonucleic acid" EXACT []
2201 synonym: "lysyl-transfer RNA" EXACT []
2202 is_a: SO:0000253 ! tRNA
2203 relationship: derives_from SO:0000222 ! lysine_tRNA_primary_transcript
2207 name: methionyl_tRNA
2208 def: "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]
2209 synonym: "methionyl tRNA" EXACT []
2210 synonym: "methionyl-transfer ribonucleic acid" EXACT []
2211 synonym: "methionyl-transfer RNA" EXACT []
2212 is_a: SO:0000253 ! tRNA
2213 relationship: derives_from SO:0000223 ! methionine_tRNA_primary_transcript
2217 name: phenylalanyl_tRNA
2218 def: "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]
2219 synonym: "phenylalanyl tRNA" EXACT []
2220 synonym: "phenylalanyl-transfer ribonucleic acid" EXACT []
2221 synonym: "phenylalanyl-transfer RNA" EXACT []
2222 is_a: SO:0000253 ! tRNA
2223 relationship: derives_from SO:0000224 ! phenylalanine_tRNA_primary_transcript
2228 def: "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]
2229 synonym: "prolyl tRNA" EXACT []
2230 synonym: "prolyl-transfer ribonucleic acid" EXACT []
2231 synonym: "prolyl-transfer RNA" EXACT []
2232 is_a: SO:0000253 ! tRNA
2233 relationship: derives_from SO:0000225 ! proline_tRNA_primary_transcript
2238 def: "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]
2239 synonym: "seryl tRNA" EXACT []
2240 synonym: "seryl-transfer ribonucleic acid" RELATED []
2241 synonym: "seryl-transfer RNA" EXACT []
2242 is_a: SO:0000253 ! tRNA
2243 relationship: derives_from SO:0000226 ! serine_tRNA_primary_transcript
2248 def: "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]
2249 synonym: "threonyl tRNA" EXACT []
2250 synonym: "threonyl-transfer ribonucleic acid" EXACT []
2251 synonym: "threonyl-transfer RNA" RELATED []
2252 is_a: SO:0000253 ! tRNA
2253 relationship: derives_from SO:0000227 ! threonine_tRNA_primary_transcript
2257 name: tryptophanyl_tRNA
2258 def: "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]
2259 synonym: "tryptophanyl tRNA" EXACT []
2260 synonym: "tryptophanyl-transfer ribonucleic acid" EXACT []
2261 synonym: "tryptophanyl-transfer RNA" EXACT []
2262 is_a: SO:0000253 ! tRNA
2263 relationship: derives_from SO:0000228 ! tryptophan_tRNA_primary_transcript
2268 def: "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]
2269 synonym: "tyrosyl tRNA" EXACT []
2270 synonym: "tyrosyl-transfer ribonucleic acid" EXACT []
2271 synonym: "tyrosyl-transfer RNA" RELATED []
2272 is_a: SO:0000253 ! tRNA
2273 relationship: derives_from SO:0000229 ! tyrosine_tRNA_primary_transcript
2278 def: "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]
2279 synonym: "valyl tRNA" EXACT []
2280 synonym: "valyl-transfer ribonucleic acid" EXACT []
2281 synonym: "valyl-transfer RNA" RELATED []
2282 is_a: SO:0000253 ! tRNA
2283 relationship: derives_from SO:0000230 ! valine_tRNA_primary_transcript
2288 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]
2289 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
2291 synonym: "small nuclear RNA" EXACT []
2292 xref: http://en.wikipedia.org/wiki/SnRNA "wiki"
2293 is_a: SO:0000655 ! ncRNA
2294 relationship: derives_from SO:0000231 ! snRNA_primary_transcript
2299 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]
2301 synonym: "small nucleolar RNA" EXACT []
2302 xref: http://en.wikipedia.org/wiki/SnoRNA "wiki"
2303 is_a: SO:0000655 ! ncRNA
2304 relationship: derives_from SO:0000232 ! snoRNA_primary_transcript
2310 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]
2312 synonym: "micro RNA" EXACT []
2313 synonym: "microRNA" EXACT []
2314 synonym: "small temporal RNA" EXACT []
2315 synonym: "stRNA" EXACT []
2316 xref: http://en.wikipedia.org/wiki/MiRNA "wiki"
2317 xref: http://en.wikipedia.org/wiki/StRNA "wiki"
2318 is_a: SO:0000370 ! small_regulatory_ncRNA
2319 relationship: part_of SO:0001244 ! pre_miRNA
2323 name: bound_by_factor
2324 def: "An attribute describing a sequence that is bound by another molecule." [SO:ke]
2325 comment: Formerly called transcript_by_bound_factor.
2326 synonym: "bound by factor" EXACT []
2327 is_a: SO:0000733 ! feature_attribute
2331 name: transcript_bound_by_nucleic_acid
2332 def: "A transcript that is bound by a nucleic acid." [SO:xp]
2333 comment: Formerly called transcript_by_bound_nucleic_acid.
2334 synonym: "transcript bound by nucleic acid" EXACT []
2335 is_a: SO:0000673 ! transcript
2336 relationship: has_quality SO:0000876 ! bound_by_nucleic_acid
2340 name: transcript_bound_by_protein
2341 def: "A transcript that is bound by a protein." [SO:xp]
2342 comment: Formerly called transcript_by_bound_protein.
2343 synonym: "transcript bound by protein" EXACT []
2344 is_a: SO:0000673 ! transcript
2345 relationship: has_quality SO:0000875 ! bound_by_protein
2349 name: engineered_gene
2350 def: "A gene that is engineered." [SO:xp]
2351 synonym: "engineered gene" EXACT []
2352 is_a: SO:0000704 ! gene
2353 is_a: SO:0000804 ! engineered_region
2354 relationship: has_quality SO:0000783 ! engineered
2358 name: engineered_foreign_gene
2359 def: "A gene that is engineered and foreign." [SO:xp]
2360 synonym: "engineered foreign gene" EXACT []
2361 is_a: SO:0000280 ! engineered_gene
2362 is_a: SO:0000285 ! foreign_gene
2363 is_a: SO:0000805 ! engineered_foreign_region
2364 relationship: has_quality SO:0000783 ! engineered
2365 relationship: has_quality SO:0000784 ! foreign
2369 name: mRNA_with_minus_1_frameshift
2370 def: "An mRNA with a minus 1 frameshift." [SO:xp]
2371 synonym: "mRNA with minus 1 frameshift" EXACT []
2372 is_a: SO:0000108 ! mRNA_with_frameshift
2373 relationship: has_quality SO:0000866 ! minus_1_frameshift
2377 name: engineered_foreign_transposable_element_gene
2378 def: "A transposable_element that is engineered and foreign." [SO:xp]
2379 synonym: "engineered foreign transposable element gene" EXACT []
2380 is_a: SO:0000111 ! transposable_element_gene
2381 is_a: SO:0000281 ! engineered_foreign_gene
2382 relationship: has_quality SO:0000783 ! engineered
2383 relationship: has_quality SO:0000784 ! foreign
2387 name: type_I_enzyme_restriction_site
2388 def: "The recognition site is bipartite and interrupted." [http://www.promega.com]
2394 def: "A gene that is foreign." [SO:xp]
2395 synonym: "foreign gene" EXACT []
2396 is_a: SO:0000704 ! gene
2397 relationship: has_quality SO:0000784 ! foreign
2401 name: long_terminal_repeat
2402 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]
2403 synonym: "direct terminal repeat" RELATED []
2404 synonym: "long terminal repeat" EXACT []
2405 synonym: "LTR" EXACT []
2406 xref: http://en.wikipedia.org/wiki/Long_terminal_repeat "wiki"
2407 is_a: SO:0000657 ! repeat_region
2408 relationship: part_of SO:0000186 ! LTR_retrotransposon
2413 def: "A gene that is a fusion." [SO:xp]
2414 synonym: "fusion gene" EXACT []
2415 xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki"
2416 is_a: SO:0000704 ! gene
2417 relationship: has_quality SO:0000806 ! fusion
2421 name: engineered_fusion_gene
2422 def: "A fusion gene that is engineered." [SO:xp]
2423 synonym: "engineered fusion gene" EXACT []
2424 is_a: SO:0000280 ! engineered_gene
2425 is_a: SO:0000287 ! fusion_gene
2426 relationship: has_quality SO:0000783 ! engineered
2430 name: microsatellite
2431 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]
2433 synonym: "microsatellite locus" EXACT []
2434 synonym: "microsatellite marker" EXACT []
2435 synonym: "VNTR" EXACT []
2436 xref: http://en.wikipedia.org/wiki/Microsatellite "wiki"
2437 is_a: SO:0000005 ! satellite_DNA
2441 name: dinucleotide_repeat_microsatellite_feature
2442 synonym: "dinucleotide repeat microsatellite" EXACT []
2443 synonym: "dinucleotide repeat microsatellite feature" EXACT []
2444 synonym: "dinucleotide repeat microsatellite locus" EXACT []
2445 synonym: "dinucleotide repeat microsatellite marker" EXACT []
2446 is_a: SO:0000289 ! microsatellite
2450 name: trinucleotide_repeat_microsatellite_feature
2451 synonym: "dinucleotide repeat microsatellite marker" RELATED []
2452 synonym: "rinucleotide repeat microsatellite" EXACT []
2453 synonym: "trinucleotide repeat microsatellite feature" EXACT []
2454 synonym: "trinucleotide repeat microsatellite locus" EXACT []
2455 is_a: SO:0000289 ! microsatellite
2459 name: repetitive_element
2464 name: engineered_foreign_repetitive_element
2465 def: "A repetitive element that is engineered and foreign." [SO:xp]
2466 synonym: "engineered foreign repetitive element" EXACT []
2467 is_a: SO:0000657 ! repeat_region
2468 is_a: SO:0000805 ! engineered_foreign_region
2469 relationship: has_quality SO:0000783 ! engineered
2470 relationship: has_quality SO:0000784 ! foreign
2474 name: inverted_repeat
2475 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]
2477 synonym: "inverted repeat" EXACT []
2478 synonym: "inverted repeat sequence" EXACT []
2479 xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki"
2480 is_a: SO:0000657 ! repeat_region
2485 def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]
2486 comment: May have either GT-AC or AT-AC 5' and 3' boundaries.
2487 synonym: "U12 intron" EXACT []
2488 synonym: "U12-dependent intron" EXACT []
2489 is_a: SO:0000662 ! spliceosomal_intron
2493 name: origin_of_replication
2494 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]
2496 synonym: "ori" EXACT []
2497 synonym: "origin of replication" EXACT []
2498 xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki"
2499 is_a: SO:0001411 ! biological_region
2500 relationship: part_of SO:0001235 ! replicon
2505 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]
2506 synonym: "D-loop" EXACT []
2507 synonym: "displacement loop" RELATED []
2508 xref: http://en.wikipedia.org/wiki/D_loop "wiki"
2509 is_a: SO:0000296 ! origin_of_replication
2513 name: recombination_feature
2514 synonym: "recombination feature" EXACT []
2515 is_a: SO:0001411 ! biological_region
2519 name: specific_recombination_site
2520 synonym: "specific recombination site" EXACT []
2521 is_a: SO:0000669 ! sequence_rearrangement_feature
2525 name: recombination_feature_of_rearranged_gene
2526 synonym: "recombination feature of rearranged gene" EXACT []
2527 is_a: SO:0000299 ! specific_recombination_site
2531 name: vertebrate_immune_system_gene_recombination_feature
2532 synonym: "vertebrate immune system gene recombination feature" EXACT []
2533 is_a: SO:0000300 ! recombination_feature_of_rearranged_gene
2537 name: J_gene_recombination_feature
2538 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#]
2539 synonym: "J gene recombination feature" EXACT []
2540 synonym: "J-RS" EXACT []
2541 is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
2546 def: "Part of the primary transcript that is clipped off during processing." [SO:ke]
2548 is_a: SO:0000835 ! primary_transcript_region
2552 name: type_II_enzyme_restriction_site
2553 def: "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com]
2558 name: modified_DNA_base
2559 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]
2560 comment: Modified base:<modified_base>.
2562 synonym: "modified base site" EXACT []
2563 is_a: SO:0001236 ! base
2564 is_a: SO:0001720 ! epigenetically_modified_region
2568 name: methylated_DNA_base_feature
2569 def: "A nucleotide modified by methylation." [SO:ke]
2571 synonym: "methylated base feature" EXACT []
2572 is_a: SO:0000305 ! modified_DNA_base
2577 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]
2579 synonym: "CG island" EXACT []
2580 synonym: "CpG island" EXACT []
2581 xref: http://en.wikipedia.org/wiki/CpG_island "wiki"
2582 is_a: SO:0001411 ! biological_region
2586 name: sequence_feature_locating_method
2591 name: computed_feature
2596 name: predicted_ab_initio_computation
2601 name: computed_feature_by_similarity
2603 comment: similar to:<sequence_id>
2608 name: experimentally_determined
2609 def: "Attribute to describe a feature that has been experimentally verified." [SO:ke]
2610 synonym: "experimentally determined" EXACT []
2611 is_a: SO:0000789 ! validated
2617 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]
2618 synonym: "RNA_hairpin_loop" EXACT []
2619 synonym: "stem loop" EXACT []
2620 synonym: "stem-loop" EXACT []
2621 xref: http://en.wikipedia.org/wiki/Stem_loop "wiki"
2622 is_a: SO:0000122 ! RNA_sequence_secondary_structure
2627 def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke]
2629 synonym: "direct repeat" EXACT []
2630 xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki"
2631 is_a: SO:0000657 ! repeat_region
2636 def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]
2638 synonym: "transcription start site" EXACT []
2639 synonym: "transcription_start_site" EXACT []
2640 is_a: SO:0000835 ! primary_transcript_region
2645 def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]
2647 synonym: "coding sequence" EXACT []
2648 synonym: "coding_sequence" EXACT []
2649 is_a: SO:0000836 ! mRNA_region
2654 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]
2655 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
2656 synonym: "cDNA clone" EXACT []
2657 is_a: SO:0000151 ! clone
2658 relationship: has_quality SO:0000756 ! cDNA
2663 def: "First codon to be translated by a ribosome." [SO:ke]
2665 synonym: "initiation codon" EXACT []
2666 synonym: "start codon" EXACT []
2667 xref: http://en.wikipedia.org/wiki/Start_codon "wiki"
2668 is_a: SO:0000360 ! codon
2673 def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]
2675 synonym: "stop codon" EXACT []
2676 xref: http://en.wikipedia.org/wiki/Stop_codon "wiki"
2677 is_a: SO:0000360 ! codon
2681 name: intronic_splice_enhancer
2682 def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke]
2683 synonym: "intronic splice enhancer" EXACT []
2684 is_a: SO:0000344 ! splice_enhancer
2685 relationship: part_of SO:0000841 ! spliceosomal_intron_region
2689 name: mRNA_with_plus_1_frameshift
2690 def: "An mRNA with a plus 1 frameshift." [SO:ke]
2691 synonym: "mRNA with plus 1 frameshift" EXACT []
2692 is_a: SO:0000108 ! mRNA_with_frameshift
2693 relationship: has_quality SO:0000868 ! plus_1_frameshift
2697 name: nuclease_hypersensitive_site
2698 synonym: "nuclease hypersensitive site" EXACT []
2699 is_a: SO:0000684 ! nuclease_sensitive_site
2704 def: "The first base to be translated into protein." [SO:ke]
2705 synonym: "coding start" EXACT []
2706 synonym: "translation initiation site" EXACT []
2707 synonym: "translation start" RELATED []
2708 is_a: SO:0000851 ! CDS_region
2713 def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]
2715 is_a: SO:0000696 ! oligo
2719 name: rRNA_large_subunit_primary_transcript
2720 def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]
2722 synonym: "35S rRNA primary transcript" EXACT []
2723 synonym: "rRNA large subunit primary transcript" EXACT []
2724 is_a: SO:0000209 ! rRNA_primary_transcript
2729 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]
2731 synonym: "SAGE tag" EXACT []
2732 is_a: SO:0000324 ! tag
2737 def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke]
2738 synonym: "coding end" EXACT []
2739 synonym: "translation termination site" EXACT []
2740 synonym: "translation_end" EXACT []
2741 is_a: SO:0000851 ! CDS_region
2745 name: microarray_oligo
2746 synonym: "microarray oligo" EXACT []
2747 synonym: "microarray oligonucleotide" EXACT []
2748 is_a: SO:0000051 ! probe
2752 name: mRNA_with_plus_2_frameshift
2753 def: "An mRNA with a plus 2 frameshift." [SO:xp]
2754 synonym: "mRNA with plus 2 frameshift" EXACT []
2755 is_a: SO:0000108 ! mRNA_with_frameshift
2756 relationship: has_quality SO:0000869 ! plus_2_framshift
2760 name: conserved_region
2761 def: "Region of sequence similarity by descent from a common ancestor." [SO:ke]
2763 synonym: "conserved region" EXACT []
2764 xref: http://en.wikipedia.org/wiki/Conserved_region "wiki"
2765 is_a: SO:0001410 ! experimental_feature
2770 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]
2772 synonym: "sequence tag site" EXACT []
2773 is_a: SO:0000324 ! tag
2777 name: coding_conserved_region
2778 def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke]
2780 synonym: "coding conserved region" EXACT []
2781 is_a: SO:0000330 ! conserved_region
2786 def: "The boundary between two exons in a processed transcript." [SO:ke]
2788 synonym: "exon junction" EXACT []
2789 is_a: SO:0000699 ! junction
2790 relationship: part_of SO:0000233 ! mature_transcript
2794 name: nc_conserved_region
2795 def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]
2797 synonym: "nc conserved region" EXACT []
2798 synonym: "noncoding conserved region" EXACT []
2799 is_a: SO:0000330 ! conserved_region
2803 name: mRNA_with_minus_2_frameshift
2804 def: "A mRNA with a minus 2 frameshift." [SO:ke]
2805 synonym: "mRNA with minus 2 frameshift" EXACT []
2806 is_a: SO:0000108 ! mRNA_with_frameshift
2807 relationship: has_quality SO:0000867 ! minus_2_frameshift
2812 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]
2814 xref: http://en.wikipedia.org/wiki/Pseudogene "wiki"
2815 is_a: SO:0001411 ! biological_region
2816 relationship: non_functional_homolog_of SO:0000704 ! gene
2821 def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]
2823 synonym: "RNAi reagent" EXACT []
2824 is_a: SO:0000442 ! ds_oligo
2829 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]
2830 synonym: "miniature inverted repeat transposable element" EXACT []
2831 is_a: SO:0000208 ! terminal_inverted_repeat_element
2835 name: recombination_hotspot
2836 def: "A region in a genome which promotes recombination." [SO:rd]
2837 synonym: "recombination hotspot" EXACT []
2838 xref: http://en.wikipedia.org/wiki/Recombination_hotspot "wiki"
2839 is_a: SO:0000298 ! recombination_feature
2844 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]
2845 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
2847 xref: http://en.wikipedia.org/wiki/Chromosome "wiki"
2848 is_a: SO:0001235 ! replicon
2852 name: chromosome_band
2853 def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]
2855 synonym: "chromosome band" EXACT []
2856 synonym: "cytoband" EXACT []
2857 synonym: "cytological band" EXACT []
2858 xref: http://en.wikipedia.org/wiki/Cytological_band "wiki"
2859 is_a: SO:0000830 ! chromosome_part
2863 name: site_specific_recombination_target_region
2864 synonym: "site specific recombination target region" EXACT []
2865 is_a: SO:0000299 ! specific_recombination_site
2870 def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]
2872 is_a: SO:0001410 ! experimental_feature
2876 name: splice_enhancer
2877 def: "Region of a transcript that regulates splicing." [SO:ke]
2879 synonym: "splice enhancer" EXACT []
2880 is_a: SO:0000165 ! enhancer
2881 is_a: SO:0001056 ! splicing_regulatory_region
2886 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]
2887 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
2889 synonym: "expressed sequence tag" EXACT []
2890 is_a: SO:0000324 ! tag
2891 relationship: derives_from SO:0000234 ! mRNA
2896 synonym: "Cre-recombination target region" RELATED []
2897 synonym: "loxP site" EXACT []
2898 is_a: SO:0000947 ! resolution_site
2902 name: nucleotide_match
2903 def: "A match against a nucleotide sequence." [SO:ke]
2905 synonym: "nucleotide match" EXACT []
2906 is_a: SO:0000343 ! match
2911 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]
2912 synonym: "nucleic acid" EXACT []
2913 xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki"
2914 is_a: SO:0000443 ! polymer_attribute
2919 def: "A match against a protein sequence." [SO:ke]
2921 synonym: "protein match" EXACT []
2922 is_a: SO:0000343 ! match
2927 def: "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]
2928 synonym: "FLP recombination target region" EXACT []
2929 synonym: "FRT site" EXACT []
2930 is_a: SO:0000948 ! inversion_site
2934 name: synthetic_sequence
2935 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]
2936 synonym: "synthetic sequence" EXACT []
2937 is_a: SO:0000443 ! polymer_attribute
2942 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]
2943 is_a: SO:0000348 ! nucleic_acid
2947 name: sequence_assembly
2948 def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]
2950 synonym: "sequence assembly" EXACT []
2951 xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki"
2952 is_a: SO:0001248 ! assembly
2956 name: group_1_intron_homing_endonuclease_target_region
2957 def: "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]
2958 synonym: "group 1 intron homing endonuclease target region" EXACT []
2959 is_a: SO:0000684 ! nuclease_sensitive_site
2963 name: haplotype_block
2964 def: "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]
2965 synonym: "haplotype block" EXACT []
2966 is_a: SO:0000298 ! recombination_feature
2971 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]
2972 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
2973 is_a: SO:0000348 ! nucleic_acid
2978 def: "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]
2979 is_a: SO:0000733 ! feature_attribute
2984 def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]
2985 xref: http://en.wikipedia.org/wiki/Floxed "wiki"
2986 is_a: SO:0000357 ! flanked
2991 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]
2993 xref: http://en.wikipedia.org/wiki/Codon "wiki"
2994 is_a: SO:0000851 ! CDS_region
2999 def: "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]
3000 synonym: "FRT flanked" EXACT []
3001 is_a: SO:0000357 ! flanked
3005 name: invalidated_by_chimeric_cDNA
3006 def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]
3007 synonym: "invalidated by chimeric cDNA" EXACT []
3008 is_a: SO:0000790 ! invalidated
3013 def: "A transgene that is floxed." [SO:xp]
3014 synonym: "floxed gene" EXACT []
3015 is_a: SO:0000902 ! transgene
3016 relationship: has_quality SO:0000359 ! floxed
3020 name: transposable_element_flanking_region
3021 def: "The region of sequence surrounding a transposable element." [SO:ke]
3022 synonym: "transposable element flanking region" EXACT []
3023 is_a: SO:0000239 ! flanking_region
3028 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]
3029 xref: http://en.wikipedia.org/wiki/Integron "wiki"
3030 is_a: SO:0001039 ! integrated_mobile_genetic_element
3034 name: insertion_site
3035 def: "The junction where an insertion occurred." [SO:ke]
3037 synonym: "insertion site" EXACT []
3038 is_a: SO:0000699 ! junction
3043 def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]
3044 synonym: "attI site" EXACT []
3045 is_a: SO:0000946 ! integration_excision_site
3046 relationship: part_of SO:0000365 ! integron
3050 name: transposable_element_insertion_site
3051 def: "The junction in a genome where a transposable_element has inserted." [SO:ke]
3053 synonym: "transposable element insertion site" EXACT []
3054 is_a: SO:0000366 ! insertion_site
3058 name: integrase_coding_region
3063 name: small_regulatory_ncRNA
3064 def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
3066 synonym: "small regulatory ncRNA" EXACT []
3067 is_a: SO:0000655 ! ncRNA
3071 name: conjugative_transposon
3072 def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]
3073 synonym: "conjugative transposon" EXACT []
3074 is_a: SO:0000182 ! DNA_transposon
3079 def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
3080 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.
3082 synonym: "enzymatic RNA" EXACT []
3083 is_a: SO:0000673 ! transcript
3084 relationship: has_quality SO:0001185 ! enzymatic
3088 name: recombinationally_inverted_gene
3089 def: "A recombinationally rearranged gene by inversion." [SO:xp]
3090 synonym: "recombinationally inverted gene" EXACT []
3091 is_a: SO:0000456 ! recombinationally_rearranged_gene
3092 relationship: has_quality SO:1000036 ! inversion
3097 def: "An RNA with catalytic activity." [SO:ma]
3099 xref: http://en.wikipedia.org/wiki/Ribozyme "wiki"
3100 is_a: SO:0000372 ! enzymatic_RNA
3101 relationship: has_quality SO:0001186 ! ribozymic
3106 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]
3108 synonym: "5.8S LSU rRNA" EXACT []
3109 synonym: "5.8S ribosomal RNA" EXACT []
3110 synonym: "5.8S rRNA" EXACT []
3111 synonym: "rRNA 5 8S" EXACT []
3112 xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki"
3113 is_a: SO:0000651 ! large_subunit_rRNA
3118 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]
3119 synonym: "6S RNA" EXACT []
3120 synonym: "RNA 6S" EXACT []
3121 xref: http://en.wikipedia.org/wiki/6S_RNA "wiki"
3122 is_a: SO:0000370 ! small_regulatory_ncRNA
3127 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]
3128 synonym: "CsrB RsmB RNA" EXACT []
3129 synonym: "CsrB-RsmB RNA" EXACT []
3130 is_a: SO:0000370 ! small_regulatory_ncRNA
3135 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]
3136 synonym: "DsrA RNA" EXACT []
3137 xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki"
3138 is_a: SO:0000370 ! small_regulatory_ncRNA
3143 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]
3144 synonym: "GcvB RNA" EXACT []
3145 xref: http://en.wikipedia.org/wiki/GcvB_RNA "wiki"
3146 is_a: SO:0000378 ! DsrA_RNA
3150 name: hammerhead_ribozyme
3151 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]
3153 synonym: "hammerhead ribozyme" EXACT []
3154 xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki"
3155 is_a: SO:0000715 ! RNA_motif
3156 relationship: has_quality SO:0001186 ! ribozymic
3160 name: group_IIA_intron
3161 synonym: "group IIA intron" EXACT []
3162 is_a: SO:0000603 ! group_II_intron
3166 name: group_IIB_intron
3167 synonym: "group IIB intron" EXACT []
3168 is_a: SO:0000603 ! group_II_intron
3173 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]
3174 synonym: "MicF RNA" EXACT []
3175 xref: http://en.wikipedia.org/wiki/MicF_RNA "wiki"
3176 is_a: SO:0000644 ! antisense_RNA
3181 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]
3182 synonym: "OxyS RNA" EXACT []
3183 xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki"
3184 is_a: SO:0000370 ! small_regulatory_ncRNA
3189 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]
3191 synonym: "RNase MRP RNA" EXACT []
3192 is_a: SO:0000655 ! ncRNA
3197 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]
3199 synonym: "RNase P RNA" EXACT []
3200 is_a: SO:0000655 ! ncRNA
3205 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]
3206 synonym: "RprA RNA" EXACT []
3207 xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki"
3208 is_a: SO:0000370 ! small_regulatory_ncRNA
3213 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]
3214 synonym: "RRE RNA" EXACT []
3215 is_a: SO:0000370 ! small_regulatory_ncRNA
3220 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]
3221 synonym: "spot-42 RNA" EXACT []
3222 xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki"
3223 is_a: SO:0000370 ! small_regulatory_ncRNA
3227 name: telomerase_RNA
3228 def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
3230 synonym: "telomerase RNA" EXACT []
3231 xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki"
3232 is_a: SO:0000655 ! ncRNA
3237 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]
3239 synonym: "small nuclear RNA U1" EXACT [RSC:cb]
3240 synonym: "snRNA U1" EXACT [RSC:cb]
3241 synonym: "U1 small nuclear RNA" EXACT [RSC:cb]
3242 synonym: "U1 snRNA" EXACT []
3243 xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki"
3244 is_a: SO:0000274 ! snRNA
3249 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]
3251 synonym: "small nuclear RNA U2" EXACT [RSC:CB]
3252 synonym: "snRNA U2" EXACT [RSC:CB]
3253 synonym: "U2 small nuclear RNA" EXACT [RSC:CB]
3254 synonym: "U2 snRNA" EXACT []
3255 xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki"
3256 is_a: SO:0000274 ! snRNA
3261 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]
3263 synonym: "small nuclear RNA U4" EXACT [RSC:cb]
3264 synonym: "snRNA U4" EXACT [RSC:cb]
3265 synonym: "U4 small nuclear RNA" EXACT [RSC:cb]
3266 synonym: "U4 snRNA" EXACT []
3267 xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki"
3268 is_a: SO:0000274 ! snRNA
3273 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]
3275 synonym: "small nuclear RNA U4atac" EXACT [RSC:cb]
3276 synonym: "snRNA U4atac" EXACT [RSC:cb]
3277 synonym: "U4atac small nuclear RNA" EXACT [RSC:cb]
3278 synonym: "U4atac snRNA" EXACT []
3279 is_a: SO:0000274 ! snRNA
3284 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]
3286 synonym: "small nuclear RNA U5" EXACT [RSC:cb]
3287 synonym: "snRNA U5" EXACT [RSC:cb]
3288 synonym: "U5 small nuclear RNA" EXACT [RSC:cb]
3289 synonym: "U5 snRNA" EXACT []
3290 xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki"
3291 is_a: SO:0000274 ! snRNA
3296 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]
3298 synonym: "small nuclear RNA U6" EXACT [RSC:cb]
3299 synonym: "snRNA U6" EXACT [RSC:cb]
3300 synonym: "U6 small nuclear RNA" EXACT [RSC:cb]
3301 synonym: "U6 snRNA" EXACT []
3302 xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki"
3303 is_a: SO:0000274 ! snRNA
3308 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]
3310 synonym: "snRNA U6atac" EXACT [RSC:cb]
3311 synonym: "U6atac small nuclear RNA" EXACT [RSC:cb]
3312 synonym: "U6atac snRNA" EXACT [RSC:cb]
3313 is_a: SO:0000274 ! snRNA
3318 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]
3320 synonym: "small nuclear RNA U11" EXACT [RSC:cb]
3321 synonym: "snRNA U11" EXACT [RSC:cb]
3322 synonym: "U11 small nuclear RNA" EXACT [RSC:cb]
3323 synonym: "U11 snRNA" EXACT []
3324 xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki"
3325 is_a: SO:0000274 ! snRNA
3330 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]
3332 synonym: "small nuclear RNA U12" EXACT [RSC:cb]
3333 synonym: "snRNA U12" EXACT [RSC:cb]
3334 synonym: "U12 small nuclear RNA" EXACT [RSC:cb]
3335 synonym: "U12 snRNA" EXACT []
3336 xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki"
3337 is_a: SO:0000274 ! snRNA
3341 name: sequence_attribute
3342 def: "An attribute describes a quality of sequence." [SO:ke]
3343 synonym: "sequence attribute" EXACT []
3347 name: gene_attribute
3348 synonym: "gene attribute" EXACT []
3349 is_a: SO:0000733 ! feature_attribute
3353 name: enhancer_attribute
3360 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]
3361 comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
3363 synonym: "small nucleolar RNA U14" EXACT []
3364 synonym: "snoRNA U14" EXACT []
3365 synonym: "U14 small nucleolar RNA" EXACT []
3366 synonym: "U14 snoRNA" EXACT []
3367 is_a: SO:0000593 ! C_D_box_snoRNA
3368 relationship: derives_from SO:0005837 ! U14_snoRNA_primary_transcript
3373 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]
3375 synonym: "vault RNA" EXACT []
3376 xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki"
3377 is_a: SO:0000655 ! ncRNA
3382 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]
3384 synonym: "Y RNA" EXACT []
3385 xref: http://en.wikipedia.org/wiki/Y_RNA "wiki"
3386 is_a: SO:0000655 ! ncRNA
3391 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]
3392 xref: http://en.wikipedia.org/wiki/Twintron "wiki"
3393 is_a: SO:0000188 ! intron
3398 def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]
3400 synonym: "18S ribosomal RNA" EXACT []
3401 synonym: "18S rRNA" EXACT []
3402 synonym: "rRNA 18S" EXACT []
3403 xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki"
3404 is_a: SO:0000650 ! small_subunit_rRNA
3409 def: "The interbase position where something (eg an aberration) occurred." [SO:ke]
3416 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]
3417 comment: See GO:0005488 : binding.
3420 synonym: "binding_or_interaction_site" EXACT []
3421 synonym: "site" RELATED []
3422 xref: http://en.wikipedia.org/wiki/Binding_site "wiki"
3423 is_a: SO:0001411 ! biological_region
3427 name: protein_binding_site
3428 def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]
3429 comment: See GO:0042277 : peptide binding.
3431 synonym: "protein binding site" EXACT []
3432 is_a: SO:0000409 ! binding_site
3437 def: "A region that rescues." [SO:xp]
3438 synonym: "rescue fragment" EXACT []
3439 synonym: "rescue region" EXACT []
3440 synonym: "rescue segment" RELATED []
3441 is_a: SO:0000695 ! reagent
3442 relationship: has_quality SO:0000814 ! rescue
3446 name: restriction_fragment
3447 def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]
3449 synonym: "restriction fragment" EXACT []
3450 xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki"
3451 is_a: SO:0000143 ! assembly_component
3455 name: sequence_difference
3456 def: "A region where the sequence differs from that of a specified sequence." [SO:ke]
3458 synonym: "sequence difference" EXACT []
3459 is_a: SO:0000700 ! remark
3463 name: invalidated_by_genomic_contamination
3464 def: "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]
3465 synonym: "invalidated by genomic contamination" EXACT []
3466 is_a: SO:0000790 ! invalidated
3470 name: invalidated_by_genomic_polyA_primed_cDNA
3471 def: "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]
3472 synonym: "invalidated by genomic polyA primed cDNA" EXACT []
3473 is_a: SO:0000790 ! invalidated
3477 name: invalidated_by_partial_processing
3478 def: "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]
3479 synonym: "invalidated by partial processing" EXACT []
3480 is_a: SO:0000790 ! invalidated
3484 name: polypeptide_domain
3488 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]
3489 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.
3491 synonym: "domain" BROAD BS [uniprot:feature_type]
3492 synonym: "polypeptide domain" EXACT []
3493 synonym: "polypeptide_structural_domain" EXACT BS []
3494 synonym: "structural domain" BROAD BS []
3495 is_a: SO:0001070 ! polypeptide_structural_region
3496 is_a: SO:0100021 ! polypeptide_conserved_region
3500 name: signal_peptide
3502 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]
3503 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.
3506 synonym: "signal" RELATED [uniprot:feature_type]
3507 synonym: "signal peptide" EXACT []
3508 synonym: "signal peptide coding sequence" EXACT []
3509 xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki"
3510 is_a: SO:0001527 ! peptide_localization_signal
3511 relationship: part_of SO:0001062 ! propeptide
3515 name: mature_protein_region
3517 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]
3518 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.
3521 synonym: "chain" RELATED [uniprot:feature_type]
3522 synonym: "mature peptide" RELATED []
3523 synonym: "mature protein region" EXACT []
3524 is_a: SO:0000839 ! polypeptide_region
3525 relationship: part_of SO:0001063 ! immature_peptide_region
3529 name: five_prime_terminal_inverted_repeat
3530 synonym: "5' TIR" EXACT []
3531 synonym: "five prime terminal inverted repeat" EXACT []
3532 is_a: SO:0000481 ! terminal_inverted_repeat
3536 name: three_prime_terminal_inverted_repeat
3537 synonym: "3' TIR" EXACT []
3538 synonym: "three prime terminal inverted repeat" EXACT []
3539 is_a: SO:0000481 ! terminal_inverted_repeat
3544 synonym: "U5 long terminal repeat region" EXACT []
3545 synonym: "U5 LTR region" EXACT []
3546 is_a: SO:0000848 ! LTR_component
3551 synonym: "R long terminal repeat region" EXACT []
3552 synonym: "R LTR region" EXACT []
3553 is_a: SO:0000848 ! LTR_component
3558 synonym: "U3 long terminal repeat region" EXACT []
3559 synonym: "U3 LTR region" EXACT []
3560 is_a: SO:0000848 ! LTR_component
3564 name: five_prime_LTR
3565 synonym: "5' long terminal repeat" EXACT []
3566 synonym: "5' LTR" EXACT []
3567 synonym: "five prime LTR" EXACT []
3568 is_a: SO:0000286 ! long_terminal_repeat
3572 name: three_prime_LTR
3573 synonym: "3' long terminal repeat" EXACT []
3574 synonym: "3' LTR" EXACT []
3575 synonym: "three prime LTR" EXACT []
3576 is_a: SO:0000286 ! long_terminal_repeat
3580 name: R_five_prime_LTR_region
3581 synonym: "R 5' long term repeat region" EXACT []
3582 synonym: "R five prime LTR region" EXACT []
3583 is_a: SO:0000423 ! R_LTR_region
3584 is_a: SO:0000850 ! five_prime_LTR_component
3588 name: U5_five_prime_LTR_region
3589 synonym: "U5 5' long terminal repeat region" EXACT []
3590 synonym: "U5 five prime LTR region" EXACT []
3591 is_a: SO:0000422 ! U5_LTR_region
3592 is_a: SO:0000850 ! five_prime_LTR_component
3596 name: U3_five_prime_LTR_region
3597 synonym: "U3 5' long term repeat region" EXACT []
3598 synonym: "U3 five prime LTR region" EXACT []
3599 is_a: SO:0000424 ! U3_LTR_region
3600 is_a: SO:0000850 ! five_prime_LTR_component
3604 name: R_three_prime_LTR_region
3605 synonym: "R 3' long terminal repeat region" EXACT []
3606 synonym: "R three prime LTR region" EXACT []
3607 is_a: SO:0000849 ! three_prime_LTR_component
3611 name: U3_three_prime_LTR_region
3612 synonym: "U3 3' long terminal repeat region" EXACT []
3613 synonym: "U3 three prime LTR region" EXACT []
3614 is_a: SO:0000849 ! three_prime_LTR_component
3618 name: U5_three_prime_LTR_region
3619 synonym: "U5 3' long terminal repeat region" EXACT []
3620 synonym: "U5 three prime LTR region" EXACT []
3621 is_a: SO:0000849 ! three_prime_LTR_component
3625 name: non_LTR_retrotransposon_polymeric_tract
3626 def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]
3627 synonym: "non LTR retrotransposon polymeric tract" EXACT []
3628 is_a: SO:0000657 ! repeat_region
3629 is_a: SO:0000840 ! repeat_component
3630 relationship: part_of SO:0000189 ! non_LTR_retrotransposon
3634 name: target_site_duplication
3635 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]
3636 synonym: "target site duplication" EXACT []
3637 is_a: SO:0000314 ! direct_repeat
3638 relationship: derives_from SO:0000101 ! transposable_element
3643 def: "A polypurine tract within an LTR_retrotransposon." [SO:ke]
3644 synonym: "LTR retrotransposon poly purine tract" RELATED []
3645 synonym: "RR tract" EXACT []
3646 is_a: SO:0000330 ! conserved_region
3647 relationship: part_of SO:0000186 ! LTR_retrotransposon
3652 def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]
3654 synonym: "autonomously replicating sequence" EXACT []
3655 is_a: SO:0000296 ! origin_of_replication
3659 name: assortment_derived_duplication
3664 name: gene_not_polyadenylated
3669 name: inverted_ring_chromosome
3670 synonym: "inverted ring chromosome" EXACT []
3671 is_a: SO:1000030 ! chromosomal_inversion
3672 is_a: SO:1000045 ! ring_chromosome
3676 name: vector_replicon
3677 def: "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]
3678 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
3679 synonym: "vector" EXACT []
3680 synonym: "vector replicon" EXACT []
3681 xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology) "wiki"
3682 is_a: SO:0001235 ! replicon
3683 relationship: part_of SO:0000151 ! clone
3688 def: "A single stranded oligonucleotide." [SO:ke]
3689 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
3691 synonym: "single strand oligo" EXACT []
3692 synonym: "single strand oligonucleotide" EXACT []
3693 synonym: "single stranded oligonucleotide" EXACT []
3694 synonym: "ss oligo" EXACT []
3695 synonym: "ss oligonucleotide" EXACT []
3696 is_a: SO:0000696 ! oligo
3701 def: "A double stranded oligonucleotide." [SO:ke]
3702 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
3704 synonym: "double stranded oligonucleotide" EXACT []
3705 synonym: "ds oligo" EXACT []
3706 synonym: "ds-oligonucleotide" EXACT []
3707 is_a: SO:0000696 ! oligo
3711 name: polymer_attribute
3712 def: "An attribute to describe the kind of biological sequence." [SO:ke]
3713 synonym: "polymer attribute" EXACT []
3714 is_a: SO:0000400 ! sequence_attribute
3718 name: three_prime_noncoding_exon
3719 def: "Non-coding exon in the 3' UTR." [SO:ke]
3720 synonym: "three prime noncoding exon" EXACT []
3721 is_a: SO:0000198 ! noncoding_exon
3725 name: five_prime_noncoding_exon
3726 def: "Non-coding exon in the 5' UTR." [SO:ke]
3727 synonym: "5' nc exon" EXACT []
3728 synonym: "5' non coding exon" EXACT []
3729 synonym: "five prime noncoding exon" EXACT []
3730 is_a: SO:0000198 ! noncoding_exon
3735 def: "Intron located in the untranslated region." [SO:ke]
3736 synonym: "UTR intron" EXACT []
3737 is_a: SO:0000188 ! intron
3741 name: five_prime_UTR_intron
3742 def: "An intron located in the 5' UTR." [SO:ke]
3743 synonym: "five prime UTR intron" EXACT []
3744 is_a: SO:0000446 ! UTR_intron
3748 name: three_prime_UTR_intron
3749 def: "An intron located in the 3' UTR." [SO:ke]
3750 synonym: "three prime UTR intron" EXACT []
3751 is_a: SO:0000446 ! UTR_intron
3755 name: random_sequence
3756 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]
3757 synonym: "random sequence" EXACT []
3758 is_a: SO:0000351 ! synthetic_sequence
3763 def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma]
3764 synonym: "chromosome interband" RELATED []
3765 is_a: SO:0000830 ! chromosome_part
3769 name: gene_with_polyadenylated_mRNA
3770 def: "A gene that encodes a polyadenylated mRNA." [SO:xp]
3771 synonym: "gene with polyadenylated mRNA" EXACT []
3772 is_a: SO:0001217 ! protein_coding_gene
3773 relationship: transcribed_to SO:0000871 ! polyadenylated_mRNA
3777 name: transgene_attribute
3782 name: chromosomal_transposition
3783 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]
3784 synonym: "chromosomal transposition" EXACT []
3785 synonym: "transposition" NARROW []
3786 is_a: SO:1000183 ! chromosome_structure_variation
3791 def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]
3793 synonym: "repeat associated small interfering RNA" EXACT []
3794 xref: http://en.wikipedia.org/wiki/RasiRNA "wiki"
3795 is_a: SO:0000655 ! ncRNA
3799 name: gene_with_mRNA_with_frameshift
3800 def: "A gene that encodes an mRNA with a frameshift." [SO:xp]
3801 synonym: "gene with mRNA with frameshift" EXACT []
3802 is_a: SO:0001217 ! protein_coding_gene
3803 relationship: has_quality SO:0000865 ! frameshift
3807 name: recombinationally_rearranged_gene
3808 def: "A gene that is recombinationally rearranged." [SO:ke]
3809 synonym: "recombinationally rearranged gene" EXACT []
3810 is_a: SO:0000704 ! gene
3811 relationship: has_quality SO:0000940 ! recombinationally_rearranged
3815 name: interchromosomal_duplication
3816 def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke]
3817 synonym: "interchromosomal duplication" EXACT []
3818 is_a: SO:1000037 ! chromosomal_duplication
3822 name: D_gene_segment
3823 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#]
3824 synonym: "D gene" EXACT []
3825 synonym: "D-GENE" EXACT []
3826 is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
3830 name: gene_with_trans_spliced_transcript
3831 def: "A gene with a transcript that is trans-spliced." [SO:xp]
3832 synonym: "gene with trans spliced transcript" EXACT []
3833 is_a: SO:0000704 ! gene
3834 relationship: transcribed_to SO:0000479 ! trans_spliced_transcript
3838 name: vertebrate_immunoglobulin_T_cell_receptor_segment
3839 comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
3840 synonym: "vertebrate immunoglobulin T cell receptor segment" EXACT []
3841 synonym: "vertebrate_immunoglobulin/T-cell receptor gene" EXACT []
3842 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
3846 name: inversion_derived_bipartite_deficiency
3847 def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]
3848 synonym: "inversion derived bipartite deficiency" EXACT []
3849 is_a: SO:1000029 ! chromosomal_deletion
3853 name: pseudogenic_region
3854 def: "A non-functional descendant of a functional entity." [SO:cjm]
3856 synonym: "pseudogenic region" EXACT []
3857 is_a: SO:0001411 ! biological_region
3861 name: encodes_alternately_spliced_transcripts
3862 def: "A gene that encodes more than one transcript." [SO:ke]
3863 synonym: "encodes alternately spliced transcripts" EXACT []
3864 is_a: SO:0000401 ! gene_attribute
3869 def: "A non-functional descendant of an exon." [SO:ke]
3871 synonym: "decayed exon" EXACT []
3872 is_a: SO:0000462 ! pseudogenic_region
3873 relationship: non_functional_homolog_of SO:0000147 ! exon
3877 name: inversion_derived_deficiency_plus_duplication
3878 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]
3879 synonym: "inversion derived deficiency plus duplication" EXACT []
3880 is_a: SO:1000029 ! chromosomal_deletion
3881 is_a: SO:1000038 ! intrachromosomal_duplication
3885 name: V_gene_segment
3886 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#]
3887 synonym: "V gene" EXACT []
3888 synonym: "V-GENE" EXACT []
3889 synonym: "variable_gene" EXACT []
3890 is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
3894 name: post_translationally_regulated_by_protein_stability
3895 def: "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]
3896 synonym: "post translationally regulated by protein stability" EXACT []
3897 synonym: "post-translationally regulated by protein stability" EXACT []
3898 is_a: SO:0000130 ! post_translationally_regulated
3902 name: golden_path_fragment
3903 def: "One of the pieces of sequence that make up a golden path." [SO:rd]
3905 synonym: "golden path fragment" EXACT []
3906 is_a: SO:0000143 ! assembly_component
3907 relationship: part_of SO:0000688 ! golden_path
3911 name: post_translationally_regulated_by_protein_modification
3912 def: "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]
3913 synonym: "post translationally regulated by protein modification" EXACT []
3914 synonym: "post-translationally regulated by protein modification" EXACT []
3915 is_a: SO:0000130 ! post_translationally_regulated
3919 name: J_gene_segment
3920 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#]
3921 synonym: "J gene" EXACT []
3922 synonym: "J-GENE" EXACT []
3923 is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
3928 def: "The gene product is involved in its own transcriptional regulation." [SO:ke]
3929 is_a: SO:0000123 ! transcriptionally_regulated
3934 def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]
3936 synonym: "tiling path" EXACT []
3937 is_a: SO:0000353 ! sequence_assembly
3941 name: negatively_autoregulated
3942 def: "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]
3943 synonym: "negatively autoregulated" EXACT []
3944 is_a: SO:0000126 ! transcriptionally_repressed
3945 is_a: SO:0000471 ! autoregulated
3949 name: tiling_path_fragment
3950 def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]
3952 synonym: "tiling path fragment" EXACT []
3953 is_a: SO:0000143 ! assembly_component
3954 relationship: part_of SO:0000472 ! tiling_path
3958 name: positively_autoregulated
3959 def: "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]
3960 synonym: "positively autoregulated" EXACT []
3961 is_a: SO:0000125 ! transcriptionally_induced
3962 is_a: SO:0000471 ! autoregulated
3967 def: "A DNA sequencer read which is part of a contig." [SO:ke]
3968 synonym: "contig read" EXACT []
3969 is_a: SO:0000150 ! read
3973 name: polycistronic_gene
3974 def: "A gene that is polycistronic." [SO:ke]
3979 name: C_gene_segment
3980 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#]
3981 synonym: "C gene" EXACT []
3982 synonym: "C_GENE" EXACT []
3983 synonym: "constant gene" EXACT []
3984 is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
3988 name: trans_spliced_transcript
3989 def: "A transcript that is trans-spliced." [SO:xp]
3990 synonym: "trans spliced transcript" EXACT []
3991 synonym: "trans-spliced transcript" EXACT []
3992 is_a: SO:0000673 ! transcript
3993 relationship: has_quality SO:0000870 ! trans_spliced
3997 name: tiling_path_clone
3998 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]
3999 synonym: "tiling path clone" EXACT []
4000 is_a: SO:0000151 ! clone
4001 is_a: SO:0000474 ! tiling_path_fragment
4005 name: terminal_inverted_repeat
4006 def: "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]
4007 synonym: "terminal inverted repeat" EXACT []
4008 synonym: "TIR" EXACT []
4009 is_a: SO:0000294 ! inverted_repeat
4010 relationship: part_of SO:0000208 ! terminal_inverted_repeat_element
4014 name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4015 synonym: "vertebrate immunoglobulin T cell receptor gene cluster" EXACT []
4016 synonym: "vertebrate_immunoglobulin/T-cell receptor gene cluster" EXACT []
4017 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
4021 name: nc_primary_transcript
4022 def: "A primary transcript that is never translated into a protein." [SO:ke]
4024 synonym: "nc primary transcript" EXACT []
4025 synonym: "noncoding primary transcript" EXACT []
4026 is_a: SO:0000185 ! primary_transcript
4030 name: three_prime_coding_exon_noncoding_region
4031 def: "The sequence of the 3' exon that is not coding." [SO:ke]
4033 synonym: "three prime coding exon noncoding region" EXACT []
4034 synonym: "three_prime_exon_noncoding_region" EXACT []
4035 is_a: SO:0001214 ! noncoding_region_of_exon
4036 relationship: part_of SO:0000202 ! three_prime_coding_exon
4041 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#]
4042 synonym: "(DJ)-J-CLUSTER" EXACT []
4043 synonym: "DJ J cluster" EXACT []
4044 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4045 relationship: has_part SO:0000470 ! J_gene_segment
4046 relationship: has_part SO:0000572 ! DJ_gene_segment
4050 name: five_prime_coding_exon_noncoding_region
4051 def: "The sequence of the 5' exon preceding the start codon." [SO:ke]
4053 synonym: "five prime coding exon noncoding region" EXACT []
4054 synonym: "five_prime_exon_noncoding_region" EXACT []
4055 is_a: SO:0001214 ! noncoding_region_of_exon
4056 relationship: part_of SO:0000200 ! five_prime_coding_exon
4060 name: VDJ_J_C_cluster
4061 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#]
4062 synonym: "(VDJ)-J-C-CLUSTER" EXACT []
4063 synonym: "VDJ J C cluster" EXACT []
4064 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4065 relationship: has_part SO:0000470 ! J_gene_segment
4066 relationship: has_part SO:0000478 ! C_gene_segment
4067 relationship: has_part SO:0000574 ! VDJ_gene_segment
4072 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#]
4073 synonym: "(VDJ)-J-CLUSTER" EXACT []
4074 synonym: "VDJ J cluster" EXACT []
4075 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4076 relationship: has_part SO:0000470 ! J_gene_segment
4077 relationship: has_part SO:0000574 ! VDJ_gene_segment
4082 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#]
4083 synonym: "(VJ)-C-CLUSTER" RELATED []
4084 synonym: "VJ C cluster" EXACT []
4085 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4086 relationship: has_part SO:0000478 ! C_gene_segment
4087 relationship: has_part SO:0000576 ! VJ_gene_segment
4091 name: VJ_J_C_cluster
4092 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#]
4093 synonym: "(VJ)-J-C-CLUSTER" EXACT []
4094 synonym: "VJ J C cluster" EXACT []
4095 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4096 relationship: has_part SO:0000470 ! J_gene_segment
4097 relationship: has_part SO:0000478 ! C_gene_segment
4098 relationship: has_part SO:0000576 ! VJ_gene_segment
4103 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#]
4104 synonym: "(VJ)-J-CLUSTER" EXACT []
4105 synonym: "VJ J cluster" EXACT []
4106 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4107 relationship: has_part SO:0000470 ! J_gene_segment
4108 relationship: has_part SO:0000576 ! VJ_gene_segment
4112 name: D_gene_recombination_feature
4113 synonym: "D gene recombination feature" EXACT []
4114 is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
4118 name: three_prime_D_heptamer
4119 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#]
4120 synonym: "3'D-HEPTAMER" EXACT []
4121 synonym: "three prime D heptamer" EXACT []
4122 is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
4123 relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
4127 name: three_prime_D_nonamer
4128 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#]
4129 synonym: "3'D-NOMAMER" EXACT []
4130 synonym: "three prime D nonamer" EXACT []
4131 is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
4132 relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
4136 name: three_prime_D_spacer
4137 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#]
4138 synonym: "3'D-SPACER" EXACT []
4139 synonym: "three prime D spacer" EXACT []
4140 is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
4141 relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
4145 name: five_prime_D_heptamer
4146 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#]
4147 synonym: "5'D-HEPTAMER" EXACT []
4148 synonym: "five prime D heptamer" EXACT []
4149 is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
4150 relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
4154 name: five_prime_D_nonamer
4155 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#]
4156 synonym: "5'D-NONAMER" EXACT []
4157 synonym: "five prime D nonamer" EXACT []
4158 is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
4159 relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
4163 name: five_prime_D_spacer
4164 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#]
4165 synonym: "5'-SPACER" EXACT []
4166 synonym: "five prime D spacer" EXACT []
4167 synonym: "five prime D-spacer" EXACT []
4168 is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
4169 relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
4173 name: virtual_sequence
4174 def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]
4176 synonym: "virtual sequence" EXACT []
4177 is_a: SO:0000353 ! sequence_assembly
4181 name: Hoogsteen_base_pair
4182 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]
4183 synonym: "Hoogsteen base pair" EXACT []
4184 xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair "wiki"
4185 is_a: SO:0000028 ! base_pair
4189 name: reverse_Hoogsteen_base_pair
4190 def: "A type of non-canonical base-pairing." [SO:ke]
4191 synonym: "reverse Hoogsteen base pair" EXACT []
4192 is_a: SO:0000028 ! base_pair
4196 name: transcribed_region
4197 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]
4198 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.
4204 name: alternately_spliced_gene_encodeing_one_transcript
4209 name: D_DJ_C_cluster
4210 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#]
4211 synonym: "D DJ C cluster" EXACT []
4212 synonym: "D-(DJ)-C-CLUSTER" EXACT []
4213 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4214 relationship: has_part SO:0000458 ! D_gene_segment
4215 relationship: has_part SO:0000478 ! C_gene_segment
4216 relationship: has_part SO:0000572 ! DJ_gene_segment
4221 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#]
4222 synonym: "D DJ cluster" EXACT []
4223 synonym: "D-(DJ)-CLUSTER" EXACT []
4224 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4225 relationship: has_part SO:0000458 ! D_gene_segment
4226 relationship: has_part SO:0000572 ! DJ_gene_segment
4230 name: D_DJ_J_C_cluster
4231 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#]
4232 synonym: "D DJ J C cluster" EXACT []
4233 synonym: "D-(DJ)-J-C-CLUSTER" EXACT []
4234 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4235 relationship: has_part SO:0000458 ! D_gene_segment
4236 relationship: has_part SO:0000470 ! J_gene_segment
4237 relationship: has_part SO:0000478 ! C_gene_segment
4238 relationship: has_part SO:0000572 ! DJ_gene_segment
4242 name: pseudogenic_exon
4243 def: "A non functional descendant of an exon, part of a pseudogene." [SO:ke]
4244 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.
4245 synonym: "pseudogenic exon" EXACT []
4246 is_a: SO:0000462 ! pseudogenic_region
4247 relationship: non_functional_homolog_of SO:0000147 ! exon
4248 relationship: part_of SO:0000516 ! pseudogenic_transcript
4252 name: D_DJ_J_cluster
4253 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#]
4254 synonym: "D DJ J cluster" EXACT []
4255 synonym: "D-(DJ)-J-CLUSTER" EXACT []
4256 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4257 relationship: has_part SO:0000458 ! D_gene_segment
4258 relationship: has_part SO:0000470 ! J_gene_segment
4259 relationship: has_part SO:0000572 ! DJ_gene_segment
4264 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#]
4265 synonym: "D J C cluster" EXACT []
4266 synonym: "D-J-C-CLUSTER" EXACT []
4267 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4268 relationship: has_part SO:0000458 ! D_gene_segment
4269 relationship: has_part SO:0000470 ! J_gene_segment
4270 relationship: has_part SO:0000478 ! C_gene_segment
4274 name: VD_gene_segment
4275 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#]
4276 synonym: "V_D_GENE" EXACT []
4277 synonym: "VD gene" EXACT []
4278 is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
4283 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#]
4284 synonym: "J C cluster" EXACT []
4285 synonym: "J-C-CLUSTER" EXACT []
4286 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4287 relationship: has_part SO:0000470 ! J_gene_segment
4288 relationship: has_part SO:0000478 ! C_gene_segment
4292 name: inversion_derived_deficiency_plus_aneuploid
4293 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]
4294 synonym: "inversion derived deficiency plus aneuploid" EXACT []
4295 is_a: SO:1000029 ! chromosomal_deletion
4300 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#]
4301 synonym: "J cluster" EXACT []
4302 synonym: "J-CLUSTER" EXACT []
4303 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4304 relationship: has_part SO:0000470 ! J_gene_segment
4309 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#]
4310 synonym: "J nonamer" EXACT []
4311 synonym: "J-NONAMER" EXACT []
4312 is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
4313 relationship: part_of SO:0000302 ! J_gene_recombination_feature
4318 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#]
4319 synonym: "J heptamer" EXACT []
4320 synonym: "J-HEPTAMER" EXACT []
4321 is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
4322 relationship: part_of SO:0000302 ! J_gene_recombination_feature
4326 name: pseudogenic_transcript
4327 def: "A non functional descendant of a transcript, part of a pseudogene." [SO:ke]
4328 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.
4329 synonym: "pseudogenic transcript" EXACT []
4330 is_a: SO:0000462 ! pseudogenic_region
4331 relationship: non_functional_homolog_of SO:0000673 ! transcript
4332 relationship: part_of SO:0000336 ! pseudogene
4337 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#]
4338 synonym: "J spacer" EXACT []
4339 synonym: "J-SPACER" EXACT []
4340 is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
4341 relationship: part_of SO:0000302 ! J_gene_recombination_feature
4346 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#]
4347 synonym: "V DJ cluster" EXACT []
4348 synonym: "V-(DJ)-CLUSTER" EXACT []
4349 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4350 relationship: has_part SO:0000466 ! V_gene_segment
4351 relationship: has_part SO:0000572 ! DJ_gene_segment
4355 name: V_DJ_J_cluster
4356 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#]
4357 synonym: "V DJ J cluster" EXACT []
4358 synonym: "V-(DJ)-J-CLUSTER" RELATED []
4359 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4360 relationship: has_part SO:0000466 ! V_gene_segment
4361 relationship: has_part SO:0000470 ! J_gene_segment
4362 relationship: has_part SO:0000572 ! DJ_gene_segment
4366 name: V_VDJ_C_cluster
4367 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#]
4368 synonym: "V VDJ C cluster" EXACT []
4369 synonym: "V-(VDJ)-C-CLUSTER" EXACT []
4370 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4371 relationship: has_part SO:0000466 ! V_gene_segment
4372 relationship: has_part SO:0000478 ! C_gene_segment
4373 relationship: has_part SO:0000574 ! VDJ_gene_segment
4378 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#]
4379 synonym: "V VDJ cluster" EXACT []
4380 synonym: "V-(VDJ)-CLUSTER" EXACT []
4381 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4382 relationship: has_part SO:0000466 ! V_gene_segment
4383 relationship: has_part SO:0000574 ! VDJ_gene_segment
4387 name: V_VDJ_J_cluster
4388 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#]
4389 synonym: "V VDJ J cluster" EXACT []
4390 synonym: "V-(VDJ)-J-CLUSTER" RELATED []
4391 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4392 relationship: has_part SO:0000466 ! V_gene_segment
4393 relationship: has_part SO:0000470 ! J_gene_segment
4394 relationship: has_part SO:0000574 ! VDJ_gene_segment
4398 name: V_VJ_C_cluster
4399 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#]
4400 synonym: "V VJ C cluster" EXACT []
4401 synonym: "V-(VJ)-C-CLUSTER" EXACT []
4402 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4403 relationship: has_part SO:0000466 ! V_gene_segment
4404 relationship: has_part SO:0000478 ! C_gene_segment
4405 relationship: has_part SO:0000576 ! VJ_gene_segment
4410 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#]
4411 synonym: "V VJ cluster" EXACT []
4412 synonym: "V-(VJ)-CLUSTER" EXACT []
4413 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4414 relationship: has_part SO:0000466 ! V_gene_segment
4415 relationship: has_part SO:0000576 ! VJ_gene_segment
4419 name: V_VJ_J_cluster
4420 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#]
4421 synonym: "V VJ J cluster" EXACT []
4422 synonym: "V-(VJ)-J-CLUSTER" EXACT []
4423 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4424 relationship: has_part SO:0000466 ! V_gene_segment
4425 relationship: has_part SO:0000470 ! J_gene_segment
4426 relationship: has_part SO:0000576 ! VJ_gene_segment
4431 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#]
4432 synonym: "V cluster" EXACT []
4433 synonym: "V-CLUSTER" EXACT []
4434 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4435 relationship: has_part SO:0000466 ! V_gene_segment
4439 name: V_D_DJ_C_cluster
4440 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#]
4441 synonym: "V D DJ C cluster" EXACT []
4442 synonym: "V-D-(DJ)-C-CLUSTER" EXACT []
4443 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4444 relationship: has_part SO:0000458 ! D_gene_segment
4445 relationship: has_part SO:0000466 ! V_gene_segment
4446 relationship: has_part SO:0000478 ! C_gene_segment
4447 relationship: has_part SO:0000572 ! DJ_gene_segment
4451 name: V_D_DJ_cluster
4452 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#]
4453 synonym: "V D DJ cluster" EXACT []
4454 synonym: "V-D-(DJ)-CLUSTER" EXACT []
4455 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4456 relationship: has_part SO:0000458 ! D_gene_segment
4457 relationship: has_part SO:0000466 ! V_gene_segment
4458 relationship: has_part SO:0000572 ! DJ_gene_segment
4462 name: V_D_DJ_J_C_cluster
4463 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#]
4464 synonym: "V D DJ J C cluster" EXACT []
4465 synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT []
4466 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4467 relationship: has_part SO:0000458 ! D_gene_segment
4468 relationship: has_part SO:0000466 ! V_gene_segment
4469 relationship: has_part SO:0000470 ! J_gene_segment
4470 relationship: has_part SO:0000478 ! C_gene_segment
4471 relationship: has_part SO:0000572 ! DJ_gene_segment
4475 name: V_D_DJ_J_cluster
4476 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#]
4477 synonym: "V D DJ J cluster" EXACT []
4478 synonym: "V-D-(DJ)-J-CLUSTER" EXACT []
4479 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4480 relationship: has_part SO:0000458 ! D_gene_segment
4481 relationship: has_part SO:0000466 ! V_gene_segment
4482 relationship: has_part SO:0000470 ! J_gene_segment
4483 relationship: has_part SO:0000572 ! DJ_gene_segment
4487 name: V_D_J_C_cluster
4488 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#]
4489 synonym: "V D J C cluster" EXACT []
4490 synonym: "V-D-J-C-CLUSTER" EXACT []
4491 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4492 relationship: has_part SO:0000458 ! D_gene_segment
4493 relationship: has_part SO:0000466 ! V_gene_segment
4494 relationship: has_part SO:0000470 ! J_gene_segment
4495 relationship: has_part SO:0000478 ! C_gene_segment
4500 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#]
4501 synonym: "V D J cluster" EXACT []
4502 synonym: "V-D-J-CLUSTER" EXACT []
4503 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4504 relationship: has_part SO:0000458 ! D_gene_segment
4505 relationship: has_part SO:0000466 ! V_gene_segment
4506 relationship: has_part SO:0000470 ! J_gene_segment
4511 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#]
4512 synonym: "V heptamer" EXACT []
4513 synonym: "V-HEPTAMER" EXACT []
4514 is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
4515 relationship: part_of SO:0000538 ! V_gene_recombination_feature
4520 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#]
4521 synonym: "V J cluster" EXACT []
4522 synonym: "V-J-CLUSTER" EXACT []
4523 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4524 relationship: has_part SO:0000466 ! V_gene_segment
4525 relationship: has_part SO:0000470 ! J_gene_segment
4530 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#]
4531 synonym: "V J C cluster" EXACT []
4532 synonym: "V-J-C-CLUSTER" EXACT []
4533 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4534 relationship: has_part SO:0000466 ! V_gene_segment
4535 relationship: has_part SO:0000470 ! J_gene_segment
4536 relationship: has_part SO:0000478 ! C_gene_segment
4541 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#]
4542 synonym: "V nonamer" EXACT []
4543 synonym: "V-NONAMER" EXACT []
4544 is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
4545 relationship: part_of SO:0000538 ! V_gene_recombination_feature
4550 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#]
4551 synonym: "V spacer" EXACT []
4552 synonym: "V-SPACER" EXACT []
4553 is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
4554 relationship: part_of SO:0000538 ! V_gene_recombination_feature
4558 name: V_gene_recombination_feature
4559 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#]
4560 synonym: "V gene recombination feature" EXACT []
4561 synonym: "V-RS" EXACT []
4562 is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
4567 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#]
4568 synonym: "(DJ)-C-CLUSTER" EXACT []
4569 synonym: "DJ C cluster" EXACT []
4570 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4571 relationship: has_part SO:0000478 ! C_gene_segment
4572 relationship: has_part SO:0000572 ! DJ_gene_segment
4576 name: DJ_J_C_cluster
4577 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#]
4578 synonym: "(DJ)-J-C-CLUSTER" EXACT []
4579 synonym: "DJ J C cluster" EXACT []
4580 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4581 relationship: has_part SO:0000470 ! J_gene_segment
4582 relationship: has_part SO:0000478 ! C_gene_segment
4583 relationship: has_part SO:0000572 ! DJ_gene_segment
4588 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#]
4589 synonym: "(VDJ)-C-CLUSTER" EXACT []
4590 synonym: "VDJ C cluster" EXACT []
4591 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4592 relationship: has_part SO:0000478 ! C_gene_segment
4593 relationship: has_part SO:0000574 ! VDJ_gene_segment
4597 name: V_DJ_C_cluster
4598 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#]
4599 synonym: "V DJ C cluster" EXACT []
4600 synonym: "V-(DJ)-C-CLUSTER" EXACT []
4601 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4602 relationship: has_part SO:0000466 ! V_gene_segment
4603 relationship: has_part SO:0000478 ! C_gene_segment
4604 relationship: has_part SO:0000572 ! DJ_gene_segment
4608 name: alternately_spliced_gene_encoding_greater_than_one_transcript
4614 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]
4615 synonym: "ISCR" RELATED []
4616 xref: http://en.wikipedia.org/wiki/Helitron "wiki"
4617 is_a: SO:0000182 ! DNA_transposon
4621 name: recoding_pseudoknot
4622 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]
4623 synonym: "recoding pseudoknot" EXACT []
4624 is_a: SO:0000591 ! pseudoknot
4625 relationship: part_of SO:1001268 ! recoding_stimulatory_region
4629 name: designed_sequence
4630 synonym: "designed sequence" EXACT []
4631 is_a: SO:0000351 ! synthetic_sequence
4635 name: inversion_derived_bipartite_duplication
4636 def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]
4637 synonym: "inversion derived bipartite duplication" EXACT []
4638 is_a: SO:1000038 ! intrachromosomal_duplication
4642 name: gene_with_edited_transcript
4643 def: "A gene that encodes a transcript that is edited." [SO:xp]
4644 synonym: "gene with edited transcript" EXACT []
4645 is_a: SO:0001217 ! protein_coding_gene
4646 relationship: transcribed_to SO:0000873 ! edited_transcript
4650 name: inversion_derived_duplication_plus_aneuploid
4651 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]
4652 synonym: "inversion derived duplication plus aneuploid" EXACT []
4653 is_a: SO:1000038 ! intrachromosomal_duplication
4657 name: aneuploid_chromosome
4658 def: "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]
4659 comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
4660 synonym: "aneuploid chromosome" EXACT []
4661 is_a: SO:1000183 ! chromosome_structure_variation
4665 name: polyA_signal_sequence
4666 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]
4668 synonym: "poly(A) signal" EXACT []
4669 synonym: "polyA signal sequence" EXACT []
4670 synonym: "polyadenylation termination signal" EXACT []
4671 is_a: SO:0001679 ! transcription_regulatory_region
4675 name: Shine_Dalgarno_sequence
4676 def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]
4677 comment: Not found in Eukaryotic sequence.
4678 synonym: "five prime ribosome binding site" EXACT []
4679 synonym: "RBS" RELATED []
4680 synonym: "Shine Dalgarno sequence" EXACT []
4681 synonym: "Shine-Dalgarno sequence" EXACT []
4682 xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki"
4683 is_a: SO:0000139 ! ribosome_entry_site
4689 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]
4691 synonym: "polyA cleavage site" EXACT []
4692 synonym: "polyA junction" EXACT []
4693 synonym: "polyA site" EXACT []
4694 synonym: "polyA_junction" EXACT []
4695 synonym: "polyadenylation site" RELATED []
4696 is_a: SO:0000699 ! junction
4697 relationship: part_of SO:0000205 ! three_prime_UTR
4698 relationship: part_of SO:0000233 ! mature_transcript
4702 name: assortment_derived_deficiency_plus_duplication
4707 name: five_prime_clip
4708 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]
4709 synonym: "5' clip" RELATED []
4710 synonym: "five prime clip" EXACT []
4711 is_a: SO:0000303 ! clip
4715 name: five_prime_D_recombination_signal_sequence
4716 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#]
4717 synonym: "5'RS" EXACT []
4718 synonym: "five prime D recombination signal sequence" EXACT []
4719 synonym: "five prime D-recombination signal sequence" EXACT []
4720 is_a: SO:0000492 ! D_gene_recombination_feature
4724 name: three_prime_clip
4725 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]
4726 synonym: "3'-clip" EXACT []
4727 synonym: "three prime clip" EXACT []
4728 is_a: SO:0000303 ! clip
4733 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#]
4734 synonym: "C cluster" EXACT []
4735 synonym: "C-CLUSTER" EXACT []
4736 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4737 relationship: has_part SO:0000478 ! C_gene_segment
4742 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#]
4743 synonym: "D cluster" EXACT []
4744 synonym: "D-CLUSTER" EXACT []
4745 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4746 relationship: has_part SO:0000458 ! D_gene_segment
4751 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#]
4752 synonym: "D J cluster" EXACT []
4753 synonym: "D-J-CLUSTER" EXACT []
4754 is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
4755 relationship: has_part SO:0000458 ! D_gene_segment
4756 relationship: has_part SO:0000470 ! J_gene_segment
4760 name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
4761 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#]
4762 synonym: "HEPTAMER" RELATED []
4763 synonym: "heptamer of recombination feature of vertebrate immune system gene" EXACT []
4764 is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
4768 name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
4769 synonym: "nonamer of recombination feature of vertebrate immune system gene" EXACT []
4770 is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
4774 name: vertebrate_immune_system_gene_recombination_spacer
4775 synonym: "vertebrate immune system gene recombination spacer" EXACT []
4776 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
4780 name: V_DJ_J_C_cluster
4781 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#]
4782 synonym: "V DJ J C cluster" EXACT []
4783 synonym: "V-(DJ)-J-C-CLUSTER" EXACT []
4784 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4785 relationship: has_part SO:0000466 ! V_gene_segment
4786 relationship: has_part SO:0000470 ! J_gene_segment
4787 relationship: has_part SO:0000478 ! C_gene_segment
4788 relationship: has_part SO:0000572 ! DJ_gene_segment
4792 name: V_VDJ_J_C_cluster
4793 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#]
4794 synonym: "V VDJ J C cluster" EXACT []
4795 synonym: "V-(VDJ)-J-C-CLUSTER" EXACT []
4796 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4797 relationship: has_part SO:0000466 ! V_gene_segment
4798 relationship: has_part SO:0000470 ! J_gene_segment
4799 relationship: has_part SO:0000478 ! C_gene_segment
4800 relationship: has_part SO:0000574 ! VDJ_gene_segment
4804 name: V_VJ_J_C_cluster
4805 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#]
4806 synonym: "V VJ J C cluster" EXACT []
4807 synonym: "V-(VJ)-J-C-CLUSTER" EXACT []
4808 is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
4809 relationship: has_part SO:0000466 ! V_gene_segment
4810 relationship: has_part SO:0000470 ! J_gene_segment
4811 relationship: has_part SO:0000478 ! C_gene_segment
4812 relationship: has_part SO:0000576 ! VJ_gene_segment
4816 name: inversion_derived_aneuploid_chromosome
4817 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]
4818 synonym: "inversion derived aneuploid chromosome" EXACT []
4819 is_a: SO:0000550 ! aneuploid_chromosome
4823 name: bidirectional_promoter
4824 def: "An unregulated promoter that allows continuous expression." [SO:ke]
4825 synonym: "bidirectional promoter" EXACT []
4826 is_a: SO:0000167 ! promoter
4830 name: retrotransposed
4832 def: "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke]
4833 comment: GO:0003964 RNA-directed DNA polymerase activity.
4834 xref: http://en.wikipedia.org/wiki/Retrotransposed "wiki"
4835 is_a: SO:0000733 ! feature_attribute
4839 name: three_prime_D_recombination_signal_sequence
4840 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#]
4841 synonym: "3'D-RS" EXACT []
4842 synonym: "three prime D recombination signal sequence" EXACT []
4843 synonym: "three_prime_D-recombination_signal_sequence" EXACT []
4844 is_a: SO:0000492 ! D_gene_recombination_feature
4848 name: miRNA_encoding
4849 synonym: "miRNA encoding" EXACT []
4850 is_a: SO:0000011 ! non_protein_coding
4854 name: DJ_gene_segment
4855 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#]
4856 synonym: "D-J-GENE" EXACT []
4857 synonym: "DJ gene" EXACT []
4858 is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
4863 synonym: "rRNA encoding" EXACT []
4864 is_a: SO:0000011 ! non_protein_coding
4868 name: VDJ_gene_segment
4869 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#]
4870 synonym: "V-D-J-GENE" EXACT []
4871 synonym: "VDJ gene" EXACT []
4872 is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
4876 name: scRNA_encoding
4877 synonym: "scRNA encoding" EXACT []
4878 is_a: SO:0000011 ! non_protein_coding
4882 name: VJ_gene_segment
4883 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#]
4884 synonym: "V-J-GENE" EXACT []
4885 synonym: "VJ gene" EXACT []
4886 is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
4891 def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]
4893 xref: http://en.wikipedia.org/wiki/Centromere "wiki"
4894 is_a: SO:0000628 ! chromosomal_structural_element
4898 name: snoRNA_encoding
4899 synonym: "snoRNA encoding" EXACT []
4900 is_a: SO:0000011 ! non_protein_coding
4904 name: edited_transcript_feature
4905 def: "A locatable feature on a transcript that is edited." [SO:ma]
4906 synonym: "edited transcript feature" EXACT []
4907 is_a: SO:0000833 ! transcript_region
4911 name: methylation_guide_snoRNA_primary_transcript
4912 def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]
4913 synonym: "methylation guide snoRNA primary transcript" EXACT []
4914 is_a: SO:0000232 ! snoRNA_primary_transcript
4919 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]
4921 xref: http://en.wikipedia.org/wiki/5%27_cap "wiki"
4922 is_a: SO:0001411 ! biological_region
4926 name: rRNA_cleavage_snoRNA_primary_transcript
4927 def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]
4928 synonym: "rRNA cleavage snoRNA primary transcript" EXACT []
4929 is_a: SO:0000232 ! snoRNA_primary_transcript
4933 name: pre_edited_region
4934 def: "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]
4935 synonym: "pre edited region" EXACT []
4936 synonym: "pre-edited region" EXACT []
4937 is_a: SO:0000579 ! edited_transcript_feature
4942 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]
4943 synonym: "10Sa RNA" RELATED []
4944 synonym: "ssrA" RELATED []
4945 xref: http://en.wikipedia.org/wiki/TmRNA "wiki"
4946 is_a: SO:0000370 ! small_regulatory_ncRNA
4950 name: C_D_box_snoRNA_encoding
4951 synonym: "C/D box snoRNA encoding" EXACT []
4952 is_a: SO:0000578 ! snoRNA_encoding
4956 name: tmRNA_primary_transcript
4957 def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]
4958 synonym: "10Sa RNA primary transcript" RELATED []
4959 synonym: "ssrA RNA primary transcript" RELATED []
4960 synonym: "tmRNA primary transcript" EXACT []
4961 is_a: SO:0000483 ! nc_primary_transcript
4965 name: group_I_intron
4966 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]
4967 comment: GO:0000372.
4969 synonym: "group I intron" EXACT []
4970 xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki"
4971 is_a: SO:0000588 ! autocatalytically_spliced_intron
4975 name: autocatalytically_spliced_intron
4976 def: "A self spliced intron." [SO:ke]
4978 synonym: "autocatalytically spliced intron" EXACT []
4979 is_a: SO:0000188 ! intron
4980 relationship: has_quality SO:0001186 ! ribozymic
4984 name: SRP_RNA_primary_transcript
4985 def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke]
4986 synonym: "SRP RNA primary transcript" EXACT []
4987 is_a: SO:0000483 ! nc_primary_transcript
4992 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]
4994 synonym: "7S RNA" RELATED []
4995 synonym: "signal recognition particle RNA" RELATED []
4996 synonym: "SRP RNA" EXACT []
4997 is_a: SO:0000655 ! ncRNA
4998 relationship: derives_from SO:0000589 ! SRP_RNA_primary_transcript
5003 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]
5004 xref: http://en.wikipedia.org/wiki/Pseudoknot "wiki"
5005 is_a: SO:0000002 ! sequence_secondary_structure
5010 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]
5011 synonym: "classical pseudoknot" EXACT []
5012 synonym: "H pseudoknot" EXACT []
5013 synonym: "H-pseudoknot" EXACT []
5014 synonym: "H-type pseudoknot" EXACT []
5015 synonym: "hairpin-type pseudoknot" EXACT []
5016 is_a: SO:0000591 ! pseudoknot
5020 name: C_D_box_snoRNA
5021 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]
5023 synonym: "box C/D snoRNA" EXACT []
5024 synonym: "C D box snoRNA" EXACT []
5025 synonym: "C/D box snoRNA" EXACT []
5026 is_a: SO:0000275 ! snoRNA
5027 relationship: derives_from SO:0000595 ! C_D_box_snoRNA_primary_transcript
5031 name: H_ACA_box_snoRNA
5032 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]
5033 synonym: "box H/ACA snoRNA" EXACT []
5034 synonym: "H ACA box snoRNA" EXACT []
5035 synonym: "H/ACA box snoRNA" EXACT []
5036 is_a: SO:0000275 ! snoRNA
5037 relationship: derives_from SO:0000596 ! H_ACA_box_snoRNA_primary_transcript
5041 name: C_D_box_snoRNA_primary_transcript
5042 def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]
5043 synonym: "C/D box snoRNA primary transcript" EXACT []
5044 is_a: SO:0000232 ! snoRNA_primary_transcript
5048 name: H_ACA_box_snoRNA_primary_transcript
5049 def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]
5050 synonym: "H ACA box snoRNA primary transcript" EXACT []
5051 is_a: SO:0000232 ! snoRNA_primary_transcript
5055 name: transcript_edited_by_U_insertion/deletion
5056 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]
5061 name: edited_by_C_insertion_and_dinucleotide_insertion
5062 synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED []
5067 name: edited_by_C_to_U_substitution
5072 name: edited_by_A_to_I_substitution
5077 name: edited_by_G_addition
5083 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]
5085 synonym: "gRNA" EXACT []
5086 synonym: "guide RNA" EXACT []
5087 xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki"
5088 is_a: SO:0000655 ! ncRNA
5092 name: group_II_intron
5093 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]
5094 comment: GO:0000373.
5096 synonym: "group II intron" EXACT []
5097 xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki"
5098 is_a: SO:0000588 ! autocatalytically_spliced_intron
5103 def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]
5104 synonym: "editing block" EXACT []
5105 is_a: SO:0000579 ! edited_transcript_feature
5109 name: intergenic_region
5110 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]
5111 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
5113 synonym: "intergenic region" EXACT []
5114 xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki"
5115 is_a: SO:0001411 ! biological_region
5119 name: editing_domain
5120 def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]
5121 synonym: "editing domain" EXACT []
5122 is_a: SO:0000579 ! edited_transcript_feature
5126 name: unedited_region
5127 def: "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]
5128 synonym: "unedited region" EXACT []
5129 is_a: SO:0000579 ! edited_transcript_feature
5133 name: H_ACA_box_snoRNA_encoding
5134 synonym: "H ACA box snoRNA encoding" EXACT []
5135 is_a: SO:0000578 ! snoRNA_encoding
5140 def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]
5141 synonym: "oligo U tail" EXACT []
5142 is_a: SO:0001411 ! biological_region
5143 relationship: adjacent_to SO:0000602 ! guide_RNA
5147 name: polyA_sequence
5148 def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]
5150 synonym: "polyA sequence" EXACT []
5151 is_a: SO:0001411 ! biological_region
5152 relationship: adjacent_to SO:0000234 ! mRNA
5157 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]
5159 synonym: "branch point" EXACT []
5160 synonym: "branch site" EXACT []
5161 synonym: "branch_point" EXACT []
5162 is_a: SO:0000841 ! spliceosomal_intron_region
5166 name: polypyrimidine_tract
5167 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]
5169 synonym: "polypyrimidine tract" EXACT []
5170 xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki"
5171 is_a: SO:0000841 ! spliceosomal_intron_region
5175 name: bacterial_RNApol_promoter
5176 def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]
5177 synonym: "bacterial RNApol promoter" EXACT []
5178 is_a: SO:0000752 ! gene_group_regulatory_region
5179 is_a: SO:0001203 ! RNA_polymerase_promoter
5183 name: bacterial_terminator
5184 def: "A terminator signal for bacterial transcription." [SO:ke]
5185 synonym: "bacterial terminator" EXACT []
5186 is_a: SO:0000141 ! terminator
5187 is_a: SO:0000752 ! gene_group_regulatory_region
5191 name: terminator_of_type_2_RNApol_III_promoter
5192 def: "A terminator signal for RNA polymerase III transcription." [SO:ke]
5193 synonym: "terminator of type 2 RNApol III promoter" EXACT []
5194 is_a: SO:0000951 ! eukaryotic_terminator
5198 name: transcription_end_site
5199 def: "The base where transcription ends." [SO:ke]
5201 synonym: "transcription end site" EXACT []
5202 is_a: SO:0000835 ! primary_transcript_region
5206 name: RNApol_III_promoter_type_1
5207 synonym: "RNApol III promoter type 1" EXACT []
5208 is_a: SO:0000171 ! RNApol_III_promoter
5212 name: RNApol_III_promoter_type_2
5213 synonym: "RNApol III promoter type 2" EXACT []
5214 synonym: "tRNA promoter" RELATED []
5215 is_a: SO:0000171 ! RNApol_III_promoter
5220 def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]
5221 comment: Binds TFIIIC.
5222 synonym: "A-box" EXACT []
5223 xref: http://en.wikipedia.org/wiki/A-box "wiki"
5224 is_a: SO:0001660 ! core_promoter_element
5229 def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]
5230 comment: Binds TFIIIC.
5231 synonym: "B-box" EXACT []
5232 is_a: SO:0001660 ! core_promoter_element
5233 relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2
5237 name: RNApol_III_promoter_type_3
5238 synonym: "RNApol III promoter type 3" EXACT []
5239 is_a: SO:0000171 ! RNApol_III_promoter
5244 def: "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]
5245 synonym: "C-box" EXACT []
5246 is_a: SO:0001660 ! core_promoter_element
5247 relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
5251 name: snRNA_encoding
5252 synonym: "snRNA encoding" EXACT []
5253 is_a: SO:0000011 ! non_protein_coding
5258 def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]
5260 synonym: "telomeric DNA" EXACT []
5261 synonym: "telomeric sequence" EXACT []
5262 xref: http://en.wikipedia.org/wiki/Telomere "wiki"
5263 is_a: SO:0000628 ! chromosomal_structural_element
5268 def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]
5270 xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki"
5271 is_a: SO:0000727 ! CRM
5275 name: chromosomal_regulatory_element
5276 synonym: "chromosomal regulatory element" EXACT []
5277 is_a: SO:0000830 ! chromosome_part
5282 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]
5284 synonym: "insulator element" EXACT []
5285 xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki"
5286 is_a: SO:0001055 ! transcriptional_cis_regulatory_region
5290 name: chromosomal_structural_element
5292 synonym: "chromosomal structural element" EXACT []
5293 is_a: SO:0000830 ! chromosome_part
5297 name: five_prime_open_reading_frame
5298 synonym: "five prime open reading frame" EXACT []
5299 is_a: SO:0000836 ! mRNA_region
5300 relationship: part_of SO:0000204 ! five_prime_UTR
5304 name: upstream_AUG_codon
5305 def: "A start codon upstream of the ORF." [SO:ke]
5306 synonym: "upstream AUG codon" EXACT []
5307 is_a: SO:0000837 ! UTR_region
5308 relationship: part_of SO:0000203 ! UTR
5312 name: polycistronic_primary_transcript
5313 def: "A primary transcript encoding for more than one gene product." [SO:ke]
5314 synonym: "polycistronic primary transcript" EXACT []
5315 is_a: SO:0000078 ! polycistronic_transcript
5316 is_a: SO:0000185 ! primary_transcript
5317 relationship: has_quality SO:0000880 ! polycistronic
5321 name: monocistronic_primary_transcript
5322 def: "A primary transcript encoding for one gene product." [SO:ke]
5323 synonym: "monocistronic primary transcript" EXACT []
5324 is_a: SO:0000185 ! primary_transcript
5325 is_a: SO:0000665 ! monocistronic_transcript
5326 relationship: has_quality SO:0000878 ! monocistronic
5330 name: monocistronic_mRNA
5331 def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]
5332 synonym: "monocistronic mRNA" EXACT []
5333 synonym: "monocistronic processed transcript" EXACT []
5334 xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki"
5335 is_a: SO:0000234 ! mRNA
5336 is_a: SO:0000665 ! monocistronic_transcript
5337 relationship: has_quality SO:0000878 ! monocistronic
5341 name: polycistronic_mRNA
5342 def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]
5343 synonym: "polycistronic mRNA" EXACT []
5344 synonym: "polycistronic processed transcript" RELATED []
5345 xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki"
5346 is_a: SO:0000078 ! polycistronic_transcript
5347 is_a: SO:0000234 ! mRNA
5348 relationship: has_quality SO:0000880 ! polycistronic
5352 name: mini_exon_donor_RNA
5353 def: "A primary transcript that donates the spliced leader to other mRNA." [SO:ke]
5354 synonym: "mini exon donor RNA" EXACT []
5355 synonym: "mini-exon donor RNA" EXACT []
5356 is_a: SO:0000185 ! primary_transcript
5360 name: spliced_leader_RNA
5361 synonym: "mini-exon" RELATED []
5362 synonym: "spliced leader RNA" EXACT []
5363 is_a: SO:0000835 ! primary_transcript_region
5364 relationship: part_of SO:0000635 ! mini_exon_donor_RNA
5368 name: engineered_plasmid
5369 def: "A plasmid that is engineered." [SO:xp]
5370 synonym: "engineered plasmid" EXACT []
5371 synonym: "engineered plasmid gene" RELATED []
5372 is_a: SO:0000155 ! plasmid
5373 is_a: SO:0000804 ! engineered_region
5374 relationship: has_quality SO:0000783 ! engineered
5378 name: transcribed_spacer_region
5379 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]
5380 synonym: "transcribed spacer region" EXACT []
5381 is_a: SO:0000838 ! rRNA_primary_transcript_region
5385 name: internal_transcribed_spacer_region
5386 def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]
5387 synonym: "internal transcribed spacer region" EXACT []
5388 is_a: SO:0000638 ! transcribed_spacer_region
5392 name: external_transcribed_spacer_region
5393 def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]
5394 synonym: "external transcribed spacer region" EXACT []
5395 is_a: SO:0000638 ! transcribed_spacer_region
5399 name: tetranucleotide_repeat_microsatellite_feature
5400 synonym: "tetranucleotide repeat microsatellite feature" EXACT []
5401 is_a: SO:0000289 ! microsatellite
5405 name: SRP_RNA_encoding
5406 synonym: "SRP RNA encoding" EXACT []
5407 is_a: SO:0000011 ! non_protein_coding
5412 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]
5414 xref: http://en.wikipedia.org/wiki/Minisatellite "wiki"
5415 is_a: SO:0000005 ! satellite_DNA
5420 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]
5422 synonym: "antisense RNA" EXACT []
5423 xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki"
5424 is_a: SO:0000655 ! ncRNA
5425 relationship: derives_from SO:0000645 ! antisense_primary_transcript
5429 name: antisense_primary_transcript
5430 def: "The reverse complement of the primary transcript." [SO:ke]
5432 synonym: "antisense primary transcript" EXACT []
5433 is_a: SO:0000185 ! primary_transcript
5438 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]
5440 synonym: "small interfering RNA" EXACT []
5441 xref: http://en.wikipedia.org/wiki/SiRNA "wiki"
5442 is_a: SO:0000655 ! ncRNA
5446 name: miRNA_primary_transcript
5448 def: "A primary transcript encoding a micro RNA." [SO:ke]
5449 synonym: "micro RNA primary transcript" EXACT []
5450 synonym: "miRNA primary transcript" EXACT []
5451 synonym: "small temporal RNA primary transcript" EXACT []
5452 synonym: "stRNA primary transcript" EXACT []
5453 synonym: "stRNA_primary_transcript" EXACT []
5454 is_a: SO:0000483 ! nc_primary_transcript
5455 relationship: has_part SO:0001244 ! pre_miRNA
5459 name: small_subunit_rRNA
5460 def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]
5462 synonym: "small subunit rRNA" EXACT []
5463 synonym: "SSU RNA" EXACT [RSC:cb]
5464 synonym: "SSU rRNA" EXACT [RSC:cb]
5465 is_a: SO:0000252 ! rRNA
5466 relationship: derives_from SO:0000255 ! rRNA_small_subunit_primary_transcript
5470 name: large_subunit_rRNA
5471 def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]
5473 synonym: "large subunit rRNA" EXACT []
5474 synonym: "LSU RNA" EXACT [RSC:cb]
5475 synonym: "LSU rRNA" EXACT [RSC:cb]
5476 is_a: SO:0000252 ! rRNA
5477 relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript
5482 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]
5484 synonym: "5S LSU rRNA" EXACT []
5485 synonym: "5S ribosomal RNA" EXACT []
5486 synonym: "5S rRNA" EXACT []
5487 synonym: "rRNA 5S" EXACT []
5488 xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki"
5489 is_a: SO:0000651 ! large_subunit_rRNA
5494 def: "A component of the large ribosomal subunit." [SO:ke]
5496 synonym: "28S LSU rRNA" EXACT []
5497 synonym: "28S ribosomal RNA" EXACT []
5498 synonym: "28S rRNA" EXACT []
5499 synonym: "rRNA 28S" EXACT []
5500 xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki"
5501 is_a: SO:0000651 ! large_subunit_rRNA
5505 name: maxicircle_gene
5506 def: "A mitochondrial gene located in a maxicircle." [SO:xp]
5507 synonym: "maxi-circle gene" EXACT []
5508 synonym: "maxicircle gene" EXACT []
5509 is_a: SO:0000089 ! kinetoplast_gene
5510 relationship: part_of SO:0000742 ! maxicircle
5515 def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]
5516 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.
5518 synonym: "noncoding RNA" EXACT []
5519 xref: http://en.wikipedia.org/wiki/NcRNA "wiki"
5520 is_a: SO:0000233 ! mature_transcript
5524 name: stRNA_encoding
5525 synonym: "stRNA encoding" EXACT []
5526 is_a: SO:0000011 ! non_protein_coding
5531 def: "A region of sequence containing one or more repeat units." [SO:ke]
5533 synonym: "repeat region" EXACT []
5534 is_a: SO:0001411 ! biological_region
5535 relationship: has_part SO:0000726 ! repeat_unit
5539 name: dispersed_repeat
5540 def: "A repeat that is located at dispersed sites in the genome." [SO:ke]
5542 synonym: "dispersed repeat" EXACT []
5543 synonym: "interspersed repeat" EXACT []
5544 xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki"
5545 is_a: SO:0000657 ! repeat_region
5549 name: tmRNA_encoding
5550 synonym: "tmRNA encoding" EXACT []
5551 is_a: SO:0000011 ! non_protein_coding
5555 name: DNA_invertase_target_sequence
5560 name: intron_attribute
5565 name: spliceosomal_intron
5566 def: "An intron which is spliced by the spliceosome." [SO:ke]
5567 comment: GO:0000398.
5569 synonym: "spliceosomal intron" EXACT []
5570 is_a: SO:0000188 ! intron
5575 synonym: "tRNA encoding" EXACT []
5576 is_a: SO:0000011 ! non_protein_coding
5580 name: introgressed_chromosome_region
5581 synonym: "introgressed chromosome region" EXACT []
5582 is_a: SO:0000830 ! chromosome_part
5586 name: monocistronic_transcript
5587 def: "A transcript that is monocistronic." [SO:xp]
5588 synonym: "monocistronic transcript" EXACT []
5589 is_a: SO:0000673 ! transcript
5590 relationship: has_quality SO:0000878 ! monocistronic
5595 def: "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]
5596 synonym: "mobile intron" EXACT []
5597 is_a: SO:0000188 ! intron
5598 is_a: SO:0001037 ! mobile_genetic_element
5599 relationship: has_quality SO:0001234 ! mobile
5605 def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]
5608 synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
5609 synonym: "nucleotide insertion" EXACT []
5610 synonym: "nucleotide_insertion" EXACT []
5611 xref: loinc:LA6687-3 "Insertion"
5612 is_a: SO:0001059 ! sequence_alteration
5613 is_a: SO:0001411 ! biological_region
5618 def: "A match against an EST sequence." [SO:ke]
5620 synonym: "EST match" EXACT []
5621 is_a: SO:0000102 ! expressed_sequence_match
5625 name: sequence_rearrangement_feature
5626 synonym: "sequence rearrangement feature" EXACT []
5627 is_a: SO:0000298 ! recombination_feature
5631 name: chromosome_breakage_sequence
5632 def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]
5633 synonym: "chromosome breakage sequence" EXACT []
5634 is_a: SO:0000669 ! sequence_rearrangement_feature
5638 name: internal_eliminated_sequence
5639 def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]
5640 synonym: "internal eliminated sequence" EXACT []
5641 is_a: SO:0000669 ! sequence_rearrangement_feature
5645 name: macronucleus_destined_segment
5646 def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]
5647 synonym: "macronucleus destined segment" EXACT []
5648 is_a: SO:0000669 ! sequence_rearrangement_feature
5653 def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]
5655 xref: http://en.wikipedia.org/wiki/RNA "wiki"
5656 is_a: SO:0000831 ! gene_member_region
5660 name: non_canonical_splice_site
5661 def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke]
5662 synonym: "non canonical splice site" EXACT []
5663 synonym: "non-canonical splice site" EXACT []
5665 consider: SO:0000678
5666 consider: SO:0000679
5670 name: canonical_splice_site
5671 def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke]
5672 synonym: "canonical splice site" EXACT []
5674 consider: SO:0000676
5675 consider: SO:0000677
5679 name: canonical_three_prime_splice_site
5680 def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke]
5681 synonym: "canonical 3' splice site" EXACT []
5682 synonym: "canonical three prime splice site" EXACT []
5683 is_a: SO:0000164 ! three_prime_cis_splice_site
5687 name: canonical_five_prime_splice_site
5688 def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke]
5689 synonym: "canonical 5' splice site" EXACT []
5690 synonym: "canonical five prime splice site" EXACT []
5691 is_a: SO:0000163 ! five_prime_cis_splice_site
5695 name: non_canonical_three_prime_splice_site
5696 def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke]
5697 synonym: "non canonical 3' splice site" RELATED []
5698 synonym: "non canonical three prime splice site" EXACT []
5699 synonym: "non-canonical three prime splice site" EXACT []
5700 is_a: SO:0000164 ! three_prime_cis_splice_site
5704 name: non_canonical_five_prime_splice_site
5705 def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke]
5706 synonym: "non canonical 5' splice site" EXACT []
5707 synonym: "non canonical five prime splice site" EXACT []
5708 synonym: "non-canonical five prime splice site" EXACT []
5709 is_a: SO:0000163 ! five_prime_cis_splice_site
5713 name: non_canonical_start_codon
5714 def: "A start codon that is not the usual AUG sequence." [SO:ke]
5715 synonym: "non ATG start codon" EXACT []
5716 synonym: "non canonical start codon" EXACT []
5717 synonym: "non-canonical start codon" EXACT []
5718 is_a: SO:0000318 ! start_codon
5722 name: aberrant_processed_transcript
5723 def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke]
5724 synonym: "aberrant processed transcript" EXACT []
5725 is_a: SO:0000673 ! transcript
5729 name: splicing_feature
5734 name: exonic_splice_enhancer
5735 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]
5736 synonym: "exonic splice enhancer" EXACT []
5737 is_a: SO:0000344 ! splice_enhancer
5741 name: nuclease_sensitive_site
5742 def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]
5744 synonym: "nuclease sensitive site" EXACT []
5745 is_a: SO:0000059 ! nuclease_binding_site
5749 name: DNAseI_hypersensitive_site
5750 synonym: "DHS" EXACT []
5751 synonym: "DNAseI hypersensitive site" EXACT []
5752 is_a: SO:0000322 ! nuclease_hypersensitive_site
5756 name: translocation_element
5757 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]
5758 synonym: "translocation element" EXACT []
5759 is_a: SO:1000044 ! chromosomal_translocation
5763 name: deletion_junction
5764 def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]
5766 synonym: "deletion junction" EXACT []
5767 is_a: SO:0000699 ! junction
5772 def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]
5774 synonym: "golden path" EXACT []
5775 is_a: SO:0000353 ! sequence_assembly
5780 def: "A match against cDNA sequence." [SO:ke]
5782 synonym: "cDNA match" EXACT []
5783 is_a: SO:0000102 ! expressed_sequence_match
5787 name: gene_with_polycistronic_transcript
5788 def: "A gene that encodes a polycistronic transcript." [SO:xp]
5789 synonym: "gene with polycistronic transcript" EXACT []
5790 is_a: SO:0000704 ! gene
5791 relationship: transcribed_to SO:0000078 ! polycistronic_transcript
5795 name: cleaved_initiator_methionine
5797 def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]
5799 synonym: "cleaved initiator methionine" EXACT []
5800 synonym: "init_met" RELATED [uniprot:feature_type]
5801 synonym: "initiator methionine" RELATED []
5802 is_a: SO:0100011 ! cleaved_peptide_region
5806 name: gene_with_dicistronic_transcript
5807 def: "A gene that encodes a dicistronic transcript." [SO:xp]
5808 synonym: "gene with dicistronic transcript" EXACT []
5809 is_a: SO:0000690 ! gene_with_polycistronic_transcript
5810 relationship: transcribed_to SO:0000079 ! dicistronic_transcript
5814 name: gene_with_recoded_mRNA
5815 def: "A gene that encodes an mRNA that is recoded." [SO:xp]
5816 synonym: "gene with recoded mRNA" EXACT []
5817 is_a: SO:0001217 ! protein_coding_gene
5818 relationship: has_quality SO:0000881 ! recoded
5823 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]
5825 synonym: "single nucleotide polymorphism" EXACT []
5826 is_a: SO:0001483 ! SNV
5831 def: "A sequence used in experiment." [SO:ke]
5832 comment: Requested by Lynn Crosby, jan 2006.
5834 is_a: SO:0001409 ! biomaterial_region
5839 def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]
5841 synonym: "oligonucleotide" EXACT []
5842 xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki"
5843 is_a: SO:0000695 ! reagent
5847 name: gene_with_stop_codon_read_through
5848 def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp]
5849 synonym: "gene with stop codon read through" EXACT []
5850 is_a: SO:0000693 ! gene_with_recoded_mRNA
5851 relationship: has_part SO:0000883 ! stop_codon_read_through
5855 name: gene_with_stop_codon_redefined_as_pyrrolysine
5856 def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]
5857 synonym: "gene with stop codon redefined as pyrrolysine" EXACT []
5858 is_a: SO:0000697 ! gene_with_stop_codon_read_through
5859 relationship: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine
5864 def: "A sequence_feature with an extent of zero." [SO:ke]
5865 comment: A junction is a boundary between regions. A boundary has an extent of zero.
5867 synonym: "boundary" EXACT []
5868 synonym: "breakpoint" EXACT []
5869 is_a: SO:0000110 ! sequence_feature
5874 def: "A comment about the sequence." [SO:ke]
5876 is_a: SO:0001410 ! experimental_feature
5880 name: possible_base_call_error
5881 def: "A region of sequence where the validity of the base calling is questionable." [SO:ke]
5883 synonym: "possible base call error" EXACT []
5884 is_a: SO:0000413 ! sequence_difference
5888 name: possible_assembly_error
5889 def: "A region of sequence where there may have been an error in the assembly." [SO:ke]
5891 synonym: "possible assembly error" EXACT []
5892 is_a: SO:0000413 ! sequence_difference
5896 name: experimental_result_region
5897 def: "A region of sequence implicated in an experimental result." [SO:ke]
5899 synonym: "experimental result region" EXACT []
5900 is_a: SO:0000700 ! remark
5905 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]
5906 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
5908 xref: http://en.wikipedia.org/wiki/Gene "wiki"
5909 is_a: SO:0001411 ! biological_region
5910 relationship: member_of SO:0005855 ! gene_group
5915 def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]
5917 synonym: "tandem repeat" EXACT []
5918 xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki"
5919 xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
5920 is_a: SO:0000657 ! repeat_region
5924 name: trans_splice_acceptor_site
5925 def: "The 3' splice site of the acceptor primary transcript." [SO:ke]
5926 comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
5928 synonym: "3' trans splice site" RELATED []
5929 synonym: "trans splice acceptor site" EXACT []
5930 is_a: SO:0001420 ! trans_splice_site
5934 name: trans_splice_donor_site
5935 def: "The 5' five prime splice site region of the donor RNA." [SO:ke]
5936 comment: SL RNA contains a donor site.
5937 synonym: "5 prime trans splice site" RELATED []
5938 synonym: "trans splice donor site" EXACT []
5939 synonym: "trans-splice donor site" EXACT []
5940 is_a: SO:0001420 ! trans_splice_site
5944 name: SL1_acceptor_site
5945 def: "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]
5946 synonym: "SL1 acceptor site" EXACT []
5947 is_a: SO:0000706 ! trans_splice_acceptor_site
5951 name: SL2_acceptor_site
5952 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]
5953 synonym: "SL2 acceptor site" EXACT []
5954 is_a: SO:0000706 ! trans_splice_acceptor_site
5958 name: gene_with_stop_codon_redefined_as_selenocysteine
5959 def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]
5960 synonym: "gene with stop codon redefined as selenocysteine" EXACT []
5961 is_a: SO:0000697 ! gene_with_stop_codon_read_through
5962 relationship: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine
5966 name: gene_with_mRNA_recoded_by_translational_bypass
5967 def: "A gene with mRNA recoded by translational bypass." [SO:xp]
5968 synonym: "gene with mRNA recoded by translational bypass" EXACT []
5969 is_a: SO:0000693 ! gene_with_recoded_mRNA
5970 relationship: has_quality SO:0000886 ! recoded_by_translational_bypass
5974 name: gene_with_transcript_with_translational_frameshift
5975 def: "A gene encoding a transcript that has a translational frameshift." [SO:xp]
5976 synonym: "gene with transcript with translational frameshift" EXACT []
5977 is_a: SO:0000693 ! gene_with_recoded_mRNA
5978 relationship: has_quality SO:0000887 ! translationally_frameshifted
5983 def: "A motif that is active in the DNA form of the sequence." [SO:ke]
5984 synonym: "DNA motif" EXACT []
5985 xref: http://en.wikipedia.org/wiki/DNA_motif "wiki"
5986 is_a: SO:0000714 ! nucleotide_motif
5990 name: nucleotide_motif
5991 def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke]
5993 synonym: "nucleotide motif" EXACT []
5994 is_a: SO:0001683 ! sequence_motif
5999 def: "A motif that is active in RNA sequence." [SO:ke]
6001 synonym: "RNA motif" EXACT []
6002 is_a: SO:0000714 ! nucleotide_motif
6006 name: dicistronic_mRNA
6007 def: "An mRNA that has the quality dicistronic." [SO:ke]
6008 synonym: "dicistronic mRNA" EXACT []
6009 synonym: "dicistronic processed transcript" RELATED []
6010 is_a: SO:0000079 ! dicistronic_transcript
6011 is_a: SO:0000634 ! polycistronic_mRNA
6012 relationship: has_quality SO:0000879 ! dicistronic
6017 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]
6018 comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
6020 synonym: "reading frame" EXACT []
6021 xref: http://en.wikipedia.org/wiki/Reading_frame "wiki"
6022 is_a: SO:0001410 ! experimental_feature
6026 name: blocked_reading_frame
6027 def: "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]
6028 comment: Term requested by Rama from SGD.
6029 synonym: "blocked reading frame" EXACT []
6030 is_a: SO:0000717 ! reading_frame
6035 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]
6037 synonym: "superscaffold" RELATED []
6038 is_a: SO:0001876 ! partial_genomic_sequence_assembly
6042 name: foreign_transposable_element
6043 def: "A transposable element that is foreign." [SO:ke]
6044 comment: requested by Michael on 19 Nov 2004.
6045 synonym: "foreign transposable element" EXACT []
6046 is_a: SO:0000101 ! transposable_element
6047 relationship: has_quality SO:0000784 ! foreign
6051 name: gene_with_dicistronic_primary_transcript
6052 def: "A gene that encodes a dicistronic primary transcript." [SO:xp]
6053 comment: Requested by Michael, 19 nov 2004.
6054 synonym: "gene with dicistronic primary transcript" EXACT []
6055 is_a: SO:0000692 ! gene_with_dicistronic_transcript
6056 relationship: transcribed_to SO:1001197 ! dicistronic_primary_transcript
6060 name: gene_with_dicistronic_mRNA
6061 def: "A gene that encodes a polycistronic mRNA." [SO:xp]
6062 comment: Requested by MA nov 19 2004.
6063 synonym: "gene with dicistronic mRNA" EXACT []
6064 synonym: "gene with dicistronic processed transcript" EXACT []
6065 is_a: SO:0000692 ! gene_with_dicistronic_transcript
6066 relationship: transcribed_to SO:0000716 ! dicistronic_mRNA
6071 def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]
6072 synonym: "intervening DNA" EXACT []
6073 xref: http://en.wikipedia.org/wiki/IDNA "wiki"
6074 is_a: SO:0000298 ! recombination_feature
6079 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]
6081 synonym: "origin of transfer" EXACT []
6082 xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki"
6083 is_a: SO:0000296 ! origin_of_replication
6087 name: transit_peptide
6089 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]
6090 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.
6093 synonym: "signal" RELATED []
6094 synonym: "transit" RELATED [uniprot:feature_type]
6095 synonym: "transit peptide" EXACT []
6096 is_a: SO:0001527 ! peptide_localization_signal
6101 def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke]
6102 comment: Added to comply with the feature table. A single repeat.
6103 synonym: "repeat unit" EXACT []
6104 xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
6105 is_a: SO:0001411 ! biological_region
6110 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]
6111 comment: Requested by Stephen Grossmann Dec 2004.
6113 synonym: "cis regulatory module" EXACT []
6114 synonym: "TF module" EXACT []
6115 synonym: "transcription factor module" EXACT []
6116 is_a: SO:0001055 ! transcriptional_cis_regulatory_region
6117 relationship: has_part SO:0000235 ! TF_binding_site
6122 def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]
6123 comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
6124 synonym: "protein intron" RELATED []
6125 xref: http://en.wikipedia.org/wiki/Intein "wiki"
6126 is_a: SO:0100011 ! cleaved_peptide_region
6130 name: intein_containing
6131 def: "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]
6132 synonym: "intein containing" EXACT []
6133 is_a: SO:0000010 ! protein_coding
6138 def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]
6140 is_a: SO:0000143 ! assembly_component
6141 relationship: part_of SO:0000353 ! sequence_assembly
6146 def: "An attribute to describe a feature that is incomplete." [SO:ke]
6147 comment: Term added because of request by MO people.
6148 synonym: "fragment" EXACT []
6149 is_a: SO:0000905 ! status
6154 def: "An attribute describing an unverified region." [SO:ke]
6155 xref: http://en.wikipedia.org/wiki/Predicted "wiki"
6156 is_a: SO:0000905 ! status
6160 name: feature_attribute
6161 def: "An attribute describing a located_sequence_feature." [SO:ke]
6162 synonym: "feature attribute" EXACT []
6163 is_a: SO:0000400 ! sequence_attribute
6168 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]
6169 comment: Added for the MO people.
6170 synonym: "exemplar mRNA" EXACT []
6171 is_a: SO:0000234 ! mRNA
6172 relationship: has_quality SO:0000864 ! exemplar
6176 name: sequence_location
6177 synonym: "sequence location" EXACT []
6178 is_a: SO:0000400 ! sequence_attribute
6182 name: organelle_sequence
6183 synonym: "organelle sequence" EXACT []
6184 is_a: SO:0000735 ! sequence_location
6188 name: mitochondrial_sequence
6189 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
6190 synonym: "mitochondrial sequence" EXACT []
6191 is_a: SO:0000736 ! organelle_sequence
6195 name: nuclear_sequence
6196 synonym: "nuclear sequence" EXACT []
6197 is_a: SO:0000736 ! organelle_sequence
6201 name: nucleomorphic_sequence
6202 synonym: "nucleomorphic sequence" EXACT []
6203 is_a: SO:0000736 ! organelle_sequence
6207 name: plastid_sequence
6208 synonym: "plastid sequence" EXACT []
6209 is_a: SO:0000736 ! organelle_sequence
6215 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]
6216 synonym: "kinetoplast_chromosome" EXACT []
6217 xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki"
6218 is_a: SO:0001026 ! genome
6219 relationship: has_part SO:0000742 ! maxicircle
6220 relationship: has_part SO:0000980 ! minicircle
6226 def: "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]
6227 synonym: "maxicircle_chromosome" EXACT []
6228 is_a: SO:0001235 ! replicon
6232 name: apicoplast_sequence
6233 synonym: "apicoplast sequence" EXACT []
6234 is_a: SO:0000740 ! plastid_sequence
6238 name: chromoplast_sequence
6239 synonym: "chromoplast sequence" EXACT []
6240 is_a: SO:0000740 ! plastid_sequence
6244 name: chloroplast_sequence
6245 synonym: "chloroplast sequence" EXACT []
6246 is_a: SO:0000740 ! plastid_sequence
6250 name: cyanelle_sequence
6251 synonym: "cyanelle sequence" EXACT []
6252 is_a: SO:0000740 ! plastid_sequence
6256 name: leucoplast_sequence
6257 synonym: "leucoplast sequence" EXACT []
6258 is_a: SO:0000740 ! plastid_sequence
6262 name: proplastid_sequence
6263 synonym: "proplastid sequence" EXACT []
6264 is_a: SO:0000740 ! plastid_sequence
6268 name: plasmid_location
6269 synonym: "plasmid location" EXACT []
6270 is_a: SO:0000735 ! sequence_location
6274 name: amplification_origin
6275 def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]
6276 synonym: "amplification origin" EXACT []
6277 is_a: SO:0000296 ! origin_of_replication
6281 name: proviral_location
6282 synonym: "proviral location" EXACT []
6283 is_a: SO:0000735 ! sequence_location
6287 name: gene_group_regulatory_region
6289 synonym: "gene group regulatory region" EXACT []
6290 is_a: SO:0001679 ! transcription_regulatory_region
6291 relationship: member_of SO:0005855 ! gene_group
6296 def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]
6298 synonym: "clone insert" EXACT []
6299 is_a: SO:0000695 ! reagent
6300 relationship: part_of SO:0000151 ! clone
6305 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]
6306 synonym: "lambda vector" EXACT []
6307 is_a: SO:0000440 ! vector_replicon
6311 name: plasmid_vector
6312 synonym: "plasmid vector" EXACT []
6313 xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors "wiki"
6314 is_a: SO:0000440 ! vector_replicon
6315 relationship: derives_from SO:0000155 ! plasmid
6320 def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]
6321 synonym: "complementary DNA" EXACT []
6322 xref: http://en.wikipedia.org/wiki/CDNA "wiki"
6323 is_a: SO:0000352 ! DNA
6327 name: single_stranded_cDNA
6328 synonym: "single strand cDNA" EXACT []
6329 synonym: "single stranded cDNA" EXACT []
6330 synonym: "single-strand cDNA" RELATED []
6331 is_a: SO:0000756 ! cDNA
6335 name: double_stranded_cDNA
6336 synonym: "double strand cDNA" RELATED []
6337 synonym: "double stranded cDNA" EXACT []
6338 synonym: "double-strand cDNA" RELATED []
6339 is_a: SO:0000756 ! cDNA
6353 name: phagemid_clone
6359 synonym: "P1_clone" RELATED []
6379 name: pyrrolysyl_tRNA
6380 def: "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]
6381 synonym: "pyrrolysyl tRNA" EXACT []
6382 synonym: "pyrrolysyl-transfer ribonucleic acid" EXACT []
6383 synonym: "pyrrolysyl-transfer RNA" EXACT []
6384 is_a: SO:0000253 ! tRNA
6385 relationship: derives_from SO:0001178 ! pyrrolysine_tRNA_primary_transcript
6389 name: clone_insert_start
6395 def: "A plasmid that may integrate with a chromosome." [SO:ma]
6396 is_a: SO:0000155 ! plasmid
6400 name: tmRNA_coding_piece
6401 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]
6402 comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005.
6403 synonym: "tmRNA coding piece" EXACT []
6404 is_a: SO:0000847 ! tmRNA_region
6408 name: tmRNA_acceptor_piece
6409 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]
6410 comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005.
6411 synonym: "tmRNA acceptor piece" EXACT []
6412 is_a: SO:0000847 ! tmRNA_region
6417 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/]
6418 comment: Added in respose to request by Simon Twigger November 14th 2005.
6419 synonym: "quantitative trait locus" EXACT []
6420 is_a: SO:0001411 ! biological_region
6424 name: genomic_island
6425 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]
6426 comment: Genomic islands are transmissible elements characterized by large size (>10kb).
6427 synonym: "genomic island" EXACT []
6428 xref: http://en.wikipedia.org/wiki/Genomic_island "wiki"
6429 is_a: SO:0001039 ! integrated_mobile_genetic_element
6433 name: pathogenic_island
6434 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]
6435 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.
6436 synonym: "pathogenic island" EXACT []
6437 is_a: SO:0000772 ! genomic_island
6441 name: metabolic_island
6442 def: "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
6443 comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
6444 synonym: "metabolic island" EXACT []
6445 is_a: SO:0000772 ! genomic_island
6449 name: adaptive_island
6450 def: "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]
6451 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.
6452 synonym: "adaptive island" EXACT []
6453 is_a: SO:0000772 ! genomic_island
6457 name: symbiosis_island
6458 def: "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
6459 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.
6460 synonym: "symbiosis island" EXACT []
6461 is_a: SO:0000772 ! genomic_island
6465 name: pseudogenic_rRNA
6466 def: "A non functional descendant of an rRNA." [SO:ke]
6467 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.
6469 synonym: "pseudogenic rRNA" EXACT []
6470 is_a: SO:0000462 ! pseudogenic_region
6474 name: pseudogenic_tRNA
6475 def: "A non functional descendent of a tRNA." [SO:ke]
6476 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.
6478 synonym: "pseudogenic tRNA" EXACT []
6479 is_a: SO:0000462 ! pseudogenic_region
6483 name: engineered_episome
6484 def: "An episome that is engineered." [SO:xp]
6485 comment: Requested by Lynn Crosby Jan 2006.
6486 synonym: "engineered episome" EXACT []
6487 is_a: SO:0000637 ! engineered_plasmid
6488 is_a: SO:0000768 ! episome
6489 relationship: has_quality SO:0000783 ! engineered
6493 name: transposable_element_attribute
6494 comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs
6500 def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke]
6501 is_a: SO:0000733 ! feature_attribute
6506 def: "An attribute describing a feature that occurs in nature." [SO:ke]
6507 is_a: SO:0000733 ! feature_attribute
6512 def: "An attribute to describe a region that was modified in vitro." [SO:ke]
6513 is_a: SO:0000733 ! feature_attribute
6518 def: "An attribute to describe a region from another species." [SO:ke]
6519 is_a: SO:0000733 ! feature_attribute
6524 comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
6525 synonym: "cloned region" EXACT []
6526 synonym: "cloned segment" EXACT []
6527 is_a: SO:0000695 ! reagent
6528 relationship: part_of SO:0000753 ! clone_insert
6532 name: reagent_attribute
6533 comment: Added jan 2006 by KE.
6534 synonym: "reagent attribute" EXACT []
6539 name: clone_attribute
6550 def: "An attribute to describe a feature that has been proven." [SO:ke]
6551 is_a: SO:0000905 ! status
6556 def: "An attribute describing a feature that is invalidated." [SO:ke]
6557 is_a: SO:0000905 ! status
6561 name: cloned_genomic
6571 name: engineered_DNA
6576 name: engineered_rescue_region
6577 def: "A rescue region that is engineered." [SO:xp]
6578 synonym: "engineered rescue fragment" EXACT []
6579 synonym: "engineered rescue region" EXACT []
6580 synonym: "engineered rescue segment" EXACT []
6581 is_a: SO:0000411 ! rescue_region
6582 is_a: SO:0000804 ! engineered_region
6583 relationship: has_quality SO:0000783 ! engineered
6587 name: rescue_mini_gene
6588 def: "A mini_gene that rescues." [SO:xp]
6589 synonym: "rescue mini gene" EXACT []
6590 synonym: "rescue mini-gene" EXACT []
6591 is_a: SO:0000815 ! mini_gene
6592 relationship: has_quality SO:0000814 ! rescue
6596 name: transgenic_transposable_element
6597 def: "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]
6598 comment: Modified as requested by Lynn - FB. May 2007.
6599 synonym: "transgenic transposable element" EXACT []
6600 is_a: SO:0000101 ! transposable_element
6601 relationship: derives_from SO:0000151 ! clone
6602 relationship: has_quality SO:0000781 ! transgenic
6606 name: natural_transposable_element
6607 def: "TE that exists (or existed) in nature." [FB:mc]
6608 synonym: "natural transposable element" EXACT []
6609 is_a: SO:0000101 ! transposable_element
6610 is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
6611 relationship: has_quality SO:0000782 ! natural
6615 name: engineered_transposable_element
6616 def: "TE that has been modified by manipulations in vitro." [FB:mc]
6617 synonym: "engineered transposable element" EXACT []
6618 is_a: SO:0000101 ! transposable_element
6619 is_a: SO:0000804 ! engineered_region
6620 relationship: has_quality SO:0000783 ! engineered
6624 name: engineered_foreign_transposable_element
6625 def: "A transposable_element that is engineered and foreign." [FB:mc]
6626 synonym: "engineered foreign transposable element" EXACT []
6627 is_a: SO:0000720 ! foreign_transposable_element
6628 is_a: SO:0000798 ! engineered_transposable_element
6629 is_a: SO:0000805 ! engineered_foreign_region
6630 relationship: has_quality SO:0000783 ! engineered
6631 relationship: has_quality SO:0000784 ! foreign
6635 name: assortment_derived_duplication
6636 def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]
6637 synonym: "assortment derived duplication" EXACT []
6638 is_a: SO:0001504 ! assortment_derived_variation
6642 name: assortment_derived_deficiency_plus_duplication
6643 def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]
6644 synonym: "assortment derived deficiency plus duplication" EXACT []
6645 is_a: SO:0001504 ! assortment_derived_variation
6649 name: assortment_derived_deficiency
6650 def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]
6651 synonym: "assortment-derived deficiency" EXACT []
6652 is_a: SO:0001504 ! assortment_derived_variation
6656 name: assortment_derived_aneuploid
6657 def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]
6658 synonym: "assortment derived aneuploid" EXACT []
6659 is_a: SO:0001504 ! assortment_derived_variation
6663 name: engineered_region
6664 def: "A region that is engineered." [SO:xp]
6665 synonym: "construct" EXACT []
6666 synonym: "engineered region" EXACT []
6667 synonym: "engineered sequence" EXACT []
6668 is_a: SO:0001409 ! biomaterial_region
6669 relationship: has_quality SO:0000783 ! engineered
6673 name: engineered_foreign_region
6674 def: "A region that is engineered and foreign." [SO:xp]
6675 synonym: "engineered foreign region" EXACT []
6676 is_a: SO:0000804 ! engineered_region
6677 relationship: has_quality SO:0000783 ! engineered
6678 relationship: has_quality SO:0000784 ! foreign
6683 is_a: SO:0000733 ! feature_attribute
6687 name: engineered_tag
6688 def: "A tag that is engineered." [SO:xp]
6689 synonym: "engineered tag" EXACT []
6690 is_a: SO:0000324 ! tag
6691 is_a: SO:0000804 ! engineered_region
6692 relationship: has_quality SO:0000783 ! engineered
6696 name: validated_cDNA_clone
6697 def: "A cDNA clone that has been validated." [SO:xp]
6698 synonym: "validated cDNA clone" EXACT []
6699 is_a: SO:0000317 ! cDNA_clone
6700 relationship: has_quality SO:0000789 ! validated
6704 name: invalidated_cDNA_clone
6705 def: "A cDNA clone that is invalid." [SO:xp]
6706 synonym: "invalidated cDNA clone" EXACT []
6707 is_a: SO:0000317 ! cDNA_clone
6708 relationship: has_quality SO:0000790 ! invalidated
6712 name: chimeric_cDNA_clone
6713 def: "A cDNA clone invalidated because it is chimeric." [SO:xp]
6714 synonym: "chimeric cDNA clone" EXACT []
6715 is_a: SO:0000809 ! invalidated_cDNA_clone
6716 relationship: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA
6720 name: genomically_contaminated_cDNA_clone
6721 def: "A cDNA clone invalidated by genomic contamination." [SO:xp]
6722 synonym: "genomically contaminated cDNA clone" EXACT []
6723 is_a: SO:0000809 ! invalidated_cDNA_clone
6724 relationship: has_quality SO:0000414 ! invalidated_by_genomic_contamination
6728 name: polyA_primed_cDNA_clone
6729 def: "A cDNA clone invalidated by polyA priming." [SO:xp]
6730 synonym: "polyA primed cDNA clone" EXACT []
6731 is_a: SO:0000809 ! invalidated_cDNA_clone
6732 relationship: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA
6736 name: partially_processed_cDNA_clone
6737 def: "A cDNA invalidated clone by partial processing." [SO:xp]
6738 synonym: "partially processed cDNA clone" EXACT []
6739 is_a: SO:0000809 ! invalidated_cDNA_clone
6740 relationship: has_quality SO:0000416 ! invalidated_by_partial_processing
6745 def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]
6746 is_a: SO:0000733 ! feature_attribute
6751 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]
6752 synonym: "mini gene" EXACT []
6753 is_a: SO:0000236 ! ORF
6758 def: "A gene that rescues." [SO:xp]
6759 synonym: "rescue gene" EXACT []
6760 is_a: SO:0000704 ! gene
6761 relationship: has_quality SO:0000814 ! rescue
6766 def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]
6767 synonym: "wild type" EXACT []
6768 xref: http://en.wikipedia.org/wiki/Wild_type "wiki"
6769 xref: loinc:LA9658-1 "wild type"
6770 is_a: SO:0000733 ! feature_attribute
6774 name: wild_type_rescue_gene
6775 def: "A gene that rescues." [SO:xp]
6776 synonym: "wild type rescue gene" EXACT []
6777 is_a: SO:0000816 ! rescue_gene
6778 relationship: has_quality SO:0000817 ! wild_type
6782 name: mitochondrial_chromosome
6783 def: "A chromosome originating in a mitochondria." [SO:xp]
6784 synonym: "mitochondrial chromosome" EXACT []
6785 is_a: SO:0000340 ! chromosome
6786 relationship: has_origin SO:0000737 ! mitochondrial_sequence
6790 name: chloroplast_chromosome
6791 def: "A chromosome originating in a chloroplast." [SO:xp]
6792 synonym: "chloroplast chromosome" EXACT []
6793 is_a: SO:0000340 ! chromosome
6794 relationship: has_origin SO:0000745 ! chloroplast_sequence
6798 name: chromoplast_chromosome
6799 def: "A chromosome originating in a chromoplast." [SO:xp]
6800 synonym: "chromoplast chromosome" EXACT []
6801 is_a: SO:0000340 ! chromosome
6802 relationship: has_origin SO:0000744 ! chromoplast_sequence
6806 name: cyanelle_chromosome
6807 def: "A chromosome originating in a cyanelle." [SO:xp]
6808 synonym: "cyanelle chromosome" EXACT []
6809 is_a: SO:0000340 ! chromosome
6810 relationship: has_origin SO:0000746 ! cyanelle_sequence
6814 name: leucoplast_chromosome
6815 def: "A chromosome with origin in a leucoplast." [SO:xp]
6816 synonym: "leucoplast chromosome" EXACT []
6817 is_a: SO:0000340 ! chromosome
6818 relationship: has_origin SO:0000747 ! leucoplast_sequence
6822 name: macronuclear_chromosome
6823 def: "A chromosome originating in a macronucleus." [SO:xp]
6824 synonym: "macronuclear chromosome" EXACT []
6825 is_a: SO:0000340 ! chromosome
6826 relationship: has_origin SO:0000083 ! macronuclear_sequence
6830 name: micronuclear_chromosome
6831 def: "A chromosome originating in a micronucleus." [SO:xp]
6832 synonym: "micronuclear chromosome" EXACT []
6833 is_a: SO:0000340 ! chromosome
6834 relationship: has_origin SO:0000084 ! micronuclear_sequence
6838 name: nuclear_chromosome
6839 def: "A chromosome originating in a nucleus." [SO:xp]
6840 synonym: "nuclear chromosome" EXACT []
6841 is_a: SO:0000340 ! chromosome
6842 relationship: has_origin SO:0000738 ! nuclear_sequence
6846 name: nucleomorphic_chromosome
6847 def: "A chromosome originating in a nucleomorph." [SO:xp]
6848 synonym: "nucleomorphic chromosome" EXACT []
6849 is_a: SO:0000340 ! chromosome
6850 relationship: has_origin SO:0000739 ! nucleomorphic_sequence
6854 name: chromosome_part
6855 def: "A region of a chromosome." [SO:ke]
6856 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.
6858 synonym: "chromosome part" EXACT []
6859 is_a: SO:0001411 ! biological_region
6860 relationship: part_of SO:0000340 ! chromosome
6864 name: gene_member_region
6865 def: "A region of a gene." [SO:ke]
6866 comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.
6868 synonym: "gene member region" EXACT []
6869 is_a: SO:0001411 ! biological_region
6870 relationship: member_of SO:0000704 ! gene
6874 name: promoter_region
6875 def: "A region of sequence which is part of a promoter." [SO:ke]
6876 comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
6881 name: transcript_region
6882 def: "A region of a transcript." [SO:ke]
6883 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.
6885 synonym: "transcript region" EXACT []
6886 is_a: SO:0001411 ! biological_region
6887 relationship: part_of SO:0000673 ! transcript
6891 name: mature_transcript_region
6892 def: "A region of a mature transcript." [SO:ke]
6893 comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
6895 synonym: "mature transcript region" EXACT []
6896 is_a: SO:0000833 ! transcript_region
6900 name: primary_transcript_region
6901 def: "A part of a primary transcript." [SO:ke]
6902 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.
6904 synonym: "primary transcript region" EXACT []
6905 is_a: SO:0000833 ! transcript_region
6906 relationship: part_of SO:0000185 ! primary_transcript
6911 def: "A region of an mRNA." [SO:cb]
6912 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.
6914 synonym: "mRNA region" EXACT []
6915 is_a: SO:0000834 ! mature_transcript_region
6916 relationship: part_of SO:0000234 ! mRNA
6921 def: "A region of UTR." [SO:ke]
6922 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.
6924 synonym: "UTR region" EXACT []
6925 is_a: SO:0000836 ! mRNA_region
6929 name: rRNA_primary_transcript_region
6930 def: "A region of an rRNA primary transcript." [SO:ke]
6931 comment: To allow transcribed_spacer_region to have a path to the root.
6932 synonym: "rRNA primary transcript region" EXACT []
6933 is_a: SO:0000835 ! primary_transcript_region
6934 relationship: part_of SO:0000209 ! rRNA_primary_transcript
6938 name: polypeptide_region
6941 def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]
6942 comment: Added to allow the polypeptide regions to have is_a paths back to the root.
6945 synonym: "positional" RELATED []
6946 synonym: "positional polypeptide feature" RELATED []
6947 synonym: "region" NARROW [uniprot:feature_type]
6948 synonym: "region or site annotation" RELATED []
6949 synonym: "site" NARROW [uniprot:feature_type]
6950 is_a: SO:0001411 ! biological_region
6951 relationship: part_of SO:0000104 ! polypeptide
6955 name: repeat_component
6956 def: "A region of a repeated sequence." [SO:ke]
6957 comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root.
6958 synonym: "repeat component" EXACT []
6959 is_a: SO:0001412 ! topologically_defined_region
6963 name: spliceosomal_intron_region
6964 def: "A region within an intron." [SO:ke]
6965 comment: A terms added to allow the parts of introns to have is_a paths to the root.
6967 synonym: "spliceosomal intron region" EXACT []
6968 is_a: SO:0000835 ! primary_transcript_region
6969 relationship: part_of SO:0000662 ! spliceosomal_intron
6973 name: gene_component_region
6975 synonym: "gene component region" EXACT []
6976 is_a: SO:0001411 ! biological_region
6977 relationship: part_of SO:0000704 ! gene
6981 name: bacterial_RNApol_promoter_region
6982 def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke]
6983 comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
6988 name: RNApol_II_promoter_region
6989 def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke]
6990 comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
6995 name: RNApol_III_promoter_type_1_region
6996 def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke]
6997 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.
7002 name: RNApol_III_promoter_type_2_region
7003 def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke]
7004 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.
7010 def: "A region of a tmRNA." [SO:cb]
7011 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.
7012 synonym: "tmRNA region" EXACT []
7013 is_a: SO:0000834 ! mature_transcript_region
7014 relationship: part_of SO:0000584 ! tmRNA
7019 synonym: "long term repeat component" EXACT []
7020 synonym: "LTR component" EXACT []
7021 is_a: SO:0000840 ! repeat_component
7022 relationship: part_of SO:0000286 ! long_terminal_repeat
7026 name: three_prime_LTR_component
7027 synonym: "3' long terminal repeat component" EXACT []
7028 synonym: "three prime LTR component" EXACT []
7029 is_a: SO:0000848 ! LTR_component
7030 relationship: part_of SO:0000426 ! three_prime_LTR
7034 name: five_prime_LTR_component
7035 synonym: "5' long term repeat component" EXACT []
7036 synonym: "five prime LTR component" EXACT []
7037 is_a: SO:0000848 ! LTR_component
7038 relationship: part_of SO:0000425 ! five_prime_LTR
7043 def: "A region of a CDS." [SO:cb]
7045 synonym: "CDS region" EXACT []
7046 is_a: SO:0000836 ! mRNA_region
7047 relationship: part_of SO:0000316 ! CDS
7052 def: "A region of an exon." [RSC:cb]
7054 synonym: "exon region" EXACT []
7055 is_a: SO:0000833 ! transcript_region
7056 relationship: part_of SO:0000147 ! exon
7060 name: homologous_region
7061 def: "A region that is homologous to another region." [SO:ke]
7062 synonym: "homolog" EXACT []
7063 synonym: "homologous region" EXACT []
7064 synonym: "homologue" EXACT []
7065 xref: http://en.wikipedia.org/wiki/Homology_(biology) "wiki"
7066 is_a: SO:0000330 ! conserved_region
7067 relationship: has_quality SO:0000857 ! homologous
7071 name: paralogous_region
7072 def: "A homologous_region that is paralogous to another region." [SO:ke]
7073 comment: A term to be used in conjunction with the paralogous_to relationship.
7074 synonym: "paralog" EXACT []
7075 synonym: "paralogous region" EXACT []
7076 synonym: "paralogue" EXACT []
7077 xref: http://en.wikipedia.org/wiki/Paralog#Paralogy "wiki"
7078 is_a: SO:0000853 ! homologous_region
7079 relationship: has_quality SO:0000859 ! paralogous
7083 name: orthologous_region
7084 def: "A homologous_region that is orthologous to another region." [SO:ke]
7085 comment: This term should be used in conjunction with the similarity relationships defined in SO.
7086 synonym: "ortholog" EXACT []
7087 synonym: "orthologous region" EXACT []
7088 synonym: "orthologue" EXACT []
7089 xref: http://en.wikipedia.org/wiki/Ortholog#Orthology "wiki"
7090 is_a: SO:0000853 ! homologous_region
7091 relationship: has_quality SO:0000858 ! orthologous
7096 is_a: SO:0000733 ! feature_attribute
7101 def: "Similarity due to common ancestry." [SO:ke]
7102 is_a: SO:0000856 ! conserved
7107 def: "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]
7108 is_a: SO:0000857 ! homologous
7113 def: "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]
7114 is_a: SO:0000857 ! homologous
7119 def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]
7120 xref: http://en.wikipedia.org/wiki/Syntenic "wiki"
7121 is_a: SO:0000856 ! conserved
7125 name: capped_primary_transcript
7126 def: "A primary transcript that is capped." [SO:xp]
7127 synonym: "capped primary transcript" EXACT []
7128 is_a: SO:0000185 ! primary_transcript
7129 relationship: adjacent_to SO:0000581 ! cap
7130 relationship: has_quality SO:0000146 ! capped
7135 def: "An mRNA that is capped." [SO:xp]
7136 synonym: "capped mRNA" EXACT []
7137 is_a: SO:0000234 ! mRNA
7138 relationship: adjacent_to SO:0000581 ! cap
7139 relationship: has_quality SO:0000146 ! capped
7143 name: mRNA_attribute
7144 def: "An attribute describing an mRNA feature." [SO:ke]
7145 synonym: "mRNA attribute" EXACT []
7146 is_a: SO:0000237 ! transcript_attribute
7151 def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]
7152 is_a: SO:0000863 ! mRNA_attribute
7157 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]
7158 xref: http://en.wikipedia.org/wiki/Frameshift "wiki"
7159 is_a: SO:0000863 ! mRNA_attribute
7163 name: minus_1_frameshift
7164 def: "A frameshift caused by deleting one base." [SO:ke]
7165 synonym: "minus 1 frameshift" EXACT []
7166 is_a: SO:0000865 ! frameshift
7170 name: minus_2_frameshift
7171 def: "A frameshift caused by deleting two bases." [SO:ke]
7172 synonym: "minus 2 frameshift" EXACT []
7173 is_a: SO:0000865 ! frameshift
7177 name: plus_1_frameshift
7178 def: "A frameshift caused by inserting one base." [SO:ke]
7179 synonym: "plus 1 frameshift" EXACT []
7180 is_a: SO:0000865 ! frameshift
7184 name: plus_2_framshift
7185 def: "A frameshift caused by inserting two bases." [SO:ke]
7186 synonym: "plus 2 framshift" EXACT []
7187 is_a: SO:0000865 ! frameshift
7192 def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]
7193 synonym: "trans-spliced" EXACT []
7194 is_a: SO:0000237 ! transcript_attribute
7198 name: polyadenylated_mRNA
7199 def: "An mRNA that is polyadenylated." [SO:xp]
7200 synonym: "polyadenylated mRNA" EXACT []
7201 is_a: SO:0000234 ! mRNA
7202 relationship: adjacent_to SO:0000610 ! polyA_sequence
7203 relationship: has_quality SO:0000246 ! polyadenylated
7207 name: trans_spliced_mRNA
7208 def: "An mRNA that is trans-spliced." [SO:xp]
7209 synonym: "trans-spliced mRNA" EXACT []
7210 is_a: SO:0000234 ! mRNA
7211 is_a: SO:0000479 ! trans_spliced_transcript
7212 relationship: adjacent_to SO:0000636 ! spliced_leader_RNA
7213 relationship: has_quality SO:0000870 ! trans_spliced
7217 name: edited_transcript
7218 def: "A transcript that is edited." [SO:ke]
7219 synonym: "edited transcript" EXACT []
7220 is_a: SO:0000673 ! transcript
7221 relationship: guided_by SO:0000602 ! guide_RNA
7222 relationship: has_part SO:0000977 ! anchor_binding_site
7223 relationship: has_quality SO:0000116 ! edited
7227 name: edited_transcript_by_A_to_I_substitution
7228 def: "A transcript that has been edited by A to I substitution." [SO:ke]
7229 synonym: "edited transcript by A to I substitution" EXACT []
7230 is_a: SO:0000873 ! edited_transcript
7234 name: bound_by_protein
7235 def: "An attribute describing a sequence that is bound by a protein." [SO:ke]
7236 synonym: "bound by protein" EXACT []
7237 is_a: SO:0000277 ! bound_by_factor
7241 name: bound_by_nucleic_acid
7242 def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]
7243 synonym: "bound by nucleic acid" EXACT []
7244 is_a: SO:0000277 ! bound_by_factor
7248 name: alternatively_spliced
7249 def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]
7250 synonym: "alternatively spliced" EXACT []
7251 is_a: SO:0000237 ! transcript_attribute
7256 def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke]
7257 is_a: SO:0000237 ! transcript_attribute
7262 def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke]
7263 is_a: SO:0000880 ! polycistronic
7268 def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]
7269 is_a: SO:0000237 ! transcript_attribute
7274 def: "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]
7275 is_a: SO:0000863 ! mRNA_attribute
7279 name: codon_redefined
7280 def: "An attribute describing the alteration of codon meaning." [SO:ke]
7281 synonym: "codon redefined" EXACT []
7282 is_a: SO:0000881 ! recoded
7286 name: stop_codon_read_through
7287 def: "A stop codon redefined to be a new amino acid." [SO:ke]
7288 synonym: "stop codon read through" EXACT []
7289 synonym: "stop codon readthrough" RELATED []
7290 is_a: SO:0000145 ! recoded_codon
7294 name: stop_codon_redefined_as_pyrrolysine
7295 def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]
7296 synonym: "stop codon redefined as pyrrolysine" EXACT []
7297 is_a: SO:0000883 ! stop_codon_read_through
7301 name: stop_codon_redefined_as_selenocysteine
7302 def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]
7303 synonym: "stop codon redefined as selenocysteine" EXACT []
7304 is_a: SO:0000883 ! stop_codon_read_through
7308 name: recoded_by_translational_bypass
7309 def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke]
7310 synonym: "recoded by translational bypass" EXACT []
7311 is_a: SO:0000881 ! recoded
7315 name: translationally_frameshifted
7316 def: "Recoding by frameshifting a particular site." [SO:ke]
7317 synonym: "translationally frameshifted" EXACT []
7318 is_a: SO:0000881 ! recoded
7322 name: maternally_imprinted_gene
7323 def: "A gene that is maternally_imprinted." [SO:xp]
7324 synonym: "maternally imprinted gene" EXACT []
7325 is_a: SO:0000898 ! epigenetically_modified_gene
7326 relationship: has_quality SO:0000135 ! maternally_imprinted
7330 name: paternally_imprinted_gene
7331 def: "A gene that is paternally imprinted." [SO:xp]
7332 synonym: "paternally imprinted gene" EXACT []
7333 is_a: SO:0000898 ! epigenetically_modified_gene
7334 relationship: has_quality SO:0000136 ! paternally_imprinted
7338 name: post_translationally_regulated_gene
7339 def: "A gene that is post translationally regulated." [SO:xp]
7340 synonym: "post translationally regulated gene" EXACT []
7341 is_a: SO:0000704 ! gene
7342 relationship: has_quality SO:0000130 ! post_translationally_regulated
7346 name: negatively_autoregulated_gene
7347 def: "A gene that is negatively autoreguated." [SO:xp]
7348 synonym: "negatively autoregulated gene" EXACT []
7349 is_a: SO:0000704 ! gene
7350 relationship: has_quality SO:0000473 ! negatively_autoregulated
7354 name: positively_autoregulated_gene
7355 def: "A gene that is positively autoregulated." [SO:xp]
7356 synonym: "positively autoregulated gene" EXACT []
7357 is_a: SO:0000704 ! gene
7358 relationship: has_quality SO:0000475 ! positively_autoregulated
7363 def: "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]
7364 xref: http://en.wikipedia.org/wiki/Silenced "wiki"
7365 is_a: SO:0000126 ! transcriptionally_repressed
7369 name: silenced_by_DNA_modification
7370 def: "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]
7371 synonym: "silenced by DNA modification" EXACT []
7372 is_a: SO:0000893 ! silenced
7376 name: silenced_by_DNA_methylation
7377 def: "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]
7378 synonym: "silenced by DNA methylation" EXACT []
7379 is_a: SO:0000894 ! silenced_by_DNA_modification
7383 name: translationally_regulated_gene
7384 def: "A gene that is translationally regulated." [SO:xp]
7385 synonym: "translationally regulated gene" EXACT []
7386 is_a: SO:0000704 ! gene
7387 relationship: has_quality SO:0000131 ! translationally_regulated
7391 name: allelically_excluded_gene
7392 def: "A gene that is allelically_excluded." [SO:xp]
7393 synonym: "allelically excluded gene" EXACT []
7394 is_a: SO:0000898 ! epigenetically_modified_gene
7395 relationship: has_quality SO:0000137 ! allelically_excluded
7399 name: epigenetically_modified_gene
7400 def: "A gene that is epigenetically modified." [SO:ke]
7401 synonym: "epigenetically modified gene" EXACT []
7402 is_a: SO:0000704 ! gene
7403 is_a: SO:0001720 ! epigenetically_modified_region
7404 relationship: has_quality SO:0000133 ! epigenetically_modified
7408 name: nuclear_mitochondrial
7409 def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke]
7410 synonym: "nuclear mitochondrial" EXACT []
7416 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]
7421 name: unequally_crossed_over
7422 def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke]
7423 synonym: "unequally crossed over" EXACT []
7429 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]
7430 xref: http://en.wikipedia.org/wiki/Transgene "wiki"
7431 is_a: SO:0000704 ! gene
7432 relationship: has_quality SO:0000781 ! transgenic
7436 name: endogenous_retroviral_sequence
7437 synonym: "endogenous retroviral sequence" EXACT []
7438 is_a: SO:0000751 ! proviral_location
7442 name: rearranged_at_DNA_level
7443 def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]
7444 synonym: "rearranged at DNA level" EXACT []
7445 is_a: SO:0000133 ! epigenetically_modified
7450 def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke]
7451 comment: This term is the hypernym of attributes and should not be annotated to.
7452 is_a: SO:0000733 ! feature_attribute
7456 name: independently_known
7457 def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke]
7458 synonym: "independently known" EXACT []
7459 is_a: SO:0000905 ! status
7463 name: supported_by_sequence_similarity
7464 def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]
7465 synonym: "supported by sequence similarity" EXACT []
7466 is_a: SO:0000732 ! predicted
7470 name: supported_by_domain_match
7471 def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]
7472 synonym: "supported by domain match" EXACT []
7473 is_a: SO:0000907 ! supported_by_sequence_similarity
7477 name: supported_by_EST_or_cDNA
7478 def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]
7479 synonym: "supported by EST or cDNA" EXACT []
7480 is_a: SO:0000907 ! supported_by_sequence_similarity
7485 is_a: SO:0000732 ! predicted
7489 name: predicted_by_ab_initio_computation
7490 def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]
7491 synonym: "predicted by ab initio computation" EXACT []
7492 is_a: SO:0000732 ! predicted
7498 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/]
7500 synonym: "asx turn" EXACT []
7501 is_a: SO:0001128 ! polypeptide_turn_motif
7505 name: cloned_cDNA_insert
7506 def: "A clone insert made from cDNA." [SO:xp]
7507 synonym: "cloned cDNA insert" EXACT []
7508 is_a: SO:0000753 ! clone_insert
7509 relationship: has_quality SO:0000756 ! cDNA
7513 name: cloned_genomic_insert
7514 def: "A clone insert made from genomic DNA." [SO:xp]
7515 synonym: "cloned genomic insert" EXACT []
7516 is_a: SO:0000753 ! clone_insert
7517 relationship: has_quality SO:0000991 ! genomic_DNA
7521 name: engineered_insert
7522 def: "A clone insert that is engineered." [SO:xp]
7523 synonym: "engineered insert" EXACT []
7524 is_a: SO:0000753 ! clone_insert
7525 is_a: SO:0000804 ! engineered_region
7526 relationship: has_quality SO:0000783 ! engineered
7530 name: edit_operation
7531 synonym: "edit operation" EXACT []
7537 def: "An edit to insert a U." [SO:ke]
7538 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.
7539 synonym: "insert U" EXACT []
7545 def: "An edit to delete a uridine." [SO:ke]
7546 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.
7547 synonym: "delete U" EXACT []
7552 name: substitute_A_to_I
7553 def: "An edit to substitute an I for an A." [SO:ke]
7554 synonym: "substitute A to I" EXACT []
7560 def: "An edit to insert a cytidine." [SO:ke]
7561 synonym: "insert C" EXACT []
7566 name: insert_dinucleotide
7567 def: "An edit to insert a dinucleotide." [SO:ke]
7568 synonym: "insert dinucleotide" EXACT []
7573 name: substitute_C_to_U
7574 def: "An edit to substitute an U for a C." [SO:ke]
7575 synonym: "substitute C to U" EXACT []
7581 def: "An edit to insert a G." [SO:ke]
7582 synonym: "insert G" EXACT []
7588 def: "An edit to insert a GC dinucleotide." [SO:ke]
7589 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.
7590 synonym: "insert GC" EXACT []
7596 def: "An edit to insert a GU dinucleotide." [SO:ke]
7597 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.
7598 synonym: "insert GU" EXACT []
7604 def: "An edit to insert a CU dinucleotide." [SO:ke]
7605 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.
7606 synonym: "insert CU" EXACT []
7612 def: "An edit to insert a AU dinucleotide." [SO:ke]
7613 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.
7614 synonym: "insert AU" EXACT []
7620 def: "An edit to insert a AA dinucleotide." [SO:ke]
7621 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.
7622 synonym: "insert AA" EXACT []
7628 def: "An mRNA that is edited." [SO:xp]
7629 synonym: "edited mRNA" EXACT []
7630 is_a: SO:0000234 ! mRNA
7631 is_a: SO:0000873 ! edited_transcript
7632 relationship: has_quality SO:0000116 ! edited
7636 name: guide_RNA_region
7637 def: "A region of guide RNA." [SO:ma]
7638 synonym: "guide RNA region" EXACT []
7639 is_a: SO:0000834 ! mature_transcript_region
7640 relationship: part_of SO:0000602 ! guide_RNA
7645 def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]
7646 synonym: "anchor region" EXACT []
7647 is_a: SO:0000930 ! guide_RNA_region
7651 name: pre_edited_mRNA
7652 synonym: "pre-edited mRNA" EXACT []
7653 is_a: SO:0000120 ! protein_coding_primary_transcript
7658 def: "An attribute to describe a feature between stages of processing." [SO:ke]
7659 is_a: SO:0000733 ! feature_attribute
7663 name: miRNA_target_site
7664 def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]
7665 synonym: "miRNA target site" EXACT []
7666 is_a: SO:0001655 ! nucleotide_binding_site
7671 def: "A CDS that is edited." [SO:xp]
7672 synonym: "edited CDS" EXACT []
7673 is_a: SO:0000316 ! CDS
7674 relationship: has_quality SO:0000116 ! edited
7678 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
7679 synonym: "vertebrate immunoglobulin T cell receptor rearranged segment" EXACT []
7680 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
7684 name: vertebrate_immune_system_feature
7689 name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
7690 synonym: "vertebrate immunoglobulin T cell receptor rearranged gene cluster" EXACT []
7691 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
7695 name: vertebrate_immune_system_gene_recombination_signal_feature
7696 synonym: "vertebrate immune system gene recombination signal feature" EXACT []
7697 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
7701 name: recombinationally_rearranged
7702 synonym: "recombinationally rearranged" EXACT []
7703 is_a: SO:0000733 ! feature_attribute
7707 name: recombinationally_rearranged_vertebrate_immune_system_gene
7708 def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]
7709 synonym: "recombinationally rearranged vertebrate immune system gene" EXACT []
7710 is_a: SO:0000456 ! recombinationally_rearranged_gene
7715 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]
7716 synonym: "attP site" EXACT []
7717 is_a: SO:0000946 ! integration_excision_site
7718 relationship: part_of SO:0001042 ! phage_sequence
7723 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]
7724 synonym: "attB site" EXACT []
7725 is_a: SO:0000946 ! integration_excision_site
7730 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]
7731 synonym: "attBP'" RELATED []
7732 synonym: "attL site" RELATED []
7733 is_a: SO:0000946 ! integration_excision_site
7738 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]
7739 synonym: "attPB'" RELATED []
7740 synonym: "attR site" EXACT []
7741 is_a: SO:0000946 ! integration_excision_site
7745 name: integration_excision_site
7746 def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]
7747 synonym: "attachment site" RELATED []
7748 synonym: "integration excision site" EXACT []
7749 is_a: SO:0000342 ! site_specific_recombination_target_region
7753 name: resolution_site
7754 def: "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]
7755 synonym: "res site" EXACT []
7756 synonym: "resolution site" EXACT []
7757 is_a: SO:0000342 ! site_specific_recombination_target_region
7761 name: inversion_site
7762 def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]
7763 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.
7764 synonym: "inversion site" EXACT []
7765 is_a: SO:0000342 ! site_specific_recombination_target_region
7770 def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]
7771 synonym: "dif site" EXACT []
7772 is_a: SO:0000947 ! resolution_site
7777 def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]
7778 synonym: "attC site" EXACT []
7779 is_a: SO:0000946 ! integration_excision_site
7780 relationship: part_of SO:0000365 ! integron
7784 name: eukaryotic_terminator
7785 synonym: "eukaryotic terminator" EXACT []
7786 is_a: SO:0000141 ! terminator
7791 def: "An origin of vegetative replication in plasmids and phages." [SO:as]
7792 synonym: "origin of vegetative replication" EXACT []
7793 is_a: SO:0000296 ! origin_of_replication
7798 def: "An origin of bacterial chromosome replication." [SO:as]
7799 synonym: "origin of bacterial chromosome replication" EXACT []
7800 is_a: SO:0000296 ! origin_of_replication
7804 name: DNA_chromosome
7805 def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma]
7806 synonym: "DNA chromosome" EXACT []
7807 is_a: SO:0000340 ! chromosome
7808 relationship: has_quality SO:0000352 ! DNA
7812 name: double_stranded_DNA_chromosome
7813 def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]
7814 synonym: "double stranded DNA chromosome" EXACT []
7815 is_a: SO:0000954 ! DNA_chromosome
7816 relationship: has_quality SO:0000985 ! double
7820 name: single_stranded_DNA_chromosome
7821 def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]
7822 synonym: "single stranded DNA chromosome" EXACT []
7823 is_a: SO:0000954 ! DNA_chromosome
7824 relationship: has_quality SO:0000984 ! single
7828 name: linear_double_stranded_DNA_chromosome
7829 def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]
7830 synonym: "linear double stranded DNA chromosome" EXACT []
7831 is_a: SO:0000955 ! double_stranded_DNA_chromosome
7832 relationship: has_quality SO:0000987 ! linear
7836 name: circular_double_stranded_DNA_chromosome
7837 def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]
7838 synonym: "circular double stranded DNA chromosome" EXACT []
7839 is_a: SO:0000955 ! double_stranded_DNA_chromosome
7840 relationship: has_quality SO:0000988 ! circular
7844 name: linear_single_stranded_DNA_chromosome
7845 def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]
7846 synonym: "linear single stranded DNA chromosome" EXACT []
7847 is_a: SO:0000956 ! single_stranded_DNA_chromosome
7848 relationship: has_quality SO:0000987 ! linear
7852 name: circular_single_stranded_DNA_chromosome
7853 def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
7854 synonym: "circular single stranded DNA chromosome" EXACT []
7855 is_a: SO:0000956 ! single_stranded_DNA_chromosome
7856 relationship: has_quality SO:0000988 ! circular
7860 name: RNA_chromosome
7861 def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma]
7862 synonym: "RNA chromosome" EXACT []
7863 is_a: SO:0000340 ! chromosome
7864 relationship: has_quality SO:0000356 ! RNA
7868 name: single_stranded_RNA_chromosome
7869 def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]
7870 synonym: "single stranded RNA chromosome" EXACT []
7871 is_a: SO:0000961 ! RNA_chromosome
7872 relationship: has_quality SO:0000984 ! single
7876 name: linear_single_stranded_RNA_chromosome
7877 def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]
7878 synonym: "linear single stranded RNA chromosome" EXACT []
7879 is_a: SO:0000962 ! single_stranded_RNA_chromosome
7880 relationship: has_quality SO:0000987 ! linear
7884 name: linear_double_stranded_RNA_chromosome
7885 def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]
7886 synonym: "linear double stranded RNA chromosome" EXACT []
7887 is_a: SO:0000965 ! double_stranded_RNA_chromosome
7888 relationship: has_quality SO:0000987 ! linear
7892 name: double_stranded_RNA_chromosome
7893 def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]
7894 synonym: "double stranded RNA chromosome" EXACT []
7895 is_a: SO:0000961 ! RNA_chromosome
7896 relationship: has_quality SO:0000985 ! double
7900 name: circular_single_stranded_RNA_chromosome
7901 def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
7902 synonym: "circular single stranded RNA chromosome" EXACT []
7903 is_a: SO:0000962 ! single_stranded_RNA_chromosome
7904 relationship: has_quality SO:0000988 ! circular
7908 name: circular_double_stranded_RNA_chromosome
7909 def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]
7910 synonym: "circular double stranded RNA chromosome" EXACT []
7911 is_a: SO:0000965 ! double_stranded_RNA_chromosome
7912 relationship: has_quality SO:0000988 ! circular
7916 name: sequence_replication_mode
7917 comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
7918 synonym: "sequence replication mode" EXACT []
7923 name: rolling_circle
7924 comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581.
7925 synonym: "rolling circle" EXACT []
7926 xref: http://en.wikipedia.org/wiki/Rolling_circle "wiki"
7931 name: theta_replication
7932 comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582
7933 synonym: "theta replication" EXACT []
7938 name: DNA_replication_mode
7939 comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260.
7940 synonym: "DNA replication mode" EXACT []
7945 name: RNA_replication_mode
7946 comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
7947 synonym: "RNA replication mode" EXACT []
7952 name: insertion_sequence
7953 def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]
7954 synonym: "insertion sequence" EXACT []
7955 synonym: "IS" RELATED []
7956 xref: http://en.wikipedia.org/wiki/Insertion_sequence "wiki"
7957 is_a: SO:0000208 ! terminal_inverted_repeat_element
7961 name: minicircle_gene
7962 synonym: "minicircle gene" EXACT []
7963 is_a: SO:0000089 ! kinetoplast_gene
7964 relationship: part_of SO:0000980 ! minicircle
7969 def: "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke]
7970 is_a: SO:0000733 ! feature_attribute
7974 name: anchor_binding_site
7975 comment: Part of an edited transcript only.
7976 synonym: "anchor binding site" EXACT []
7977 is_a: SO:0000833 ! transcript_region
7981 name: template_region
7982 def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]
7983 synonym: "information region" EXACT []
7984 synonym: "template region" EXACT []
7985 is_a: SO:0000930 ! guide_RNA_region
7990 def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma]
7991 synonym: "gRNA encoding" EXACT []
7992 is_a: SO:0000011 ! non_protein_coding
7998 def: "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]
7999 synonym: "minicircle_chromosome" EXACT []
8000 xref: http://en.wikipedia.org/wiki/Minicircle "wiki"
8001 is_a: SO:0001235 ! replicon
8005 name: rho_dependent_bacterial_terminator
8006 synonym: "rho dependent bacterial terminator" EXACT []
8007 is_a: SO:0000614 ! bacterial_terminator
8011 name: rho_independent_bacterial_terminator
8012 synonym: "rho independent bacterial terminator" EXACT []
8013 is_a: SO:0000614 ! bacterial_terminator
8017 name: strand_attribute
8018 comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
8019 synonym: "strand attribute" EXACT []
8020 is_a: SO:0000733 ! feature_attribute
8025 comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
8026 is_a: SO:0000983 ! strand_attribute
8031 comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
8032 is_a: SO:0000983 ! strand_attribute
8036 name: topology_attribute
8037 comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
8038 synonym: "topology attribute" EXACT []
8039 is_a: SO:0000443 ! polymer_attribute
8044 def: "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]
8045 comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
8046 synonym: "two-ended" RELATED []
8047 is_a: SO:0000986 ! topology_attribute
8048 disjoint_from: SO:0000988 ! circular
8053 def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]
8054 comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
8055 synonym: "zero-ended" RELATED []
8056 is_a: SO:0000986 ! topology_attribute
8061 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]
8062 synonym: "class II RNA" EXACT []
8063 is_a: SO:0000655 ! ncRNA
8068 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]
8069 comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
8070 synonym: "class I RNA" EXACT []
8071 is_a: SO:0000655 ! ncRNA
8076 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
8077 synonym: "genomic DNA" EXACT []
8078 is_a: SO:0000352 ! DNA
8082 name: BAC_cloned_genomic_insert
8083 comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006.
8084 synonym: "BAC cloned genomic insert" EXACT []
8085 is_a: SO:0000914 ! cloned_genomic_insert
8086 relationship: derives_from SO:0000153 ! BAC
8091 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.
8092 is_a: SO:0000905 ! status
8096 name: consensus_region
8097 comment: DO not obsolete without considering MGED mapping.
8098 synonym: "consensus region" EXACT []
8099 is_a: SO:0001410 ! experimental_feature
8100 relationship: has_quality SO:0000993 ! consensus
8104 name: consensus_mRNA
8105 comment: DO not obsolete without considering MGED mapping.
8106 synonym: "consensus mRNA" EXACT []
8107 is_a: SO:0000234 ! mRNA
8108 is_a: SO:0000994 ! consensus_region
8109 relationship: has_quality SO:0000993 ! consensus
8113 name: predicted_gene
8114 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
8115 synonym: "predicted gene" EXACT []
8116 is_a: SO:0000704 ! gene
8117 relationship: has_quality SO:0000732 ! predicted
8122 comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
8123 synonym: "gene fragment" EXACT []
8124 is_a: SO:0000842 ! gene_component_region
8125 relationship: has_quality SO:0000731 ! fragmentary
8129 name: recursive_splice_site
8130 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]
8131 synonym: "recursive splice site" EXACT []
8132 is_a: SO:0001419 ! cis_splice_site
8137 def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]
8138 comment: Requested by Keith Boroevich December, 2006.
8139 synonym: "BAC end" EXACT []
8140 synonym: "BAC end sequence" EXACT []
8141 synonym: "BES" EXACT []
8142 is_a: SO:0000150 ! read
8143 relationship: part_of SO:0000153 ! BAC
8148 def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]
8150 synonym: "16S ribosomal RNA" EXACT []
8151 synonym: "16S rRNA" RELATED []
8152 synonym: "16S SSU RNA" EXACT []
8153 synonym: "rRNA 16S" EXACT []
8154 xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki"
8155 is_a: SO:0000650 ! small_subunit_rRNA
8160 def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]
8162 synonym: "23S LSU rRNA" EXACT []
8163 synonym: "23S ribosomal RNA" RELATED []
8164 synonym: "23S rRNA" EXACT []
8165 synonym: "rRNA 23S" EXACT []
8166 is_a: SO:0000651 ! large_subunit_rRNA
8171 def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]
8173 synonym: "25S LSU rRNA" EXACT []
8174 synonym: "25S ribosomal RNA" EXACT []
8175 synonym: "25S rRNA" EXACT []
8176 synonym: "rRNA 25S" EXACT []
8177 is_a: SO:0000651 ! large_subunit_rRNA
8182 def: "A recombination product between the 2 LTR of the same element." [SO:ke]
8183 comment: Requested by Hadi Quesneville January 2007.
8184 synonym: "solo LTR" EXACT []
8185 is_a: SO:0000286 ! long_terminal_repeat
8189 name: low_complexity
8190 synonym: "low complexity" EXACT []
8191 is_a: SO:0000905 ! status
8195 name: low_complexity_region
8196 synonym: "low complexity region" EXACT []
8197 is_a: SO:0001410 ! experimental_feature
8198 relationship: has_quality SO:0001004 ! low_complexity
8203 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]
8204 xref: http://en.wikipedia.org/wiki/Prophage "wiki"
8205 is_a: SO:0000113 ! proviral_region
8209 name: cryptic_prophage
8210 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]
8211 comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
8212 synonym: "cryptic prophage" EXACT []
8213 xref: http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w
8214 is_a: SO:0000772 ! genomic_island
8219 def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]
8220 xref: http://en.wikipedia.org/wiki/Tetraloop "wiki"
8221 is_a: SO:0000313 ! stem_loop
8225 name: DNA_constraint_sequence
8226 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]
8227 synonym: "DNA constraint" EXACT []
8228 synonym: "DNA constraint sequence" EXACT []
8229 is_a: SO:0000442 ! ds_oligo
8234 def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]
8235 synonym: "i motif" EXACT []
8236 synonym: "short intercalated motif" EXACT []
8237 is_a: SO:0000142 ! DNA_sequence_secondary_structure
8242 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]
8243 synonym: "peptide nucleic acid" EXACT []
8244 synonym: "PNA oligo" EXACT []
8245 xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid "wiki"
8246 is_a: SO:0001247 ! synthetic_oligo
8247 relationship: has_quality SO:0001184 ! PNA
8252 def: "A DNA sequence with catalytic activity." [SO:cb]
8253 comment: Added by request from Colin Batchelor.
8254 synonym: "catalytic DNA" EXACT []
8255 synonym: "deoxyribozyme" RELATED []
8256 synonym: "DNA enzyme" EXACT []
8257 is_a: SO:0000696 ! oligo
8258 relationship: has_quality SO:0001185 ! enzymatic
8263 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]
8264 synonym: "multiple nucleotide polymorphism" RELATED []
8265 is_a: SO:0002007 ! MNV
8270 comment: Requested by Colin Batchelor, Feb 2007.
8271 synonym: "intron domain" EXACT []
8272 is_a: SO:0000835 ! primary_transcript_region
8273 relationship: part_of SO:0000188 ! intron
8277 name: wobble_base_pair
8278 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]
8279 synonym: "wobble base pair" EXACT []
8280 synonym: "wobble pair" EXACT []
8281 xref: http://en.wikipedia.org/wiki/Wobble_base_pair "wiki"
8282 is_a: SO:0000028 ! base_pair
8286 name: internal_guide_sequence
8287 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]
8288 synonym: "IGS" EXACT []
8289 synonym: "internal guide sequence" EXACT []
8290 is_a: SO:0001014 ! intron_domain
8291 relationship: part_of SO:0000587 ! group_I_intron
8295 name: silent_mutation
8296 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]
8297 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.
8298 synonym: "silent mutation" EXACT []
8299 xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
8300 xref: loinc:LA6700-4 "Silent"
8301 is_a: SO:0001878 ! feature_variant
8306 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]
8307 comment: Requested by Trish Whetzel.
8308 xref: http://en.wikipedia.org/wiki/Epitope "wiki"
8309 is_a: SO:0000409 ! binding_site
8313 name: copy_number_variation
8314 def: "A variation that increases or decreases the copy number of a given region." [SO:ke]
8316 synonym: "CNP" EXACT []
8317 synonym: "CNV" EXACT []
8318 synonym: "copy number polymorphism" EXACT []
8319 synonym: "copy number variation" EXACT []
8320 xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki"
8321 is_a: SO:0001059 ! sequence_alteration
8325 name: sequence_variant_affecting_copy_number
8326 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
8327 synonym: "mutation affecting copy number" EXACT []
8328 synonym: "sequence variant affecting copy number" EXACT []
8330 replaced_by: SO:0001563
8334 name: chromosome_breakpoint
8336 synonym: "aberration breakpoint" EXACT []
8337 synonym: "aberration_junction" EXACT []
8338 synonym: "chromosome breakpoint" EXACT []
8339 is_a: SO:0000699 ! junction
8340 relationship: part_of SO:0000340 ! chromosome
8344 name: inversion_breakpoint
8345 def: "The point within a chromosome where an inversion begins or ends." [SO:cb]
8346 synonym: "inversion breakpoint" EXACT []
8347 is_a: SO:0001021 ! chromosome_breakpoint
8352 def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]
8353 synonym: "allelomorph" EXACT []
8354 xref: http://en.wikipedia.org/wiki/Allele "wiki"
8355 is_a: SO:0001507 ! variant_collection
8356 relationship: variant_of SO:0000704 ! gene
8361 def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]
8362 xref: http://en.wikipedia.org/wiki/Haplotype "wiki"
8363 is_a: SO:0001507 ! variant_collection
8364 relationship: variant_of SO:0000355 ! haplotype_block
8368 name: polymorphic_sequence_variant
8369 def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]
8370 synonym: "polymorphic sequence variant" EXACT []
8371 is_a: SO:0001023 ! allele
8376 def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]
8377 xref: http://en.wikipedia.org/wiki/Genome "wiki"
8378 is_a: SO:0001260 ! sequence_collection
8379 relationship: has_part SO:0001235 ! replicon
8384 def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]
8385 xref: http://en.wikipedia.org/wiki/Genotype "wiki"
8386 is_a: SO:0001507 ! variant_collection
8387 relationship: variant_of SO:0001026 ! genome
8392 def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]
8393 is_a: SO:0001507 ! variant_collection
8397 name: direction_attribute
8398 synonym: "direction attribute" EXACT []
8399 is_a: SO:0000733 ! feature_attribute
8404 def: "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]
8405 is_a: SO:0001029 ! direction_attribute
8410 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]
8411 is_a: SO:0001029 ! direction_attribute
8415 name: mitochondrial_DNA
8416 comment: This terms is used by MO.
8417 synonym: "mitochondrial DNA" EXACT []
8418 synonym: "mtDNA" EXACT []
8419 xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA "wiki"
8420 is_a: SO:0000737 ! mitochondrial_sequence
8421 relationship: has_quality SO:0000352 ! DNA
8425 name: chloroplast_DNA
8426 comment: This term is used by MO.
8427 synonym: "chloroplast DNA" EXACT []
8428 is_a: SO:0000745 ! chloroplast_sequence
8429 relationship: has_quality SO:0000352 ! DNA
8434 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]
8435 comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
8436 is_a: SO:0001014 ! intron_domain
8437 relationship: has_part SO:0001244 ! pre_miRNA
8442 def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]
8443 synonym: "piwi-associated RNA" EXACT []
8444 xref: http://en.wikipedia.org/wiki/PiRNA "wiki"
8445 is_a: SO:0000655 ! ncRNA
8450 def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]
8451 synonym: "arginyl tRNA" EXACT []
8452 is_a: SO:0000253 ! tRNA
8453 relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript
8457 name: mobile_genetic_element
8458 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]
8460 synonym: "MGE" EXACT []
8461 synonym: "mobile genetic element" EXACT []
8462 xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki"
8463 is_a: SO:0001411 ! biological_region
8464 relationship: has_quality SO:0001234 ! mobile
8468 name: extrachromosomal_mobile_genetic_element
8469 def: "An MGE that is not integrated into the host chromosome." [SO:ke]
8470 synonym: "extrachromosomal mobile genetic element" EXACT []
8471 is_a: SO:0001037 ! mobile_genetic_element
8475 name: integrated_mobile_genetic_element
8476 def: "An MGE that is integrated into the host chromosome." [SO:ke]
8478 synonym: "integrated mobile genetic element" EXACT []
8479 is_a: SO:0001037 ! mobile_genetic_element
8483 name: integrated_plasmid
8484 def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke]
8485 synonym: "integrated plasmid" EXACT []
8486 is_a: SO:0001039 ! integrated_mobile_genetic_element
8487 relationship: derives_from SO:0000155 ! plasmid
8491 name: viral_sequence
8492 def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]
8493 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.
8494 synonym: "viral sequence" EXACT []
8495 synonym: "virus sequence" EXACT []
8496 is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
8497 is_a: SO:0001235 ! replicon
8501 name: phage_sequence
8502 def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke]
8503 synonym: "bacteriophage" EXACT []
8504 synonym: "phage" EXACT []
8505 synonym: "phage sequence" EXACT []
8506 xref: http://en.wikipedia.org/wiki/Bacteriophage "wiki"
8507 is_a: SO:0001041 ! viral_sequence
8512 def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]
8513 synonym: "attCtn site" EXACT []
8514 is_a: SO:0000946 ! integration_excision_site
8515 relationship: part_of SO:0000371 ! conjugative_transposon
8519 name: nuclear_mt_pseudogene
8520 def: "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]
8521 comment: Definition change requested by Val, 3172757.
8522 synonym: "nuclear mitochondrial pseudogene" EXACT []
8523 synonym: "nuclear mt pseudogene" EXACT []
8524 synonym: "NUMT" EXACT []
8525 xref: http://en.wikipedia.org/wiki/Numt "wikipedia"
8526 is_a: SO:0001760 ! non_processed_pseudogene
8530 name: cointegrated_plasmid
8531 def: "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]
8532 synonym: "cointegrated plasmid" EXACT []
8533 synonym: "cointegrated replicon" EXACT []
8534 is_a: SO:0001039 ! integrated_mobile_genetic_element
8539 def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]
8540 synonym: "IRLinv site" EXACT []
8541 is_a: SO:0001048 ! inversion_site_part
8542 relationship: part_of SO:0000948 ! inversion_site
8547 def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]
8548 synonym: "IRRinv site" EXACT []
8549 is_a: SO:0001048 ! inversion_site_part
8550 relationship: part_of SO:0000948 ! inversion_site
8554 name: inversion_site_part
8555 def: "A region located within an inversion site." [SO:ke]
8556 comment: A term created to allow the parts of an inversion site have an is_a path back to the root.
8557 synonym: "inversion site part" EXACT []
8558 is_a: SO:0000342 ! site_specific_recombination_target_region
8562 name: defective_conjugative_transposon
8563 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]
8564 synonym: "defective conjugative transposon" EXACT []
8565 is_a: SO:0000772 ! genomic_island
8569 name: repeat_fragment
8570 def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke]
8571 comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
8572 synonym: "repeat fragment" EXACT []
8573 is_a: SO:0000840 ! repeat_component
8574 relationship: part_of SO:0001649 ! nested_repeat
8588 name: nested_transposon
8593 name: transposon_fragment
8594 def: "A portion of a transposon, interrupted by the insertion of another element." [SO:ke]
8595 synonym: "transposon fragment" EXACT []
8596 is_a: SO:0000840 ! repeat_component
8597 relationship: part_of SO:0001648 ! nested_transposon
8601 name: transcriptional_cis_regulatory_region
8602 def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]
8604 synonym: "transcription-control region" EXACT []
8605 synonym: "transcriptional cis regulatory region" EXACT []
8606 is_a: SO:0001679 ! transcription_regulatory_region
8610 name: splicing_regulatory_region
8611 def: "A regulatory_region that modulates splicing." [SO:ke]
8613 synonym: "splicing regulatory region" EXACT []
8614 is_a: SO:0001679 ! transcription_regulatory_region
8623 name: promoter_targeting_sequence
8624 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]
8625 synonym: "promoter targeting sequence" EXACT []
8626 is_a: SO:0001055 ! transcriptional_cis_regulatory_region
8630 name: sequence_alteration
8633 def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]
8634 comment: Merged with partially characterized change in nucleotide sequence.
8636 synonym: "partially characterised change in DNA sequence" NARROW []
8637 synonym: "partially_characterised_change_in_DNA_sequence" NARROW []
8638 synonym: "sequence alteration" EXACT []
8639 synonym: "sequence variation" RELATED []
8640 synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW []
8641 is_a: SO:0000110 ! sequence_feature
8645 name: sequence_variant
8646 def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
8647 synonym: "ANNOVAR:unknown" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
8648 synonym: "sequence variant" EXACT []
8649 synonym: "VAAST:sequence_variant" EXACT VAR []
8653 name: propeptide_cleavage_site
8655 def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]
8658 synonym: "propeptide cleavage site" EXACT []
8659 is_a: SO:0100011 ! cleaved_peptide_region
8660 relationship: part_of SO:0001062 ! propeptide
8666 def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]
8669 synonym: "propep" RELATED [uniprot:feature_type]
8670 xref: http://en.wikipedia.org/wiki/Propeptide "wiki"
8671 is_a: SO:0100011 ! cleaved_peptide_region
8675 name: immature_peptide_region
8677 def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]
8681 synonym: "immature peptide region" EXACT []
8682 is_a: SO:0000839 ! polypeptide_region
8686 name: active_peptide
8688 def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]
8689 comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
8691 synonym: "active peptide" EXACT []
8692 synonym: "peptide" BROAD [uniprot:feature_type]
8693 xref: http://en.wikipedia.org/wiki/Peptide "wiki"
8694 is_a: SO:0000419 ! mature_protein_region
8698 name: compositionally_biased_region_of_peptide
8700 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]
8703 synonym: "compbias" RELATED [uniprot:feature_type]
8704 synonym: "compositional bias" RELATED []
8705 synonym: "compositionally biased" RELATED []
8706 synonym: "compositionally biased region of peptide" RELATED []
8707 synonym: "compositionally_biased_region" EXACT []
8708 is_a: SO:0000839 ! polypeptide_region
8712 name: polypeptide_motif
8714 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]
8717 synonym: "motif" BROAD [uniprot:feature_type]
8718 synonym: "polypeptide motif" EXACT []
8719 is_a: SO:0100021 ! polypeptide_conserved_region
8723 name: polypeptide_repeat
8725 def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]
8728 synonym: "polypeptide repeat" EXACT []
8729 synonym: "repeat" RELATED [uniprot:feature_type]
8730 is_a: SO:0100021 ! polypeptide_conserved_region
8734 name: polypeptide_structural_region
8736 def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]
8739 synonym: "polypeptide structural region" EXACT []
8740 synonym: "structural_region" RELATED []
8741 is_a: SO:0000839 ! polypeptide_region
8745 name: membrane_structure
8747 def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]
8750 synonym: "membrane structure" EXACT []
8751 is_a: SO:0001070 ! polypeptide_structural_region
8755 name: extramembrane_polypeptide_region
8757 def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]
8760 synonym: "extramembrane" RELATED BS []
8761 synonym: "extramembrane polypeptide region" EXACT []
8762 synonym: "extramembrane_region" RELATED BS []
8763 synonym: "topo_dom" RELATED BS [uniprot:feature_type]
8764 is_a: SO:0001070 ! polypeptide_structural_region
8765 relationship: part_of SO:0001071 ! membrane_structure
8769 name: cytoplasmic_polypeptide_region
8771 def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]
8773 synonym: "cytoplasm_location" EXACT BS []
8774 synonym: "cytoplasmic polypeptide region" EXACT []
8775 synonym: "inside" RELATED BS []
8776 is_a: SO:0001072 ! extramembrane_polypeptide_region
8780 name: non_cytoplasmic_polypeptide_region
8782 def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]
8783 comment: This could be inside an organelle within the cell.
8785 synonym: "non cytoplasmic polypeptide region" EXACT []
8786 synonym: "non_cytoplasm_location" EXACT BS []
8787 synonym: "outside" RELATED BS []
8788 is_a: SO:0001072 ! extramembrane_polypeptide_region
8792 name: intramembrane_polypeptide_region
8794 def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR]
8796 synonym: "intramembrane" RELATED BS []
8797 synonym: "intramembrane polypeptide region" EXACT []
8798 is_a: SO:0001070 ! polypeptide_structural_region
8799 relationship: part_of SO:0001071 ! membrane_structure
8803 name: membrane_peptide_loop
8805 def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]
8807 synonym: "membrane peptide loop" EXACT []
8808 synonym: "membrane_loop" RELATED BS []
8809 is_a: SO:0001075 ! intramembrane_polypeptide_region
8813 name: transmembrane_polypeptide_region
8815 def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]
8817 synonym: "transmem" RELATED BS [uniprot:feature_type]
8818 synonym: "transmembrane" RELATED BS []
8819 synonym: "transmembrane polypeptide region" EXACT []
8820 is_a: SO:0001075 ! intramembrane_polypeptide_region
8824 name: polypeptide_secondary_structure
8826 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]
8827 comment: Biosapien term was secondary_structure.
8829 synonym: "2nary structure" RELATED BS []
8830 synonym: "polypeptide secondary structure" EXACT []
8831 synonym: "secondary structure" RELATED BS []
8832 synonym: "secondary structure region" RELATED BS []
8833 synonym: "secondary_structure" RELATED BS []
8834 xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki"
8835 is_a: SO:0001070 ! polypeptide_structural_region
8839 name: polypeptide_structural_motif
8841 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]
8843 synonym: "polypeptide structural motif" RELATED []
8844 synonym: "structural_motif" RELATED BS []
8845 xref: http://en.wikipedia.org/wiki/Structural_motif "wiki"
8846 is_a: SO:0001070 ! polypeptide_structural_region
8852 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]
8855 synonym: "coiled" RELATED BS [uniprot:feature_type]
8856 synonym: "coiled coil" EXACT []
8857 xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki"
8858 is_a: SO:0001079 ! polypeptide_structural_motif
8862 name: helix_turn_helix
8864 def: "A motif comprising two helices separated by a turn." [EBIBS:GAR]
8866 synonym: "helix turn helix" EXACT []
8867 synonym: "helix-turn-helix" EXACT []
8868 synonym: "HTH" RELATED BS []
8869 is_a: SO:0001079 ! polypeptide_structural_motif
8870 relationship: has_part SO:0001114 ! peptide_helix
8871 relationship: has_part SO:0001128 ! polypeptide_turn_motif
8875 name: polypeptide_sequencing_information
8877 def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]
8880 synonym: "sequencing_information" EXACT []
8881 is_a: SO:0000700 ! remark
8885 name: non_adjacent_residues
8887 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]
8889 synonym: "non consecutive" EXACT []
8890 synonym: "non_cons" EXACT [uniprot:feature_type]
8891 is_a: SO:0001082 ! polypeptide_sequencing_information
8895 name: non_terminal_residue
8897 def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]
8900 synonym: "non terminal" EXACT []
8901 synonym: "non_ter" EXACT [uniprot:feature_type]
8902 is_a: SO:0001082 ! polypeptide_sequencing_information
8906 name: sequence_conflict
8908 def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]
8911 synonym: "conflict" EXACT [uniprot:feature_type]
8912 is_a: SO:0001082 ! polypeptide_sequencing_information
8916 name: sequence_uncertainty
8918 def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]
8920 synonym: "unsure" EXACT [uniprot:feature_type]
8921 is_a: SO:0001082 ! polypeptide_sequencing_information
8927 def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual]
8929 synonym: "cross link" EXACT []
8930 synonym: "crosslink" RELATED []
8935 name: disulfide_bond
8937 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]
8938 comment: 2 discreet & joined.
8940 synonym: "disulfid" RELATED []
8941 synonym: "disulfide" RELATED []
8942 synonym: "disulfide bond" RELATED []
8943 synonym: "disulphide" EXACT []
8944 synonym: "disulphide bond" RELATED []
8949 name: post_translationally_modified_region
8951 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]
8954 synonym: "mod_res" EXACT [uniprot:feature_type]
8955 synonym: "modified residue" EXACT []
8956 synonym: "post_translational_modification" EXACT []
8957 xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki"
8958 is_a: SO:0100001 ! biochemical_region_of_peptide
8962 name: covalent_binding_site
8964 def: "Binding involving a covalent bond." [EBIBS:GAR]
8966 synonym: "covalent binding site" EXACT []
8971 name: non_covalent_binding_site
8973 def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR]
8976 synonym: "binding" RELATED [uniprot:curation]
8977 synonym: "binding site" RELATED []
8978 synonym: "non covalent binding site" EXACT []
8983 name: polypeptide_metal_contact
8985 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]
8986 comment: Residue is part of a binding site for a metal ion.
8988 synonym: "metal_binding" RELATED []
8989 is_a: SO:0001656 ! metal_binding_site
8990 is_a: SO:0100002 ! molecular_contact_region
8994 name: protein_protein_contact
8996 def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]
8998 synonym: "protein protein contact" EXACT []
8999 synonym: "protein protein contact site" EXACT []
9000 synonym: "protein_protein_interaction" RELATED []
9001 xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki"
9002 is_a: SO:0000410 ! protein_binding_site
9003 is_a: SO:0100002 ! molecular_contact_region
9007 name: polypeptide_calcium_ion_contact_site
9009 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]
9010 comment: Residue involved in contact with calcium.
9012 synonym: "ca bind" RELATED []
9013 synonym: "ca_bind" EXACT BS [uniprot:feature_type]
9014 synonym: "Ca_contact_site" EXACT []
9015 synonym: "polypeptide calcium ion contact site" EXACT []
9016 is_a: SO:0001092 ! polypeptide_metal_contact
9020 name: polypeptide_cobalt_ion_contact_site
9022 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]
9024 synonym: "Co_contact_site" EXACT []
9025 synonym: "polypeptide cobalt ion contact site" EXACT []
9026 is_a: SO:0001092 ! polypeptide_metal_contact
9030 name: polypeptide_copper_ion_contact_site
9032 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]
9034 synonym: "Cu_contact_site" EXACT []
9035 synonym: "polypeptide copper ion contact site" EXACT []
9036 is_a: SO:0001092 ! polypeptide_metal_contact
9040 name: polypeptide_iron_ion_contact_site
9042 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]
9044 synonym: "Fe_contact_site" EXACT []
9045 synonym: "polypeptide iron ion contact site" EXACT []
9046 is_a: SO:0001092 ! polypeptide_metal_contact
9050 name: polypeptide_magnesium_ion_contact_site
9052 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]
9054 synonym: "Mg_contact_site" EXACT []
9055 synonym: "polypeptide magnesium ion contact site" EXACT []
9056 is_a: SO:0001092 ! polypeptide_metal_contact
9060 name: polypeptide_manganese_ion_contact_site
9062 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]
9064 synonym: "Mn_contact_site" EXACT []
9065 synonym: "polypeptide manganese ion contact site" EXACT []
9066 is_a: SO:0001092 ! polypeptide_metal_contact
9070 name: polypeptide_molybdenum_ion_contact_site
9072 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]
9074 synonym: "Mo_contact_site" EXACT []
9075 synonym: "polypeptide molybdenum ion contact site" EXACT []
9076 is_a: SO:0001092 ! polypeptide_metal_contact
9080 name: polypeptide_nickel_ion_contact_site
9082 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]
9084 synonym: "Ni_contact_site" EXACT []
9085 synonym: "polypeptide nickel ion contact site" EXACT []
9086 is_a: SO:0001092 ! polypeptide_metal_contact
9090 name: polypeptide_tungsten_ion_contact_site
9092 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]
9094 synonym: "polypeptide tungsten ion contact site" EXACT []
9095 synonym: "W_contact_site" EXACT []
9096 is_a: SO:0001092 ! polypeptide_metal_contact
9100 name: polypeptide_zinc_ion_contact_site
9102 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]
9104 synonym: "polypeptide zinc ion contact site" EXACT []
9105 synonym: "Zn_contact_site" EXACT []
9106 is_a: SO:0001092 ! polypeptide_metal_contact
9110 name: catalytic_residue
9112 def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]
9115 synonym: "act_site" RELATED [uniprot:feature_type]
9116 synonym: "active site residue" EXACT []
9117 synonym: "catalytic residue" EXACT []
9118 is_a: SO:0001237 ! amino_acid
9119 relationship: part_of SO:0100019 ! polypeptide_catalytic_motif
9123 name: polypeptide_ligand_contact
9125 def: "Residues which interact with a ligand." [EBIBS:GAR]
9127 synonym: "polypeptide ligand contact" EXACT []
9128 synonym: "protein-ligand interaction" RELATED []
9129 is_a: SO:0001657 ! ligand_binding_site
9130 is_a: SO:0100002 ! molecular_contact_region
9136 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/]
9138 synonym: "asx motif" EXACT []
9139 is_a: SO:0001078 ! polypeptide_secondary_structure
9145 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/]
9147 synonym: "beta bulge" EXACT []
9148 xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki"
9149 is_a: SO:0001078 ! polypeptide_secondary_structure
9153 name: beta_bulge_loop
9155 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/]
9157 synonym: "beta bulge loop" EXACT []
9158 is_a: SO:0001078 ! polypeptide_secondary_structure
9162 name: beta_bulge_loop_five
9164 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/]
9166 synonym: "beta bulge loop five" EXACT []
9167 is_a: SO:0001108 ! beta_bulge_loop
9171 name: beta_bulge_loop_six
9173 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/]
9175 synonym: "beta bulge loop six" EXACT []
9176 is_a: SO:0001108 ! beta_bulge_loop
9182 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]
9185 synonym: "strand" RELATED BS [uniprot:feature_type]
9186 xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki"
9187 is_a: SO:0001078 ! polypeptide_secondary_structure
9191 name: antiparallel_beta_strand
9193 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]
9196 synonym: "antiparallel beta strand" EXACT []
9197 is_a: SO:0001111 ! beta_strand
9201 name: parallel_beta_strand
9203 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]
9206 synonym: "parallel beta strand" EXACT []
9207 is_a: SO:0001111 ! beta_strand
9213 def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]
9216 synonym: "helix" RELATED BS []
9217 is_a: SO:0001078 ! polypeptide_secondary_structure
9221 name: left_handed_peptide_helix
9223 def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]
9225 synonym: "helix-l" RELATED []
9226 synonym: "left handed helix" EXACT []
9227 is_a: SO:0001114 ! peptide_helix
9231 name: right_handed_peptide_helix
9233 def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]
9235 synonym: "helix" RELATED BS []
9236 synonym: "right handed helix" EXACT []
9237 is_a: SO:0001114 ! peptide_helix
9243 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]
9246 synonym: "a-helix" RELATED BS []
9247 synonym: "helix" RELATED BS [uniprot:feature_type]
9248 xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki"
9249 is_a: SO:0001116 ! right_handed_peptide_helix
9255 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]
9258 synonym: "pi helix" EXACT []
9259 xref: http://en.wikipedia.org/wiki/Pi_helix "wiki"
9260 is_a: SO:0001116 ! right_handed_peptide_helix
9264 name: three_ten_helix
9266 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]
9269 synonym: "3(10) helix" EXACT []
9270 synonym: "3-10 helix" EXACT []
9271 synonym: "310 helix" EXACT []
9272 synonym: "three ten helix" EXACT []
9273 xref: http://en.wikipedia.org/wiki/310_helix "wiki"
9274 is_a: SO:0001116 ! right_handed_peptide_helix
9278 name: polypeptide_nest_motif
9280 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/]
9282 synonym: "nest" RELATED BS []
9283 synonym: "nest_motif" EXACT []
9284 synonym: "polypeptide nest motif" RELATED []
9285 is_a: SO:0001078 ! polypeptide_secondary_structure
9289 name: polypeptide_nest_left_right_motif
9291 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/]
9293 synonym: "nest_left_right" EXACT []
9294 synonym: "nest_lr" EXACT []
9295 synonym: "polypeptide nest left right motif" EXACT []
9296 is_a: SO:0001120 ! polypeptide_nest_motif
9300 name: polypeptide_nest_right_left_motif
9302 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/]
9304 synonym: "nest_right_left" EXACT []
9305 synonym: "nest_rl" EXACT []
9306 synonym: "polypeptide nest right left motif" EXACT []
9307 is_a: SO:0001120 ! polypeptide_nest_motif
9311 name: schellmann_loop
9313 def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
9315 synonym: "paperclip" RELATED BS []
9316 synonym: "paperclip loop" RELATED []
9317 synonym: "schellmann loop" EXACT []
9318 is_a: SO:0001078 ! polypeptide_secondary_structure
9322 name: schellmann_loop_seven
9324 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/]
9326 synonym: "schellmann loop seven" EXACT []
9327 synonym: "seven-residue schellmann loop" EXACT []
9328 is_a: SO:0001123 ! schellmann_loop
9332 name: schellmann_loop_six
9334 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/]
9336 synonym: "schellmann loop six" EXACT []
9337 synonym: "six-residue schellmann loop" EXACT []
9338 is_a: SO:0001123 ! schellmann_loop
9342 name: serine_threonine_motif
9344 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/]
9346 synonym: "serine/threonine motif" EXACT []
9347 synonym: "st motif" EXACT []
9348 synonym: "st_motif" EXACT []
9349 is_a: SO:0001078 ! polypeptide_secondary_structure
9353 name: serine_threonine_staple_motif
9355 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/]
9357 synonym: "serine threonine staple motif" EXACT []
9358 synonym: "st_staple" EXACT []
9359 is_a: SO:0001078 ! polypeptide_secondary_structure
9363 name: polypeptide_turn_motif
9365 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]
9368 synonym: "turn" RELATED BS []
9369 is_a: SO:0001078 ! polypeptide_secondary_structure
9373 name: asx_turn_left_handed_type_one
9375 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/]
9377 synonym: "asx turn left handed type one" EXACT []
9378 synonym: "asx_turn_il" RELATED []
9379 is_a: SO:0000912 ! asx_turn
9383 name: asx_turn_left_handed_type_two
9385 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/]
9387 synonym: "asx turn left handed type two" EXACT []
9388 synonym: "asx_turn_iil" EXACT []
9389 is_a: SO:0000912 ! asx_turn
9393 name: asx_turn_right_handed_type_two
9395 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/]
9397 synonym: "asx turn right handed type two" EXACT []
9398 synonym: "asx_turn_iir" EXACT []
9399 is_a: SO:0000912 ! asx_turn
9403 name: asx_turn_right_handed_type_one
9405 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/]
9407 synonym: "asx turn type right handed type one" EXACT []
9408 synonym: "asx_turn_ir" EXACT []
9409 is_a: SO:0000912 ! asx_turn
9415 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/]
9417 synonym: "beta turn" EXACT []
9418 is_a: SO:0001128 ! polypeptide_turn_motif
9422 name: beta_turn_left_handed_type_one
9424 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/]
9426 synonym: "beta turn left handed type one" EXACT []
9427 synonym: "beta_turn_il" EXACT []
9428 synonym: "type I' beta turn" EXACT []
9429 synonym: "type I' turn" EXACT []
9430 is_a: SO:0001133 ! beta_turn
9434 name: beta_turn_left_handed_type_two
9436 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/]
9438 synonym: "beta turn left handed type two" EXACT []
9439 synonym: "beta_turn_iil" EXACT []
9440 synonym: "type II' beta turn" EXACT []
9441 synonym: "type II' turn" EXACT []
9442 is_a: SO:0001133 ! beta_turn
9446 name: beta_turn_right_handed_type_one
9448 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/]
9450 synonym: "beta turn right handed type one" EXACT []
9451 synonym: "beta_turn_ir" EXACT []
9452 synonym: "type I beta turn" EXACT []
9453 synonym: "type I turn" EXACT []
9454 is_a: SO:0001133 ! beta_turn
9458 name: beta_turn_right_handed_type_two
9460 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/]
9462 synonym: "beta turn right handed type two" EXACT []
9463 synonym: "beta_turn_iir" EXACT []
9464 synonym: "type II beta turn" EXACT []
9465 synonym: "type II turn" EXACT []
9466 is_a: SO:0001133 ! beta_turn
9472 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/]
9474 synonym: "gamma turn" EXACT []
9475 is_a: SO:0001128 ! polypeptide_turn_motif
9479 name: gamma_turn_classic
9481 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/]
9483 synonym: "classic gamma turn" EXACT []
9484 synonym: "gamma turn classic" EXACT []
9485 is_a: SO:0001138 ! gamma_turn
9489 name: gamma_turn_inverse
9491 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/]
9493 synonym: "gamma turn inverse" EXACT []
9494 is_a: SO:0001138 ! gamma_turn
9498 name: serine_threonine_turn
9500 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/]
9502 synonym: "serine/threonine turn" EXACT []
9503 synonym: "st_turn" EXACT []
9504 is_a: SO:0001128 ! polypeptide_turn_motif
9508 name: st_turn_left_handed_type_one
9510 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/]
9512 synonym: "st turn left handed type one" EXACT []
9513 synonym: "st_turn_il" EXACT []
9514 is_a: SO:0001141 ! serine_threonine_turn
9518 name: st_turn_left_handed_type_two
9520 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/]
9522 synonym: "st turn left handed type two" EXACT []
9523 synonym: "st_turn_iil" EXACT []
9524 is_a: SO:0001141 ! serine_threonine_turn
9528 name: st_turn_right_handed_type_one
9530 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/]
9532 synonym: "st turn right handed type one" EXACT []
9533 synonym: "st_turn_ir" EXACT []
9534 is_a: SO:0001141 ! serine_threonine_turn
9538 name: st_turn_right_handed_type_two
9540 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/]
9542 synonym: "st turn right handed type two" EXACT []
9543 synonym: "st_turn_iir" EXACT []
9544 is_a: SO:0001141 ! serine_threonine_turn
9548 name: polypeptide_variation_site
9550 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]
9551 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.
9553 synonym: "sequence_variations" EXACT []
9554 is_a: SO:0000839 ! polypeptide_region
9558 name: natural_variant_site
9560 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]
9563 synonym: "natural_variant" BROAD []
9564 synonym: "sequence variation" BROAD []
9565 synonym: "variant" BROAD [uniprot:feature_type]
9566 is_a: SO:0001146 ! polypeptide_variation_site
9570 name: mutated_variant_site
9572 def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]
9575 synonym: "mutagen" EXACT BS [uniprot:feature_type]
9576 synonym: "mutagenesis" EXACT []
9577 synonym: "mutated_site" EXACT []
9578 is_a: SO:0001146 ! polypeptide_variation_site
9582 name: alternate_sequence_site
9585 def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]
9588 synonym: "alternative_sequence" EXACT []
9589 synonym: "isoform" NARROW []
9590 synonym: "sequence variation" NARROW []
9591 synonym: "var_seq" EXACT [uniprot:feature_type]
9592 synonym: "varsplic" NARROW []
9593 is_a: SO:0001146 ! polypeptide_variation_site
9597 name: beta_turn_type_six
9598 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]
9600 synonym: "beta turn type six" EXACT []
9601 synonym: "cis-proline loop" EXACT []
9602 synonym: "type VI beta turn" EXACT []
9603 synonym: "type VI turn" EXACT []
9604 is_a: SO:0001133 ! beta_turn
9608 name: beta_turn_type_six_a
9609 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]
9611 synonym: "beta turn type six a" EXACT []
9612 synonym: "type VIa beta turn" EXACT []
9613 synonym: "type VIa turn" EXACT []
9614 is_a: SO:0001150 ! beta_turn_type_six
9618 name: beta_turn_type_six_a_one
9620 synonym: "beta turn type six a one" EXACT []
9621 synonym: "type VIa1 beta turn" EXACT []
9622 synonym: "type VIa1 turn" EXACT []
9623 is_a: SO:0001151 ! beta_turn_type_six_a
9627 name: beta_turn_type_six_a_two
9629 synonym: "beta turn type six a two" EXACT []
9630 synonym: "type VIa2 beta turn" EXACT []
9631 synonym: "type VIa2 turn" EXACT []
9632 is_a: SO:0001151 ! beta_turn_type_six_a
9636 name: beta_turn_type_six_b
9637 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]
9639 synonym: "beta turn type six b" EXACT []
9640 synonym: "type VIb beta turn" EXACT []
9641 synonym: "type VIb turn" EXACT []
9642 is_a: SO:0001150 ! beta_turn_type_six
9646 name: beta_turn_type_eight
9647 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]
9649 synonym: "beta turn type eight" EXACT []
9650 synonym: "type VIII beta turn" EXACT []
9651 synonym: "type VIII turn" EXACT []
9652 is_a: SO:0001133 ! beta_turn
9657 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]
9658 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.
9659 synonym: "DRE motif" EXACT []
9660 synonym: "NDM4" EXACT []
9661 synonym: "WATCGATW_motif" EXACT []
9662 is_a: SO:0000713 ! DNA_motif
9663 relationship: part_of SO:0000170 ! RNApol_II_promoter
9668 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]
9669 synonym: "directional motif v4" EXACT []
9670 synonym: "DMv4" EXACT []
9671 synonym: "DMv4 motif" EXACT []
9672 synonym: "motif 1 element" EXACT []
9673 synonym: "promoter motif 1" EXACT []
9674 synonym: "YGGTCACATR" NARROW []
9675 is_a: SO:0001659 ! promoter_element
9680 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]
9681 synonym: "AWCAGCTGWT" NARROW []
9682 synonym: "E box motif" EXACT []
9683 synonym: "generic E box motif" EXACT []
9684 synonym: "NDM5" RELATED []
9685 is_a: SO:0000713 ! DNA_motif
9686 relationship: part_of SO:0000170 ! RNApol_II_promoter
9691 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]
9692 synonym: "directional motif v5" EXACT []
9693 synonym: "DMv5" EXACT []
9694 synonym: "DMv5 motif" EXACT []
9695 synonym: "KTYRGTATWTTT" NARROW []
9696 synonym: "promoter motif 6" RELATED []
9697 is_a: SO:0001659 ! promoter_element
9698 relationship: part_of SO:0000170 ! RNApol_II_promoter
9703 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]
9704 synonym: "directional motif v3" EXACT []
9705 synonym: "DMv3" EXACT []
9706 synonym: "DMv3 motif" EXACT []
9707 synonym: "KNNCAKCNCTRNY" NARROW []
9708 synonym: "promoter motif 7" EXACT []
9709 is_a: SO:0001659 ! promoter_element
9710 relationship: part_of SO:0000170 ! RNApol_II_promoter
9715 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]
9716 synonym: "directional motif v2" EXACT []
9717 synonym: "DMv2" EXACT []
9718 synonym: "DMv2 motif" EXACT []
9719 synonym: "MKSYGGCARCGSYSS" NARROW []
9720 synonym: "promoter motif 8" EXACT []
9721 is_a: SO:0001659 ! promoter_element
9722 relationship: part_of SO:0000170 ! RNApol_II_promoter
9727 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]
9728 synonym: "CSARCSSAACGS" NARROW []
9729 synonym: "motif ten element" EXACT []
9730 synonym: "motif_ten_element" EXACT []
9731 is_a: SO:0001660 ! core_promoter_element
9732 relationship: part_of SO:0001669 ! RNApol_II_core_promoter
9737 def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941]
9738 synonym: "directional motif p3" EXACT []
9739 synonym: "directional promoter motif 3" EXACT []
9740 synonym: "DMp3" EXACT []
9741 synonym: "INR1 motif" EXACT []
9742 is_a: SO:0000713 ! DNA_motif
9743 relationship: part_of SO:0000170 ! RNApol_II_promoter
9748 def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941]
9749 synonym: "directional motif 5" EXACT []
9750 synonym: "directional promoter motif 5" RELATED []
9751 synonym: "DMp5" EXACT []
9752 synonym: "DPE1 motif" EXACT []
9753 is_a: SO:0001659 ! promoter_element
9754 relationship: part_of SO:0000170 ! RNApol_II_promoter
9759 def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941]
9760 synonym: "directional promoter motif v1" RELATED []
9761 synonym: "DMv1" RELATED []
9762 synonym: "DMv1 motif" EXACT []
9763 is_a: SO:0001659 ! promoter_element
9764 relationship: part_of SO:0000170 ! RNApol_II_promoter
9769 def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]
9770 synonym: "GAGA" EXACT []
9771 synonym: "GAGA motif" EXACT []
9772 synonym: "NDM1" EXACT []
9773 is_a: SO:0000713 ! DNA_motif
9774 relationship: part_of SO:0000170 ! RNApol_II_promoter
9779 def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]
9780 synonym: "NDM2" EXACT []
9781 synonym: "NDM2 motif" EXACT []
9782 synonym: "non directional promoter motif 2" EXACT []
9783 is_a: SO:0001659 ! promoter_element
9784 relationship: part_of SO:0000170 ! RNApol_II_promoter
9789 def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]
9790 synonym: "NDM3" EXACT []
9791 synonym: "NDM3 motif" EXACT []
9792 synonym: "non directional motif 3" EXACT []
9793 is_a: SO:0001659 ! promoter_element
9794 relationship: part_of SO:0000170 ! RNApol_II_promoter
9798 name: ds_RNA_viral_sequence
9799 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]
9800 synonym: "double stranded RNA virus sequence" EXACT []
9801 synonym: "ds RNA viral sequence" EXACT []
9802 is_a: SO:0001041 ! viral_sequence
9807 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]
9808 synonym: "maverick element" RELATED []
9809 is_a: SO:0000208 ! terminal_inverted_repeat_element
9814 def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]
9815 synonym: "21S LSU rRNA" EXACT []
9816 synonym: "21S ribosomal RNA" EXACT []
9817 synonym: "21S rRNA" EXACT []
9818 synonym: "rRNA 21S" EXACT []
9819 is_a: SO:0000651 ! large_subunit_rRNA
9824 def: "A region of a tRNA." [RSC:cb]
9825 synonym: "tRNA region" EXACT []
9826 is_a: SO:0000834 ! mature_transcript_region
9827 relationship: part_of SO:0000253 ! tRNA
9831 name: anticodon_loop
9832 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]
9833 synonym: "anti-codon loop" EXACT []
9834 synonym: "anticodon loop" EXACT []
9835 is_a: SO:0001172 ! tRNA_region
9840 def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]
9841 synonym: "anti-codon" EXACT []
9842 xref: http://en.wikipedia.org/wiki/Anticodon "wiki"
9843 is_a: SO:0001172 ! tRNA_region
9844 relationship: part_of SO:0001173 ! anticodon_loop
9849 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]
9850 synonym: "CCA sequence" EXACT []
9851 synonym: "CCA tail" EXACT []
9852 is_a: SO:0001172 ! tRNA_region
9857 def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]
9858 synonym: "D loop" RELATED []
9859 synonym: "DHU loop" EXACT []
9860 is_a: SO:0001172 ! tRNA_region
9865 def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]
9866 synonym: "T loop" EXACT []
9867 synonym: "TpsiC loop" EXACT []
9868 is_a: SO:0001172 ! tRNA_region
9872 name: pyrrolysine_tRNA_primary_transcript
9873 def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]
9874 synonym: "pyrrolysine tRNA primary transcript" EXACT []
9875 is_a: SO:0000210 ! tRNA_primary_transcript
9880 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]
9881 comment: The definition is most of the old definition for snoRNA (SO:0000275).
9882 synonym: "small nucleolar RNA U3" EXACT []
9883 synonym: "snoRNA U3" EXACT []
9884 synonym: "U3 small nucleolar RNA" EXACT []
9885 synonym: "U3 snoRNA" EXACT []
9886 xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 "wiki"
9887 is_a: SO:0000593 ! C_D_box_snoRNA
9891 name: AU_rich_element
9892 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]
9893 synonym: "ARE" RELATED []
9894 synonym: "AU rich element" EXACT []
9895 synonym: "AU-rich element" EXACT []
9896 xref: http://en.wikipedia.org/wiki/AU-rich_element "wiki"
9897 is_a: SO:0000837 ! UTR_region
9898 relationship: part_of SO:0000205 ! three_prime_UTR
9902 name: Bruno_response_element
9903 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]
9904 comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
9905 synonym: "BRE" RELATED []
9906 synonym: "Bruno response element" EXACT []
9907 is_a: SO:0000837 ! UTR_region
9908 relationship: part_of SO:0000205 ! three_prime_UTR
9912 name: iron_responsive_element
9913 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]
9914 synonym: "IRE" EXACT []
9915 synonym: "iron responsive element" EXACT []
9916 xref: http://en.wikipedia.org/wiki/Iron_responsive_element "wiki"
9917 is_a: SO:0000837 ! UTR_region
9918 relationship: part_of SO:0000203 ! UTR
9922 name: morpholino_backbone
9923 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]
9924 comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
9925 synonym: "morpholino backbone" EXACT []
9926 xref: http://en.wikipedia.org/wiki/Morpholino "wiki"
9927 is_a: SO:0000348 ! nucleic_acid
9932 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]
9933 comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
9934 synonym: "peptide nucleic acid" RELATED []
9935 is_a: SO:0000348 ! nucleic_acid
9940 def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
9941 comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
9942 is_a: SO:0000733 ! feature_attribute
9947 def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]
9948 comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
9949 is_a: SO:0001185 ! enzymatic
9953 name: pseudouridylation_guide_snoRNA
9954 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]
9955 comment: Has RNA pseudouridylation guide activity (GO:0030558).
9956 synonym: "pseudouridylation guide snoRNA" EXACT []
9957 is_a: SO:0000594 ! H_ACA_box_snoRNA
9962 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]
9963 comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
9964 is_a: SO:0000348 ! nucleic_acid
9969 def: "An oligo composed of LNA residues." [RSC:cb]
9970 synonym: "LNA oligo" EXACT []
9971 synonym: "locked nucleic acid" EXACT []
9972 xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid "wiki"
9973 is_a: SO:0001247 ! synthetic_oligo
9974 relationship: has_quality SO:0001188 ! LNA
9979 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]
9980 comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
9981 is_a: SO:0000348 ! nucleic_acid
9986 def: "An oligo composed of TNA residues." [RSC:cb]
9987 synonym: "threose nucleic acid" EXACT []
9988 synonym: "TNA oligo" EXACT []
9989 xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid "wiki"
9990 is_a: SO:0001247 ! synthetic_oligo
9991 relationship: has_quality SO:0001190 ! TNA
9996 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]
9997 comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
9998 is_a: SO:0000348 ! nucleic_acid
10003 def: "An oligo composed of GNA residues." [RSC:cb]
10004 synonym: "glycerol nucleic acid" EXACT []
10005 synonym: "glycol nucleic acid" EXACT []
10006 synonym: "GNA oligo" EXACT []
10007 xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid "wiki"
10008 is_a: SO:0001247 ! synthetic_oligo
10009 relationship: has_quality SO:0001192 ! GNA
10014 def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]
10015 comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
10016 synonym: "R GNA" EXACT []
10017 is_a: SO:0001192 ! GNA
10022 def: "An oligo composed of (R)-GNA residues." [RSC:cb]
10023 synonym: "(R)-glycerol nucleic acid" EXACT []
10024 synonym: "(R)-glycol nucleic acid" EXACT []
10025 synonym: "R GNA oligo" EXACT []
10026 is_a: SO:0001193 ! GNA_oligo
10027 relationship: has_quality SO:0001194 ! R_GNA
10032 def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]
10033 comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
10034 synonym: "S GNA" EXACT []
10035 is_a: SO:0001192 ! GNA
10040 def: "An oligo composed of (S)-GNA residues." [RSC:cb]
10041 synonym: "(S)-glycerol nucleic acid" EXACT []
10042 synonym: "(S)-glycol nucleic acid" EXACT []
10043 synonym: "S GNA oligo" EXACT []
10044 is_a: SO:0001193 ! GNA_oligo
10045 relationship: has_quality SO:0001196 ! S_GNA
10049 name: ds_DNA_viral_sequence
10050 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]
10051 synonym: "double stranded DNA virus" EXACT []
10052 synonym: "ds DNA viral sequence" EXACT []
10053 is_a: SO:0001041 ! viral_sequence
10057 name: ss_RNA_viral_sequence
10058 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]
10059 synonym: "single strand RNA virus" EXACT []
10060 synonym: "ss RNA viral sequence" EXACT []
10061 is_a: SO:0001041 ! viral_sequence
10065 name: negative_sense_ssRNA_viral_sequence
10066 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]
10067 synonym: "negative sense single stranded RNA virus" RELATED []
10068 synonym: "negative sense ssRNA viral sequence" EXACT []
10069 is_a: SO:0001199 ! ss_RNA_viral_sequence
10073 name: positive_sense_ssRNA_viral_sequence
10074 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]
10075 synonym: "positive sense single stranded RNA virus" RELATED []
10076 synonym: "positive sense ssRNA viral sequence" EXACT []
10077 is_a: SO:0001199 ! ss_RNA_viral_sequence
10081 name: ambisense_ssRNA_viral_sequence
10082 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]
10083 synonym: "ambisense single stranded RNA virus" EXACT []
10084 synonym: "ambisense ssRNA viral sequence" EXACT []
10085 is_a: SO:0001199 ! ss_RNA_viral_sequence
10089 name: RNA_polymerase_promoter
10090 def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]
10091 synonym: "RNA polymerase promoter" EXACT []
10092 is_a: SO:0000167 ! promoter
10096 name: Phage_RNA_Polymerase_Promoter
10097 def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]
10098 synonym: "Phage RNA Polymerase Promoter" EXACT []
10099 is_a: SO:0001203 ! RNA_polymerase_promoter
10103 name: SP6_RNA_Polymerase_Promoter
10104 def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]
10105 synonym: "SP6 RNA Polymerase Promoter" EXACT []
10106 is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
10110 name: T3_RNA_Polymerase_Promoter
10111 def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]
10112 synonym: "T3 RNA Polymerase Promoter" EXACT []
10113 is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
10117 name: T7_RNA_Polymerase_Promoter
10118 def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]
10119 synonym: "T7 RNA Polymerase Promoter" EXACT []
10120 is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
10124 name: five_prime_EST
10125 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]
10126 synonym: "5' EST" EXACT []
10127 synonym: "five prime EST" EXACT []
10128 is_a: SO:0000345 ! EST
10132 name: three_prime_EST
10133 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]
10134 synonym: "3' EST" EXACT []
10135 synonym: "three prime EST" EXACT []
10136 is_a: SO:0000345 ! EST
10140 name: translational_frameshift
10141 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]
10142 synonym: "ribosomal frameshift" EXACT []
10143 synonym: "translational frameshift" EXACT []
10144 xref: http://en.wikipedia.org/wiki/Translational_frameshift "wiki"
10145 is_a: SO:0000836 ! mRNA_region
10149 name: plus_1_translational_frameshift
10150 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]
10151 synonym: "plus 1 ribosomal frameshift" EXACT []
10152 synonym: "plus 1 translational frameshift" EXACT []
10153 is_a: SO:0001210 ! translational_frameshift
10157 name: plus_2_translational_frameshift
10158 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]
10159 synonym: "plus 2 ribosomal frameshift" EXACT []
10160 synonym: "plus 2 translational frameshift" EXACT []
10161 is_a: SO:0001210 ! translational_frameshift
10165 name: group_III_intron
10166 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]
10167 comment: GO:0000374.
10168 synonym: "group III intron" EXACT []
10169 xref: http://en.wikipedia.org/wiki/Group_III_intron "wiki"
10170 is_a: SO:0000588 ! autocatalytically_spliced_intron
10174 name: noncoding_region_of_exon
10175 def: "The maximal intersection of exon and UTR." [SO:ke]
10176 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.
10178 synonym: "noncoding region of exon" EXACT []
10179 is_a: SO:0000852 ! exon_region
10183 name: coding_region_of_exon
10184 def: "The region of an exon that encodes for protein sequence." [SO:ke]
10185 comment: An exon containing either a start or stop codon will be partially coding and partially non coding.
10187 synonym: "coding region of exon" EXACT []
10188 is_a: SO:0000852 ! exon_region
10192 name: endonuclease_spliced_intron
10193 def: "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]
10194 synonym: "endonuclease spliced intron" EXACT []
10195 is_a: SO:0000188 ! intron
10199 name: protein_coding_gene
10200 synonym: "protein coding gene" EXACT []
10201 is_a: SO:0000704 ! gene
10202 relationship: has_quality SO:0000010 ! protein_coding
10206 name: transgenic_insertion
10207 def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]
10208 synonym: "transgenic insertion" EXACT []
10209 is_a: SO:0000667 ! insertion
10210 relationship: has_quality SO:0000781 ! transgenic
10215 is_a: SO:0000704 ! gene
10216 relationship: has_quality SO:0000569 ! retrotransposed
10220 name: silenced_by_RNA_interference
10221 def: "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]
10222 comment: RNA interference is GO:0016246.
10223 synonym: "silenced by RNA interference" EXACT []
10224 is_a: SO:0000893 ! silenced
10228 name: silenced_by_histone_modification
10229 def: "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]
10230 comment: Histone modification is GO:0016570.
10231 synonym: "silenced by histone modification" EXACT []
10232 is_a: SO:0000893 ! silenced
10236 name: silenced_by_histone_methylation
10237 def: "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]
10238 comment: Histone methylation is GO:0016571.
10239 synonym: "silenced by histone methylation" EXACT []
10240 is_a: SO:0001221 ! silenced_by_histone_modification
10244 name: silenced_by_histone_deacetylation
10245 def: "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]
10246 comment: Histone deacetylation is GO:0016573.
10247 synonym: "silenced by histone deacetylation" EXACT []
10248 is_a: SO:0001221 ! silenced_by_histone_modification
10252 name: gene_silenced_by_RNA_interference
10253 def: "A gene that is silenced by RNA interference." [SO:xp]
10254 synonym: "gene silenced by RNA interference" EXACT []
10255 synonym: "RNA interference silenced gene" EXACT []
10256 synonym: "RNAi silenced gene" EXACT []
10257 is_a: SO:0000127 ! silenced_gene
10258 relationship: has_quality SO:0001220 ! silenced_by_RNA_interference
10262 name: gene_silenced_by_histone_modification
10263 def: "A gene that is silenced by histone modification." [SO:xp]
10264 synonym: "gene silenced by histone modification" EXACT []
10265 is_a: SO:0000127 ! silenced_gene
10266 relationship: has_quality SO:0001221 ! silenced_by_histone_modification
10270 name: gene_silenced_by_histone_methylation
10271 def: "A gene that is silenced by histone methylation." [SO:xp]
10272 synonym: "gene silenced by histone methylation" EXACT []
10273 is_a: SO:0001225 ! gene_silenced_by_histone_modification
10274 relationship: has_quality SO:0001222 ! silenced_by_histone_methylation
10278 name: gene_silenced_by_histone_deacetylation
10279 def: "A gene that is silenced by histone deacetylation." [SO:xp]
10280 synonym: "gene silenced by histone deacetylation" EXACT []
10281 is_a: SO:0001225 ! gene_silenced_by_histone_modification
10282 relationship: has_quality SO:0001223 ! silenced_by_histone_deacetylation
10286 name: dihydrouridine
10287 def: "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]
10288 synonym: " D" EXACT RNAMOD []
10289 xref: http://en.wikipedia.org/wiki/Dihydrouridine "wiki"
10291 is_a: SO:0001277 ! modified_uridine
10295 name: pseudouridine
10296 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]
10297 comment: The free molecule is CHEBI:17802.
10298 synonym: " Y" EXACT RNAMOD []
10299 xref: http://en.wikipedia.org/wiki/Pseudouridine "wiki"
10301 is_a: SO:0001277 ! modified_uridine
10306 def: "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]
10307 comment: The free molecule is CHEBI:17596.
10308 synonym: "I" RELATED []
10309 synonym: "RNAMOD:017" RELATED []
10310 xref: http://en.wikipedia.org/wiki/Inosine "wiki"
10311 is_a: SO:0000250 ! modified_RNA_base_feature
10315 name: seven_methylguanine
10316 def: "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]
10317 comment: The free molecule is CHEBI:2274.
10318 synonym: "7-methylguanine" EXACT []
10319 synonym: "seven methylguanine" EXACT []
10320 is_a: SO:0000250 ! modified_RNA_base_feature
10324 name: ribothymidine
10325 def: "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]
10326 comment: The free molecule is CHEBI:30832.
10327 is_a: SO:0000250 ! modified_RNA_base_feature
10331 name: methylinosine
10332 def: "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]
10333 is_a: SO:0001274 ! modified_inosine
10338 def: "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb]
10339 xref: http://en.wikipedia.org/wiki/Mobile "wiki"
10340 is_a: SO:0000733 ! feature_attribute
10345 def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]
10347 xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki"
10348 is_a: SO:0001411 ! biological_region
10353 def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]
10355 xref: http://en.wikipedia.org/wiki/Nucleobase "wiki"
10356 is_a: SO:0001411 ! biological_region
10361 def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]
10362 comment: Probably in the future this will cross reference to Chebi.
10363 synonym: "amino acid" EXACT []
10364 xref: http://en.wikipedia.org/wiki/Amino_acid "wiki"
10365 is_a: SO:0001411 ! biological_region
10366 relationship: part_of SO:0000104 ! polypeptide
10371 synonym: "major transcription start site" EXACT []
10372 synonym: "major TSS" EXACT []
10373 is_a: SO:0000315 ! TSS
10378 synonym: "minor TSS" EXACT []
10379 is_a: SO:0000315 ! TSS
10384 def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]
10385 synonym: "TSS region" EXACT []
10386 is_a: SO:0000842 ! gene_component_region
10387 relationship: has_part SO:0000315 ! TSS
10391 name: encodes_alternate_transcription_start_sites
10392 synonym: "encodes alternate transcription start sites" EXACT []
10393 is_a: SO:0000401 ! gene_attribute
10397 name: miRNA_primary_transcript_region
10398 def: "A part of an miRNA primary_transcript." [SO:ke]
10399 synonym: "miRNA primary transcript region" EXACT []
10400 is_a: SO:0000835 ! primary_transcript_region
10405 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]
10406 synonym: "pre-miRNA" EXACT []
10407 is_a: SO:0001243 ! miRNA_primary_transcript_region
10412 def: "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]
10413 synonym: "miRNA stem" EXACT []
10414 is_a: SO:0001243 ! miRNA_primary_transcript_region
10415 relationship: part_of SO:0001244 ! pre_miRNA
10420 def: "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]
10421 synonym: "miRNA loop" EXACT []
10422 is_a: SO:0001243 ! miRNA_primary_transcript_region
10423 relationship: part_of SO:0001244 ! pre_miRNA
10427 name: synthetic_oligo
10428 def: "An oligo composed of synthetic nucleotides." [SO:ke]
10429 synonym: "synthetic oligo" EXACT []
10430 is_a: SO:0000696 ! oligo
10435 def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]
10437 xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki"
10438 is_a: SO:0001410 ! experimental_feature
10442 name: fragment_assembly
10443 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]
10444 synonym: "fragment assembly" EXACT []
10445 synonym: "physical map" EXACT []
10446 is_a: SO:0001248 ! assembly
10450 name: fingerprint_map
10451 def: "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]
10452 synonym: "BACmap" EXACT []
10453 synonym: "fingerprint map" EXACT []
10454 synonym: "FPC" EXACT []
10455 synonym: "FPCmap" EXACT []
10456 synonym: "restriction map" EXACT []
10457 is_a: SO:0001249 ! fragment_assembly
10458 relationship: has_part SO:0000412 ! restriction_fragment
10463 def: "An STS map is a physical map organized by the unique STS landmarks." [SO:ke]
10464 synonym: "STS map" EXACT []
10465 is_a: SO:0001249 ! fragment_assembly
10466 relationship: has_part SO:0000331 ! STS
10471 def: "A radiation hybrid map is a physical map." [SO:ke]
10472 synonym: "radiation hybrid map" EXACT []
10473 synonym: "RH map" EXACT []
10474 is_a: SO:0001249 ! fragment_assembly
10475 relationship: has_part SO:0000331 ! STS
10479 name: sonicate_fragment
10480 def: "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]
10481 synonym: "sonicate fragment" EXACT []
10482 is_a: SO:0000143 ! assembly_component
10487 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]
10488 xref: http://en.wikipedia.org/wiki/Polyploid "wiki"
10489 is_a: SO:1000182 ! chromosome_number_variation
10493 name: autopolyploid
10494 def: "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]
10495 xref: http://en.wikipedia.org/wiki/Autopolyploid "wiki"
10496 is_a: SO:0001254 ! polyploid
10500 name: allopolyploid
10501 def: "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]
10502 xref: http://en.wikipedia.org/wiki/Allopolyploid "wiki"
10503 is_a: SO:0001254 ! polyploid
10507 name: homing_endonuclease_binding_site
10508 def: "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]
10509 synonym: "homing endonuclease binding site" EXACT []
10510 is_a: SO:0000059 ! nuclease_binding_site
10514 name: octamer_motif
10515 def: "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]
10516 comment: Nature. 1986 Oct 16-22;323(6089):640-3.
10517 synonym: "octamer motif" EXACT []
10518 is_a: SO:0000713 ! DNA_motif
10519 relationship: part_of SO:0000170 ! RNApol_II_promoter
10523 name: apicoplast_chromosome
10524 def: "A chromosome originating in an apicoplast." [SO:xp]
10525 synonym: "apicoplast chromosome" EXACT []
10526 is_a: SO:0000340 ! chromosome
10527 relationship: has_origin SO:0000743 ! apicoplast_sequence
10531 name: sequence_collection
10532 def: "A collection of discontinuous sequences." [SO:ke]
10533 synonym: "sequence collection" EXACT []
10537 name: overlapping_feature_set
10538 def: "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]
10539 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.
10540 synonym: "overlapping feature set" EXACT []
10541 is_a: SO:0000703 ! experimental_result_region
10545 name: overlapping_EST_set
10546 def: "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]
10547 synonym: "overlapping EST set" EXACT []
10548 is_a: SO:0001261 ! overlapping_feature_set
10549 relationship: has_part SO:0000345 ! EST
10554 synonym: "ncRNA gen" EXACT []
10555 synonym: "ncRNA gene" EXACT []
10556 synonym: "non-coding RNA gene" RELATED []
10557 is_a: SO:0000704 ! gene
10562 synonym: "gRNA gene" EXACT []
10563 is_a: SO:0001263 ! ncRNA_gene
10564 relationship: has_quality SO:0000979 ! gRNA_encoding
10570 synonym: "miRNA gene" EXACT []
10571 synonym: "stRNA gene" EXACT []
10572 synonym: "stRNA_gene" EXACT []
10573 is_a: SO:0001263 ! ncRNA_gene
10574 relationship: has_quality SO:0000571 ! miRNA_encoding
10575 relationship: has_quality SO:0000656 ! stRNA_encoding
10580 synonym: "scRNA gene" EXACT []
10581 is_a: SO:0001263 ! ncRNA_gene
10582 relationship: has_quality SO:0000575 ! scRNA_encoding
10587 synonym: "snoRNA gene" EXACT []
10588 is_a: SO:0001263 ! ncRNA_gene
10589 relationship: has_quality SO:0000578 ! snoRNA_encoding
10594 synonym: "snRNA gene" EXACT []
10595 is_a: SO:0001263 ! ncRNA_gene
10596 relationship: has_quality SO:0001263 ! ncRNA_gene
10601 synonym: "SRP RNA gene" EXACT []
10602 is_a: SO:0001263 ! ncRNA_gene
10603 relationship: has_quality SO:0000642 ! SRP_RNA_encoding
10608 synonym: "tmRNA gene" EXACT []
10609 is_a: SO:0001263 ! ncRNA_gene
10610 relationship: has_quality SO:0000659 ! tmRNA_encoding
10615 synonym: "tRNA gene" EXACT []
10616 is_a: SO:0001263 ! ncRNA_gene
10617 relationship: has_quality SO:0000663 ! tRNA_encoding
10621 name: modified_adenosine
10622 def: "A modified adenine is an adenine base feature that has been altered." [SO:ke]
10623 synonym: "modified adenosine" EXACT []
10624 is_a: SO:0000250 ! modified_RNA_base_feature
10628 name: modified_inosine
10629 def: "A modified inosine is an inosine base feature that has been altered." [SO:ke]
10630 synonym: "modified inosine" EXACT []
10631 is_a: SO:0001230 ! inosine
10635 name: modified_cytidine
10636 def: "A modified cytidine is a cytidine base feature which has been altered." [SO:ke]
10637 synonym: "modified cytidine" EXACT []
10638 is_a: SO:0000250 ! modified_RNA_base_feature
10642 name: modified_guanosine
10643 synonym: "modified guanosine" EXACT []
10644 is_a: SO:0000250 ! modified_RNA_base_feature
10648 name: modified_uridine
10649 synonym: "modified uridine" EXACT []
10650 is_a: SO:0000250 ! modified_RNA_base_feature
10654 name: one_methylinosine
10655 def: "1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
10656 synonym: "1-methylinosine" EXACT []
10657 synonym: "m1I" EXACT RNAMOD []
10658 synonym: "one methylinosine" EXACT []
10660 is_a: SO:0001274 ! modified_inosine
10664 name: one_two_prime_O_dimethylinosine
10665 def: "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
10666 synonym: "1,2'-O-dimethylinosine" EXACT []
10667 synonym: "m'Im" EXACT RNAMOD []
10668 synonym: "one two prime O dimethylinosine" EXACT []
10670 is_a: SO:0001274 ! modified_inosine
10674 name: two_prime_O_methylinosine
10675 def: "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
10676 synonym: "2'-O-methylinosine" EXACT []
10677 synonym: "Im" EXACT RNAMOD []
10678 synonym: "two prime O methylinosine" EXACT []
10680 is_a: SO:0001274 ! modified_inosine
10684 name: three_methylcytidine
10685 def: "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10686 synonym: "3-methylcytidine" EXACT []
10687 synonym: "m3C" EXACT RNAMOD []
10688 synonym: "three methylcytidine" EXACT []
10690 is_a: SO:0001275 ! modified_cytidine
10694 name: five_methylcytidine
10695 def: "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10696 synonym: "5-methylcytidine" EXACT []
10697 synonym: "five methylcytidine" EXACT []
10698 synonym: "m5C" EXACT RNAMOD []
10700 is_a: SO:0001275 ! modified_cytidine
10704 name: two_prime_O_methylcytidine
10705 def: "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10706 synonym: "2'-O-methylcytidine" EXACT []
10707 synonym: "Cm" EXACT RNAMOD []
10708 synonym: "two prime O methylcytidine" EXACT []
10710 is_a: SO:0001275 ! modified_cytidine
10714 name: two_thiocytidine
10715 def: "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10716 synonym: "2-thiocytidine" EXACT []
10717 synonym: "s2C" EXACT RNAMOD []
10718 synonym: "two thiocytidine" EXACT []
10720 is_a: SO:0001275 ! modified_cytidine
10724 name: N4_acetylcytidine
10725 def: "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10726 synonym: "ac4C" EXACT RNAMOD []
10727 synonym: "N4 acetylcytidine" EXACT []
10728 synonym: "N4-acetylcytidine" EXACT []
10730 is_a: SO:0001275 ! modified_cytidine
10734 name: five_formylcytidine
10735 def: "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10736 synonym: "5-formylcytidine" EXACT []
10737 synonym: "f5C" EXACT RNAMOD []
10738 synonym: "five formylcytidine" EXACT []
10740 is_a: SO:0001275 ! modified_cytidine
10744 name: five_two_prime_O_dimethylcytidine
10745 def: "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10746 synonym: "5,2'-O-dimethylcytidine" EXACT []
10747 synonym: "five two prime O dimethylcytidine" EXACT []
10748 synonym: "m5Cm" EXACT RNAMOD []
10750 is_a: SO:0001275 ! modified_cytidine
10754 name: N4_acetyl_2_prime_O_methylcytidine
10755 def: "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10756 synonym: "ac4Cm" EXACT RNAMOD []
10757 synonym: "N4 acetyl 2 prime O methylcytidine" EXACT []
10758 synonym: "N4-acetyl-2'-O-methylcytidine" EXACT []
10760 is_a: SO:0001275 ! modified_cytidine
10765 def: "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10766 synonym: "k2C" EXACT RNAMOD []
10767 xref: http://en.wikipedia.org/wiki/Lysidine "wiki"
10769 is_a: SO:0001275 ! modified_cytidine
10773 name: N4_methylcytidine
10774 def: "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10775 synonym: "m4C" EXACT RNAMOD []
10776 synonym: "N4 methylcytidine" EXACT []
10777 synonym: "N4-methylcytidine" EXACT []
10779 is_a: SO:0001275 ! modified_cytidine
10783 name: N4_2_prime_O_dimethylcytidine
10784 def: "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10785 synonym: "m4Cm" EXACT RNAMOD []
10786 synonym: "N4 2 prime O dimethylcytidine" EXACT []
10787 synonym: "N4,2'-O-dimethylcytidine" EXACT []
10789 is_a: SO:0001275 ! modified_cytidine
10793 name: five_hydroxymethylcytidine
10794 def: "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10795 synonym: "5-hydroxymethylcytidine" EXACT []
10796 synonym: "five hydroxymethylcytidine" EXACT []
10797 synonym: "hm5C" EXACT RNAMOD []
10799 is_a: SO:0001275 ! modified_cytidine
10803 name: five_formyl_two_prime_O_methylcytidine
10804 def: "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10805 synonym: "5-formyl-2'-O-methylcytidine" EXACT []
10806 synonym: "f5Cm" EXACT RNAMOD []
10807 synonym: "five formyl two prime O methylcytidine" EXACT []
10809 is_a: SO:0001275 ! modified_cytidine
10813 name: N4_N4_2_prime_O_trimethylcytidine
10814 def: "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
10815 synonym: "m42Cm" EXACT RNAMOD []
10816 synonym: "N4,N4,2'-O-trimethylcytidine" EXACT []
10818 is_a: SO:0001275 ! modified_cytidine
10822 name: one_methyladenosine
10823 def: "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10824 synonym: "1-methyladenosine" EXACT []
10825 synonym: "m1A" EXACT RNAMOD []
10826 synonym: "one methyladenosine" EXACT []
10828 is_a: SO:0001273 ! modified_adenosine
10832 name: two_methyladenosine
10833 def: "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10834 synonym: "2-methyladenosine" EXACT []
10835 synonym: "m2A" EXACT RNAMOD []
10836 synonym: "two methyladenosine" EXACT []
10838 is_a: SO:0001273 ! modified_adenosine
10842 name: N6_methyladenosine
10843 def: "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10844 synonym: "m6A" EXACT RNAMOD []
10845 synonym: "N6 methyladenosine" EXACT []
10846 synonym: "N6-methyladenosine" EXACT []
10848 is_a: SO:0001273 ! modified_adenosine
10852 name: two_prime_O_methyladenosine
10853 def: "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10854 synonym: "2'-O-methyladenosine" EXACT []
10855 synonym: "Am" EXACT RNAMOD []
10856 synonym: "two prime O methyladenosine" EXACT []
10858 is_a: SO:0001273 ! modified_adenosine
10862 name: two_methylthio_N6_methyladenosine
10863 def: "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10864 synonym: "2-methylthio-N6-methyladenosine" EXACT []
10865 synonym: "ms2m6A" EXACT RNAMOD []
10866 synonym: "two methylthio N6 methyladenosine" EXACT []
10868 is_a: SO:0001273 ! modified_adenosine
10872 name: N6_isopentenyladenosine
10873 def: "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10874 synonym: "i6A" EXACT RNAMOD []
10875 synonym: "N6 isopentenyladenosine" EXACT []
10876 synonym: "N6-isopentenyladenosine" EXACT []
10878 is_a: SO:0001273 ! modified_adenosine
10882 name: two_methylthio_N6_isopentenyladenosine
10883 def: "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10884 synonym: "2-methylthio-N6-isopentenyladenosine" EXACT []
10885 synonym: "ms2i6A" EXACT RNAMOD []
10886 synonym: "two methylthio N6 isopentenyladenosine" EXACT []
10888 is_a: SO:0001273 ! modified_adenosine
10892 name: N6_cis_hydroxyisopentenyl_adenosine
10893 def: "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10894 synonym: "io6A" EXACT RNAMOD []
10895 synonym: "N6 cis hydroxyisopentenyl adenosine" EXACT []
10896 synonym: "N6-(cis-hydroxyisopentenyl)adenosine" EXACT []
10898 is_a: SO:0001273 ! modified_adenosine
10902 name: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
10903 def: "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10904 synonym: "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine" EXACT []
10905 synonym: "ms2io6A" EXACT RNAMOD []
10906 synonym: "two methylthio N6 cis hydroxyisopentenyl adenosine" EXACT []
10908 is_a: SO:0001273 ! modified_adenosine
10912 name: N6_glycinylcarbamoyladenosine
10913 def: "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10914 synonym: "g6A" EXACT RNAMOD []
10915 synonym: "N6 glycinylcarbamoyladenosine" EXACT []
10916 synonym: "N6-glycinylcarbamoyladenosine" EXACT []
10918 is_a: SO:0001273 ! modified_adenosine
10922 name: N6_threonylcarbamoyladenosine
10923 def: "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10924 synonym: "N6 threonylcarbamoyladenosine" EXACT []
10925 synonym: "N6-threonylcarbamoyladenosine" EXACT []
10926 synonym: "t6A" EXACT RNAMOD []
10928 is_a: SO:0001273 ! modified_adenosine
10932 name: two_methylthio_N6_threonyl_carbamoyladenosine
10933 def: "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10934 synonym: "2-methylthio-N6-threonyl carbamoyladenosine" EXACT []
10935 synonym: "ms2t6A" EXACT RNAMOD []
10936 synonym: "two methylthio N6 threonyl carbamoyladenosine" EXACT []
10938 is_a: SO:0001273 ! modified_adenosine
10942 name: N6_methyl_N6_threonylcarbamoyladenosine
10943 def: "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10944 synonym: "m6t6A" EXACT RNAMOD []
10945 synonym: "N6 methyl N6 threonylcarbamoyladenosine" EXACT []
10946 synonym: "N6-methyl-N6-threonylcarbamoyladenosine" EXACT []
10948 is_a: SO:0001273 ! modified_adenosine
10952 name: N6_hydroxynorvalylcarbamoyladenosine
10953 def: "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10954 synonym: "hn6A" EXACT RNAMOD []
10955 synonym: "N6 hydroxynorvalylcarbamoyladenosine" EXACT []
10956 synonym: "N6-hydroxynorvalylcarbamoyladenosine" EXACT []
10958 is_a: SO:0001273 ! modified_adenosine
10962 name: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
10963 def: "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10964 synonym: "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine" EXACT []
10965 synonym: "ms2hn6A" EXACT RNAMOD []
10966 synonym: "two methylthio N6 hydroxynorvalyl carbamoyladenosine" EXACT []
10968 is_a: SO:0001273 ! modified_adenosine
10972 name: two_prime_O_ribosyladenosine_phosphate
10973 def: "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10974 synonym: "2'-O-ribosyladenosine (phosphate)" EXACT []
10975 synonym: "Ar(p)" EXACT RNAMOD []
10976 synonym: "two prime O ribosyladenosine phosphate" EXACT []
10978 is_a: SO:0001273 ! modified_adenosine
10982 name: N6_N6_dimethyladenosine
10983 def: "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10984 synonym: "m62A" EXACT RNAMOD []
10985 synonym: "N6,N6-dimethyladenosine" EXACT []
10987 is_a: SO:0001273 ! modified_adenosine
10991 name: N6_2_prime_O_dimethyladenosine
10992 def: "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
10993 synonym: "m6Am" EXACT RNAMOD []
10994 synonym: "N6 2 prime O dimethyladenosine" EXACT []
10995 synonym: "N6,2'-O-dimethyladenosine" EXACT []
10997 is_a: SO:0001273 ! modified_adenosine
11001 name: N6_N6_2_prime_O_trimethyladenosine
11002 def: "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
11003 synonym: "m62Am" EXACT RNAMOD []
11004 synonym: "N6,N6,2'-O-trimethyladenosine" EXACT []
11006 is_a: SO:0001273 ! modified_adenosine
11010 name: one_two_prime_O_dimethyladenosine
11011 def: "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
11012 synonym: "1,2'-O-dimethyladenosine" EXACT []
11013 synonym: "m1Am" EXACT RNAMOD []
11014 synonym: "one two prime O dimethyladenosine" EXACT []
11016 is_a: SO:0001273 ! modified_adenosine
11020 name: N6_acetyladenosine
11021 def: "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
11022 synonym: "ac6A" EXACT RNAMOD []
11023 synonym: "N6 acetyladenosine" EXACT []
11024 synonym: "N6-acetyladenosine" EXACT []
11026 is_a: SO:0001273 ! modified_adenosine
11030 name: seven_deazaguanosine
11031 def: "7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]
11032 synonym: "7-deazaguanosine" RELATED []
11033 synonym: "seven deazaguanosine" EXACT []
11034 is_a: SO:0001276 ! modified_guanosine
11039 def: "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
11040 synonym: " Q" EXACT RNAMOD []
11041 xref: http://en.wikipedia.org/wiki/Queuosine "wiki"
11043 is_a: SO:0001316 ! seven_deazaguanosine
11047 name: epoxyqueuosine
11048 def: "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
11049 synonym: "eQ" EXACT RNAMOD []
11051 is_a: SO:0001316 ! seven_deazaguanosine
11055 name: galactosyl_queuosine
11056 def: "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
11057 synonym: "galactosyl queuosine" EXACT []
11058 synonym: "galactosyl-queuosine" EXACT []
11059 synonym: "galQ" EXACT RNAMOD []
11061 is_a: SO:0001316 ! seven_deazaguanosine
11065 name: mannosyl_queuosine
11066 def: "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
11067 synonym: "mannosyl queuosine" EXACT []
11068 synonym: "mannosyl-queuosine" EXACT []
11069 synonym: "manQ" EXACT RNAMOD []
11071 is_a: SO:0001316 ! seven_deazaguanosine
11075 name: seven_cyano_seven_deazaguanosine
11076 def: "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
11077 synonym: "7-cyano-7-deazaguanosine" EXACT []
11078 synonym: "preQ0" EXACT RNAMOD []
11079 synonym: "seven cyano seven deazaguanosine" EXACT []
11081 is_a: SO:0001316 ! seven_deazaguanosine
11085 name: seven_aminomethyl_seven_deazaguanosine
11086 def: "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
11087 synonym: "7-aminomethyl-7-deazaguanosine" EXACT []
11088 synonym: "preQ1" EXACT RNAMOD []
11089 synonym: "seven aminomethyl seven deazaguanosine" EXACT []
11091 is_a: SO:0001316 ! seven_deazaguanosine
11096 def: "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
11097 synonym: "G+" EXACT RNAMOD []
11099 is_a: SO:0001316 ! seven_deazaguanosine
11103 name: one_methylguanosine
11104 def: "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11105 synonym: "1-methylguanosine" EXACT []
11106 synonym: "m1G" EXACT RNAMOD []
11107 synonym: "one methylguanosine" EXACT []
11109 is_a: SO:0001276 ! modified_guanosine
11113 name: N2_methylguanosine
11114 def: "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11115 synonym: "m2G" EXACT RNAMOD []
11116 synonym: "N2 methylguanosine" EXACT []
11117 synonym: "N2-methylguanosine" EXACT []
11119 is_a: SO:0001276 ! modified_guanosine
11123 name: seven_methylguanosine
11124 def: "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11125 synonym: "7-methylguanosine" EXACT []
11126 synonym: "m7G" EXACT RNAMOD []
11127 synonym: "seven methylguanosine" EXACT []
11129 is_a: SO:0001276 ! modified_guanosine
11133 name: two_prime_O_methylguanosine
11134 def: "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11135 synonym: "2'-O-methylguanosine" EXACT []
11136 synonym: "Gm" EXACT RNAMOD []
11137 synonym: "two prime O methylguanosine" EXACT []
11139 is_a: SO:0001276 ! modified_guanosine
11143 name: N2_N2_dimethylguanosine
11144 def: "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11145 synonym: "m22G" EXACT RNAMOD []
11146 synonym: "N2,N2-dimethylguanosine" EXACT []
11148 is_a: SO:0001276 ! modified_guanosine
11152 name: N2_2_prime_O_dimethylguanosine
11153 def: "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11154 synonym: "m2Gm" EXACT RNAMOD []
11155 synonym: "N2 2 prime O dimethylguanosine" EXACT []
11156 synonym: "N2,2'-O-dimethylguanosine" EXACT []
11158 is_a: SO:0001276 ! modified_guanosine
11162 name: N2_N2_2_prime_O_trimethylguanosine
11163 def: "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11164 synonym: "m22Gmv" EXACT RNAMOD []
11165 synonym: "N2,N2,2'-O-trimethylguanosine" EXACT []
11167 is_a: SO:0001276 ! modified_guanosine
11171 name: two_prime_O_ribosylguanosine_phosphate
11172 def: "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11173 synonym: "2'-O-ribosylguanosine (phosphate)" EXACT []
11174 synonym: "Gr(p)" EXACT RNAMOD []
11175 synonym: "two prime O ribosylguanosine phosphate" EXACT []
11177 is_a: SO:0001276 ! modified_guanosine
11182 def: "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11183 synonym: "yW" EXACT RNAMOD []
11185 is_a: SO:0001276 ! modified_guanosine
11189 name: peroxywybutosine
11190 def: "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11191 synonym: "o2yW" EXACT RNAMOD []
11193 is_a: SO:0001276 ! modified_guanosine
11197 name: hydroxywybutosine
11198 def: "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11199 synonym: "OHyW" EXACT RNAMOD []
11201 is_a: SO:0001276 ! modified_guanosine
11205 name: undermodified_hydroxywybutosine
11206 def: "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11207 synonym: "OHyW*" EXACT RNAMOD []
11208 synonym: "undermodified hydroxywybutosine" EXACT []
11210 is_a: SO:0001276 ! modified_guanosine
11215 def: "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11216 synonym: "IMG" EXACT RNAMOD []
11218 is_a: SO:0001276 ! modified_guanosine
11222 name: methylwyosine
11223 def: "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11224 synonym: "mimG" EXACT RNAMOD []
11226 is_a: SO:0001276 ! modified_guanosine
11230 name: N2_7_dimethylguanosine
11231 def: "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11232 synonym: "m2,7G" EXACT RNAMOD []
11233 synonym: "N2 7 dimethylguanosine" EXACT []
11234 synonym: "N2,7-dimethylguanosine" EXACT []
11236 is_a: SO:0001276 ! modified_guanosine
11240 name: N2_N2_7_trimethylguanosine
11241 def: "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11242 synonym: "m2,2,7G" EXACT RNAMOD []
11243 synonym: "N2,N2,7-trimethylguanosine" EXACT []
11245 is_a: SO:0001276 ! modified_guanosine
11249 name: one_two_prime_O_dimethylguanosine
11250 def: "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11251 synonym: "1,2'-O-dimethylguanosine" EXACT []
11252 synonym: "m1Gm" EXACT RNAMOD []
11253 synonym: "one two prime O dimethylguanosine" EXACT []
11255 is_a: SO:0001276 ! modified_guanosine
11259 name: four_demethylwyosine
11260 def: "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11261 synonym: "4-demethylwyosine" EXACT []
11262 synonym: "four demethylwyosine" EXACT []
11263 synonym: "imG-14" EXACT RNAMOD []
11265 is_a: SO:0001276 ! modified_guanosine
11270 def: "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11271 synonym: "imG2" EXACT RNAMOD []
11273 is_a: SO:0001276 ! modified_guanosine
11277 name: N2_7_2prirme_O_trimethylguanosine
11278 def: "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
11279 synonym: "m2,7Gm" EXACT RNAMOD []
11280 synonym: "N2 7 2prirme O trimethylguanosine" EXACT []
11281 synonym: "N2,7,2'-O-trimethylguanosine" EXACT []
11283 is_a: SO:0001276 ! modified_guanosine
11287 name: five_methyluridine
11288 def: "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11289 synonym: "5-methyluridine" EXACT []
11290 synonym: "five methyluridine" EXACT []
11291 synonym: "m5U" EXACT RNAMOD []
11292 xref: http://en.wikipedia.org/wiki/5-methyluridine "wiki"
11294 is_a: SO:0001277 ! modified_uridine
11298 name: two_prime_O_methyluridine
11299 def: "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11300 synonym: "2'-O-methyluridine" EXACT []
11301 synonym: "two prime O methyluridine" EXACT []
11302 synonym: "Um" EXACT RNAMOD []
11304 is_a: SO:0001277 ! modified_uridine
11308 name: five_two_prime_O_dimethyluridine
11309 def: "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11310 synonym: "5,2'-O-dimethyluridine" EXACT []
11311 synonym: "five two prime O dimethyluridine" EXACT []
11312 synonym: "m5Um" EXACT RNAMOD []
11314 is_a: SO:0001277 ! modified_uridine
11318 name: one_methylpseudouridine
11319 def: "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11320 synonym: "1-methylpseudouridine" EXACT []
11321 synonym: "m1Y" EXACT RNAMOD []
11322 synonym: "one methylpseudouridine" EXACT []
11324 is_a: SO:0001277 ! modified_uridine
11328 name: two_prime_O_methylpseudouridine
11329 def: "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11330 synonym: "2'-O-methylpseudouridine" EXACT []
11331 synonym: "two prime O methylpseudouridine" EXACT []
11332 synonym: "Ym" EXACT RNAMOD []
11334 is_a: SO:0001277 ! modified_uridine
11338 name: two_thiouridine
11339 def: "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11340 synonym: "2-thiouridine" EXACT []
11341 synonym: "s2U" EXACT RNAMOD []
11342 synonym: "two thiouridine" EXACT []
11344 is_a: SO:0001277 ! modified_uridine
11348 name: four_thiouridine
11349 def: "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11350 synonym: "4-thiouridine" EXACT []
11351 synonym: "four thiouridine" EXACT []
11352 synonym: "s4U" EXACT RNAMOD []
11354 is_a: SO:0001277 ! modified_uridine
11358 name: five_methyl_2_thiouridine
11359 def: "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11360 synonym: "5-methyl-2-thiouridine" EXACT []
11361 synonym: "five methyl 2 thiouridine" EXACT []
11362 synonym: "m5s2U" EXACT RNAMOD []
11364 is_a: SO:0001277 ! modified_uridine
11368 name: two_thio_two_prime_O_methyluridine
11369 def: "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11370 synonym: "2-thio-2'-O-methyluridine" EXACT []
11371 synonym: "s2Um" EXACT RNAMOD []
11372 synonym: "two thio two prime O methyluridine" EXACT []
11374 is_a: SO:0001277 ! modified_uridine
11378 name: three_three_amino_three_carboxypropyl_uridine
11379 def: "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11380 synonym: "3-(3-amino-3-carboxypropyl)uridine" EXACT []
11381 synonym: "acp3U" EXACT RNAMOD []
11383 is_a: SO:0001277 ! modified_uridine
11387 name: five_hydroxyuridine
11388 def: "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11389 synonym: "5-hydroxyuridine" EXACT []
11390 synonym: "five hydroxyuridine" EXACT []
11391 synonym: "ho5U" EXACT RNAMOD []
11393 is_a: SO:0001277 ! modified_uridine
11397 name: five_methoxyuridine
11398 def: "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11399 synonym: "5-methoxyuridine" EXACT []
11400 synonym: "five methoxyuridine" EXACT []
11401 synonym: "mo5U" EXACT RNAMOD []
11403 is_a: SO:0001277 ! modified_uridine
11407 name: uridine_five_oxyacetic_acid
11408 def: "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11409 synonym: "cmo5U" EXACT RNAMOD []
11410 synonym: "uridine 5-oxyacetic acid" EXACT []
11411 synonym: "uridine five oxyacetic acid" EXACT []
11413 is_a: SO:0001277 ! modified_uridine
11417 name: uridine_five_oxyacetic_acid_methyl_ester
11418 def: "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11419 synonym: "mcmo5U" EXACT RNAMOD []
11420 synonym: "uridine 5-oxyacetic acid methyl ester" EXACT []
11421 synonym: "uridine five oxyacetic acid methyl ester" EXACT []
11423 is_a: SO:0001277 ! modified_uridine
11427 name: five_carboxyhydroxymethyl_uridine
11428 def: "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11429 synonym: "5-(carboxyhydroxymethyl)uridine" EXACT []
11430 synonym: "chm5U" EXACT RNAMOD []
11431 synonym: "five carboxyhydroxymethyl uridine" EXACT []
11433 is_a: SO:0001277 ! modified_uridine
11437 name: five_carboxyhydroxymethyl_uridine_methyl_ester
11438 def: "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11439 synonym: "5-(carboxyhydroxymethyl)uridine methyl ester" EXACT []
11440 synonym: "five carboxyhydroxymethyl uridine methyl ester" EXACT []
11441 synonym: "mchm5U" EXACT RNAMOD []
11443 is_a: SO:0001277 ! modified_uridine
11447 name: five_methoxycarbonylmethyluridine
11448 def: "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11449 synonym: "5-methoxycarbonylmethyluridine" EXACT []
11450 synonym: "five methoxycarbonylmethyluridine" EXACT []
11451 synonym: "mcm5U" EXACT RNAMOD []
11453 is_a: SO:0001277 ! modified_uridine
11457 name: five_methoxycarbonylmethyl_two_prime_O_methyluridine
11458 def: "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11459 synonym: "5-methoxycarbonylmethyl-2'-O-methyluridine" EXACT []
11460 synonym: "five methoxycarbonylmethyl two prime O methyluridine" EXACT []
11461 synonym: "mcm5Um" EXACT RNAMOD []
11463 is_a: SO:0001277 ! modified_uridine
11467 name: five_methoxycarbonylmethyl_two_thiouridine
11468 def: "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11469 synonym: "5-methoxycarbonylmethyl-2-thiouridine" EXACT []
11470 synonym: "five methoxycarbonylmethyl two thiouridine" EXACT []
11471 synonym: "mcm5s2U" EXACT RNAMOD []
11473 is_a: SO:0001277 ! modified_uridine
11477 name: five_aminomethyl_two_thiouridine
11478 def: "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11479 synonym: "5-aminomethyl-2-thiouridine" EXACT []
11480 synonym: "five aminomethyl two thiouridine" EXACT []
11481 synonym: "nm5s2U" EXACT RNAMOD []
11483 is_a: SO:0001277 ! modified_uridine
11487 name: five_methylaminomethyluridine
11488 def: "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11489 synonym: "5-methylaminomethyluridine" EXACT []
11490 synonym: "five methylaminomethyluridine" EXACT []
11491 synonym: "mnm5U" EXACT RNAMOD []
11493 is_a: SO:0001277 ! modified_uridine
11497 name: five_methylaminomethyl_two_thiouridine
11498 def: "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11499 synonym: "5-methylaminomethyl-2-thiouridine" EXACT []
11500 synonym: "five methylaminomethyl two thiouridine" EXACT []
11501 synonym: "mnm5s2U" EXACT RNAMOD []
11503 is_a: SO:0001277 ! modified_uridine
11507 name: five_methylaminomethyl_two_selenouridine
11508 def: "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11509 synonym: "5-methylaminomethyl-2-selenouridine" EXACT []
11510 synonym: "five methylaminomethyl two selenouridine" EXACT []
11511 synonym: "mnm5se2U" EXACT RNAMOD []
11513 is_a: SO:0001277 ! modified_uridine
11517 name: five_carbamoylmethyluridine
11518 def: "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11519 synonym: "5-carbamoylmethyluridine" EXACT []
11520 synonym: "five carbamoylmethyluridine" EXACT []
11521 synonym: "ncm5U" EXACT RNAMOD []
11523 is_a: SO:0001277 ! modified_uridine
11527 name: five_carbamoylmethyl_two_prime_O_methyluridine
11528 def: "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11529 synonym: "5-carbamoylmethyl-2'-O-methyluridine" EXACT []
11530 synonym: "five carbamoylmethyl two prime O methyluridine" EXACT []
11531 synonym: "ncm5Um" EXACT RNAMOD []
11533 is_a: SO:0001277 ! modified_uridine
11537 name: five_carboxymethylaminomethyluridine
11538 def: "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11539 synonym: "5-carboxymethylaminomethyluridine" EXACT []
11540 synonym: "cmnm5U" EXACT RNAMOD []
11541 synonym: "five carboxymethylaminomethyluridine" EXACT []
11543 is_a: SO:0001277 ! modified_uridine
11547 name: five_carboxymethylaminomethyl_two_prime_O_methyluridine
11548 def: "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11549 synonym: "5-carboxymethylaminomethyl- 2'-O-methyluridine" EXACT []
11550 synonym: "cmnm5Um" EXACT RNAMOD []
11551 synonym: "five carboxymethylaminomethyl two prime O methyluridine" EXACT []
11553 is_a: SO:0001277 ! modified_uridine
11557 name: five_carboxymethylaminomethyl_two_thiouridine
11558 def: "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11559 synonym: "5-carboxymethylaminomethyl-2-thiouridine" EXACT []
11560 synonym: "cmnm5s2U" EXACT RNAMOD []
11561 synonym: "five carboxymethylaminomethyl two thiouridine" EXACT []
11563 is_a: SO:0001277 ! modified_uridine
11567 name: three_methyluridine
11568 def: "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11569 synonym: "3-methyluridine" EXACT []
11570 synonym: "m3U" EXACT RNAMOD []
11571 synonym: "three methyluridine" EXACT []
11573 is_a: SO:0001277 ! modified_uridine
11577 name: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
11578 def: "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11579 synonym: "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine" EXACT []
11580 synonym: "m1acp3Y" EXACT RNAMOD []
11582 is_a: SO:0001277 ! modified_uridine
11586 name: five_carboxymethyluridine
11587 def: "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11588 synonym: "5-carboxymethyluridine" EXACT []
11589 synonym: "cm5U" EXACT RNAMOD []
11590 synonym: "five carboxymethyluridine" EXACT []
11592 is_a: SO:0001277 ! modified_uridine
11596 name: three_two_prime_O_dimethyluridine
11597 def: "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11598 synonym: "3,2'-O-dimethyluridine" EXACT []
11599 synonym: "m3Um" EXACT RNAMOD []
11600 synonym: "three two prime O dimethyluridine" EXACT []
11602 is_a: SO:0001277 ! modified_uridine
11606 name: five_methyldihydrouridine
11607 def: "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11608 synonym: "5-methyldihydrouridine" EXACT []
11609 synonym: "five methyldihydrouridine" EXACT []
11610 synonym: "m5D" EXACT RNAMOD []
11612 is_a: SO:0001277 ! modified_uridine
11616 name: three_methylpseudouridine
11617 def: "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11618 synonym: "3-methylpseudouridine" EXACT []
11619 synonym: "m3Y" EXACT RNAMOD []
11620 synonym: "three methylpseudouridine" EXACT []
11622 is_a: SO:0001277 ! modified_uridine
11626 name: five_taurinomethyluridine
11627 def: "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11628 synonym: "5-taurinomethyluridine" EXACT []
11629 synonym: "five taurinomethyluridine" EXACT []
11630 synonym: "tm5U" EXACT RNAMOD []
11632 is_a: SO:0001277 ! modified_uridine
11636 name: five_taurinomethyl_two_thiouridine
11637 def: "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11638 synonym: "5-taurinomethyl-2-thiouridine" EXACT []
11639 synonym: "five taurinomethyl two thiouridine" EXACT []
11640 synonym: "tm5s2U" EXACT RNAMOD []
11642 is_a: SO:0001277 ! modified_uridine
11646 name: five_isopentenylaminomethyl_uridine
11647 def: "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11648 synonym: "5-(isopentenylaminomethyl)uridine" EXACT []
11649 synonym: "five isopentenylaminomethyl uridine" EXACT []
11650 synonym: "inm5U" EXACT RNAMOD []
11652 is_a: SO:0001277 ! modified_uridine
11656 name: five_isopentenylaminomethyl_two_thiouridine
11657 def: "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11658 synonym: "5-(isopentenylaminomethyl)- 2-thiouridine" EXACT []
11659 synonym: "five isopentenylaminomethyl two thiouridine" EXACT []
11660 synonym: "inm5s2U" EXACT RNAMOD []
11662 is_a: SO:0001277 ! modified_uridine
11666 name: five_isopentenylaminomethyl_two_prime_O_methyluridine
11667 def: "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
11668 synonym: "5-(isopentenylaminomethyl)- 2'-O-methyluridine" EXACT []
11669 synonym: "five isopentenylaminomethyl two prime O methyluridine" EXACT []
11670 synonym: "inm5Um" EXACT RNAMOD []
11672 is_a: SO:0001277 ! modified_uridine
11676 name: histone_binding_site
11677 def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]
11678 synonym: "histone binding site" EXACT []
11679 is_a: SO:0001654 ! nucleotide_to_protein_binding_site
11684 synonym: "CDS fragment" EXACT []
11685 synonym: "incomplete CDS" EXACT []
11686 is_a: SO:0000316 ! CDS
11687 relationship: has_quality SO:0000731 ! fragmentary
11691 name: modified_amino_acid_feature
11692 def: "A post translationally modified amino acid feature." [SO:ke]
11693 synonym: "modified amino acid feature" EXACT []
11694 is_a: SO:0001237 ! amino_acid
11698 name: modified_glycine
11699 def: "A post translationally modified glycine amino acid feature." [SO:ke]
11700 synonym: "ModGly" EXACT AAMOD []
11701 synonym: "modified glycine" EXACT []
11703 is_a: SO:0001385 ! modified_amino_acid_feature
11707 name: modified_L_alanine
11708 def: "A post translationally modified alanine amino acid feature." [SO:ke]
11709 synonym: "ModAla" EXACT AAMOD []
11710 synonym: "modified L alanine" EXACT []
11711 synonym: "modified L-alanine" EXACT []
11713 is_a: SO:0001385 ! modified_amino_acid_feature
11717 name: modified_L_asparagine
11718 def: "A post translationally modified asparagine amino acid feature." [SO:ke]
11719 synonym: "ModAsn" EXACT AAMOD []
11720 synonym: "modified L asparagine" EXACT []
11721 synonym: "modified L-asparagine" EXACT []
11723 is_a: SO:0001385 ! modified_amino_acid_feature
11727 name: modified_L_aspartic_acid
11728 def: "A post translationally modified aspartic acid amino acid feature." [SO:ke]
11729 synonym: "ModAsp" EXACT AAMOD []
11730 synonym: "modified L aspartic acid" EXACT []
11731 synonym: "modified L-aspartic acid" EXACT []
11733 is_a: SO:0001385 ! modified_amino_acid_feature
11737 name: modified_L_cysteine
11738 def: "A post translationally modified cysteine amino acid feature." [SO:ke]
11739 synonym: "ModCys" EXACT AAMOD []
11740 synonym: "modified L cysteine" EXACT []
11741 synonym: "modified L-cysteine" EXACT []
11743 is_a: SO:0001385 ! modified_amino_acid_feature
11747 name: modified_L_glutamic_acid
11748 synonym: "ModGlu" EXACT AAMOD []
11749 synonym: "modified L glutamic acid" EXACT []
11750 synonym: "modified L-glutamic acid" EXACT []
11752 is_a: SO:0001385 ! modified_amino_acid_feature
11756 name: modified_L_threonine
11757 def: "A post translationally modified threonine amino acid feature." [SO:ke]
11758 synonym: "modified L threonine" EXACT []
11759 synonym: "modified L-threonine" EXACT []
11760 synonym: "ModThr" EXACT AAMOD []
11762 is_a: SO:0001385 ! modified_amino_acid_feature
11766 name: modified_L_tryptophan
11767 def: "A post translationally modified tryptophan amino acid feature." [SO:ke]
11768 synonym: "modified L tryptophan" EXACT []
11769 synonym: "modified L-tryptophan" EXACT []
11770 synonym: "ModTrp" EXACT AAMOD []
11772 is_a: SO:0001385 ! modified_amino_acid_feature
11776 name: modified_L_glutamine
11777 def: "A post translationally modified glutamine amino acid feature." [SO:ke]
11778 synonym: "ModGln" EXACT []
11779 synonym: "modified L glutamine" EXACT []
11780 synonym: "modified L-glutamine" EXACT []
11782 is_a: SO:0001385 ! modified_amino_acid_feature
11786 name: modified_L_methionine
11787 def: "A post translationally modified methionine amino acid feature." [SO:ke]
11788 synonym: "modified L methionine" EXACT []
11789 synonym: "modified L-methionine" EXACT []
11790 synonym: "ModMet" EXACT AAMOD []
11792 is_a: SO:0001385 ! modified_amino_acid_feature
11796 name: modified_L_isoleucine
11797 def: "A post translationally modified isoleucine amino acid feature." [SO:ke]
11798 synonym: "modified L isoleucine" EXACT []
11799 synonym: "modified L-isoleucine" EXACT []
11800 synonym: "ModIle" EXACT AAMOD []
11802 is_a: SO:0001385 ! modified_amino_acid_feature
11806 name: modified_L_phenylalanine
11807 def: "A post translationally modified phenylalanine amino acid feature." [SO:ke]
11808 synonym: "modified L phenylalanine" EXACT []
11809 synonym: "modified L-phenylalanine" EXACT []
11810 synonym: "ModPhe" EXACT AAMOD []
11812 is_a: SO:0001385 ! modified_amino_acid_feature
11816 name: modified_L_histidine
11817 def: "A post translationally modified histidine amino acid feature." [SO:ke]
11818 synonym: "ModHis" EXACT []
11819 synonym: "modified L histidine" EXACT []
11820 synonym: "modified L-histidine" EXACT []
11822 is_a: SO:0001385 ! modified_amino_acid_feature
11826 name: modified_L_serine
11827 def: "A post translationally modified serine amino acid feature." [SO:ke]
11828 synonym: "modified L serine" EXACT []
11829 synonym: "modified L-serine" EXACT []
11830 synonym: "MosSer" EXACT AAMOD []
11831 xref: MOD:00916 "http://www.psidev.info/index.php?q=node/104"
11832 is_a: SO:0001385 ! modified_amino_acid_feature
11836 name: modified_L_lysine
11837 def: "A post translationally modified lysine amino acid feature." [SO:ke]
11838 synonym: "modified L lysine" EXACT []
11839 synonym: "modified L-lysine" EXACT []
11840 synonym: "ModLys" EXACT AAMOD []
11842 is_a: SO:0001385 ! modified_amino_acid_feature
11846 name: modified_L_leucine
11847 def: "A post translationally modified leucine amino acid feature." [SO:ke]
11848 synonym: "modified L leucine" EXACT []
11849 synonym: "modified L-leucine " EXACT []
11850 synonym: "ModLeu" EXACT AAMOD []
11852 is_a: SO:0001385 ! modified_amino_acid_feature
11856 name: modified_L_selenocysteine
11857 def: "A post translationally modified selenocysteine amino acid feature." [SO:ke]
11858 synonym: "modified L selenocysteine" EXACT []
11859 synonym: "modified L-selenocysteine" EXACT []
11861 is_a: SO:0001385 ! modified_amino_acid_feature
11865 name: modified_L_valine
11866 def: "A post translationally modified valine amino acid feature." [SO:ke]
11867 synonym: "modified L valine" EXACT []
11868 synonym: "modified L-valine" EXACT []
11869 synonym: "ModVal" EXACT AAMOD []
11871 is_a: SO:0001385 ! modified_amino_acid_feature
11875 name: modified_L_proline
11876 def: "A post translationally modified proline amino acid feature." [SO:ke]
11877 synonym: "modified L proline" EXACT []
11878 synonym: "modified L-proline " EXACT []
11879 synonym: "ModPro" EXACT AAMOD []
11881 is_a: SO:0001385 ! modified_amino_acid_feature
11885 name: modified_L_tyrosine
11886 def: "A post translationally modified tyrosine amino acid feature." [SO:ke]
11887 synonym: "modified L tyrosine" EXACT []
11888 synonym: "modified L-tyrosine" EXACT []
11889 synonym: "ModTry" EXACT AAMOD []
11891 is_a: SO:0001385 ! modified_amino_acid_feature
11895 name: modified_L_arginine
11896 def: "A post translationally modified arginine amino acid feature." [SO:ke]
11897 synonym: "ModArg" EXACT AAMOD []
11898 synonym: "modified L arginine" EXACT []
11899 synonym: "modified L-arginine" EXACT []
11901 is_a: SO:0001385 ! modified_amino_acid_feature
11906 def: "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke]
11907 is_a: SO:0000443 ! polymer_attribute
11911 name: cleaved_for_gpi_anchor_region
11912 def: "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]
11913 synonym: "cleaved for gpi anchor region" EXACT []
11914 is_a: SO:0100011 ! cleaved_peptide_region
11918 name: biomaterial_region
11919 def: "A region which is intended for use in an experiment." [SO:cb]
11921 synonym: "biomaterial region" EXACT []
11922 is_a: SO:0000001 ! region
11926 name: experimental_feature
11927 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]
11929 synonym: "analysis feature" RELATED []
11930 synonym: "experimental output artefact" EXACT []
11931 synonym: "experimental_output_artefact" EXACT []
11932 is_a: SO:0000001 ! region
11936 name: biological_region
11937 def: "A region defined by its disposition to be involved in a biological process." [SO:cb]
11939 synonym: "biological region" EXACT []
11940 is_a: SO:0000001 ! region
11944 name: topologically_defined_region
11945 def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb]
11947 synonym: "topologically defined region" EXACT []
11948 is_a: SO:0000001 ! region
11952 name: translocation_breakpoint
11953 def: "The point within a chromosome where a translocation begins or ends." [SO:cb]
11954 synonym: "translocation breakpoint" EXACT []
11955 is_a: SO:0001021 ! chromosome_breakpoint
11959 name: insertion_breakpoint
11960 def: "The point within a chromosome where a insertion begins or ends." [SO:cb]
11961 synonym: "insertion breakpoint" EXACT []
11962 is_a: SO:0001021 ! chromosome_breakpoint
11966 name: deletion_breakpoint
11967 def: "The point within a chromosome where a deletion begins or ends." [SO:cb]
11968 synonym: "deletion breakpoint" EXACT []
11969 is_a: SO:0001021 ! chromosome_breakpoint
11973 name: five_prime_flanking_region
11974 def: "A flanking region located five prime of a specific region." [SO:chado]
11975 synonym: "5' flanking region" RELATED []
11976 synonym: "five prime flanking region" EXACT []
11977 is_a: SO:0000239 ! flanking_region
11981 name: three_prime_flanking_region
11982 def: "A flanking region located three prime of a specific region." [SO:chado]
11983 synonym: "3' flanking region" RELATED []
11984 synonym: "three prime flanking region" EXACT []
11985 is_a: SO:0000239 ! flanking_region
11989 name: transcribed_fragment
11990 def: "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]
11991 comment: Term requested by the MODencode group.
11992 synonym: "transcribed fragment" EXACT []
11993 synonym: "transfrag" RELATED []
11994 is_a: SO:0001410 ! experimental_feature
11998 name: cis_splice_site
11999 def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]
12001 synonym: "cis splice site" EXACT []
12002 is_a: SO:0000162 ! splice_site
12006 name: trans_splice_site
12007 def: "Primary transcript region bordering trans-splice junction." [SO:ke]
12009 synonym: "trans splice site" EXACT []
12010 is_a: SO:0000162 ! splice_site
12014 name: splice_junction
12015 def: "The boundary between an intron and an exon." [SO:ke]
12016 synonym: "splice boundary" EXACT []
12017 synonym: "splice junction" EXACT []
12018 is_a: SO:0000699 ! junction
12022 name: conformational_switch
12023 def: "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]
12024 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.
12025 synonym: "polypeptide conformational switch" EXACT []
12026 is_a: SO:0100001 ! biochemical_region_of_peptide
12030 name: dye_terminator_read
12031 def: "A read produced by the dye terminator method of sequencing." [SO:ke]
12032 synonym: "dye terminator read" RELATED []
12033 is_a: SO:0000150 ! read
12037 name: pyrosequenced_read
12038 def: "A read produced by pyrosequencing technology." [SO:ke]
12039 comment: An example is a read produced by Roche 454 technology.
12040 synonym: "pyorsequenced read" RELATED []
12041 is_a: SO:0000150 ! read
12045 name: ligation_based_read
12046 def: "A read produced by ligation based sequencing technologies." [SO:ke]
12047 comment: An example of this kind of read is one produced by ABI SOLiD.
12048 synonym: "ligation based read" RELATED []
12049 is_a: SO:0000150 ! read
12053 name: polymerase_synthesis_read
12054 def: "A read produced by the polymerase based sequence by synthesis method." [SO:ke]
12055 comment: An example is a read produced by Illumina technology.
12056 synonym: "polymerase synthesis read" RELATED []
12057 is_a: SO:0000150 ! read
12061 name: cis_regulatory_frameshift_element
12062 def: "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]
12063 synonym: "cis regulatory frameshift element" EXACT []
12064 is_a: SO:0001679 ! transcription_regulatory_region
12068 name: expressed_sequence_assembly
12069 def: "A sequence assembly derived from expressed sequences." [SO:ke]
12070 comment: From tracker [ 2372385 ] expressed_sequence_assembly.
12071 synonym: "expressed sequence assembly" EXACT []
12072 is_a: SO:0000353 ! sequence_assembly
12076 name: DNA_binding_site
12077 def: "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]
12078 synonym: "DNA binding site" EXACT []
12079 is_a: SO:0001655 ! nucleotide_binding_site
12084 def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]
12085 synonym: "cryptic gene" EXACT []
12086 is_a: SO:0000704 ! gene
12087 relationship: has_quality SO:0000976 ! cryptic
12091 name: sequence_variant_affecting_polyadenylation
12092 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
12093 synonym: "mutation affecting polyadenylation" RELATED []
12094 synonym: "sequence variant affecting polyadenylation" EXACT []
12096 replaced_by: SO:0001545
12100 name: three_prime_RACE_clone
12101 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]
12102 synonym: "3' RACE clone" RELATED []
12103 is_a: SO:0000317 ! cDNA_clone
12107 name: cassette_pseudogene
12108 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]
12109 comment: Requested by the Trypanosome community.
12110 synonym: "cassette pseudogene" EXACT []
12111 synonym: "cassette type psedogene" RELATED []
12112 is_a: SO:0001760 ! non_processed_pseudogene
12117 comment: A place holder for a cross product with chebi.
12118 synonym: "A" EXACT aa1 []
12119 synonym: "Ala" EXACT aa3 []
12120 is_a: SO:0001237 ! amino_acid
12125 comment: A place holder for a cross product with chebi.
12126 synonym: "V" EXACT aa1 []
12127 synonym: "Val" EXACT aa3 []
12128 is_a: SO:0001237 ! amino_acid
12133 comment: A place holder for a cross product with chebi.
12134 synonym: "L" EXACT aa1 []
12135 synonym: "Leu" EXACT aa3 []
12136 is_a: SO:0001237 ! amino_acid
12141 comment: A place holder for a cross product with chebi.
12142 synonym: "I" EXACT aa1 []
12143 synonym: "Ile" EXACT aa3 []
12144 is_a: SO:0001237 ! amino_acid
12149 comment: A place holder for a cross product with chebi.
12150 synonym: "P" EXACT aa1 []
12151 synonym: "Pro" EXACT aa3 []
12152 is_a: SO:0001237 ! amino_acid
12157 comment: A place holder for a cross product with chebi.
12158 synonym: "Trp" EXACT aa3 []
12159 synonym: "W" EXACT aa1 []
12160 is_a: SO:0001237 ! amino_acid
12164 name: phenylalanine
12165 comment: A place holder for a cross product with chebi.
12166 synonym: "F" EXACT aa1 []
12167 synonym: "Phe" EXACT aa3 []
12168 is_a: SO:0001237 ! amino_acid
12173 comment: A place holder for a cross product with chebi.
12174 synonym: "M" EXACT aa1 []
12175 synonym: "Met" EXACT aa3 []
12176 is_a: SO:0001237 ! amino_acid
12181 comment: A place holder for a cross product with chebi.
12182 synonym: "G" EXACT aa1 []
12183 synonym: "Gly" EXACT aa3 []
12184 is_a: SO:0001237 ! amino_acid
12189 comment: A place holder for a cross product with chebi.
12190 synonym: "S" EXACT aa1 []
12191 synonym: "Ser" EXACT aa3 []
12192 is_a: SO:0001237 ! amino_acid
12197 comment: A place holder for a cross product with chebi.
12198 synonym: "T" EXACT aa1 []
12199 synonym: "Thr" EXACT aa3 []
12200 is_a: SO:0001237 ! amino_acid
12205 comment: A place holder for a cross product with chebi.
12206 synonym: "Tyr" EXACT aa3 []
12207 synonym: "Y" EXACT aa1 []
12208 is_a: SO:0001237 ! amino_acid
12213 comment: A place holder for a cross product with chebi.
12214 synonym: "C" EXACT aa1 []
12215 synonym: "Cys" EXACT aa3 []
12216 is_a: SO:0001237 ! amino_acid
12221 comment: A place holder for a cross product with chebi.
12222 synonym: "Gln" EXACT aa3 []
12223 synonym: "Q" EXACT aa1 []
12224 is_a: SO:0001237 ! amino_acid
12229 comment: A place holder for a cross product with chebi.
12230 synonym: "Asn" EXACT aa3 []
12231 synonym: "N" EXACT aa1 []
12232 is_a: SO:0001237 ! amino_acid
12237 comment: A place holder for a cross product with chebi.
12238 synonym: "K" EXACT aa1 []
12239 synonym: "Lys" EXACT aa3 []
12240 is_a: SO:0001237 ! amino_acid
12245 comment: A place holder for a cross product with chebi.
12246 synonym: "Arg" EXACT aa3 []
12247 synonym: "R" EXACT aa1 []
12248 is_a: SO:0001237 ! amino_acid
12253 comment: A place holder for a cross product with chebi.
12254 synonym: "H" EXACT aa1 []
12255 synonym: "His" EXACT aa3 []
12256 is_a: SO:0001237 ! amino_acid
12260 name: aspartic_acid
12261 comment: A place holder for a cross product with chebi.
12262 synonym: "Asp" EXACT aa3 []
12263 synonym: "aspartic acid" EXACT []
12264 synonym: "D" EXACT aa1 []
12265 is_a: SO:0001237 ! amino_acid
12269 name: glutamic_acid
12270 comment: A place holder for a cross product with chebi.
12271 synonym: "E" EXACT aa1 []
12272 synonym: "Glu" EXACT aa3 []
12273 synonym: "glutamic acid" EXACT []
12274 is_a: SO:0001237 ! amino_acid
12278 name: selenocysteine
12279 comment: A place holder for a cross product with chebi.
12280 synonym: "Sec" EXACT aa3 []
12281 synonym: "U" EXACT aa1 []
12282 is_a: SO:0001237 ! amino_acid
12287 comment: A place holder for a cross product with chebi.
12288 synonym: "O" EXACT aa1 []
12289 synonym: "Pyl" EXACT aa3 []
12290 is_a: SO:0001237 ! amino_acid
12294 name: transcribed_cluster
12295 def: "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]
12296 comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
12297 synonym: "transcribed cluster" EXACT []
12298 synonym: "unigene cluster" RELATED []
12299 is_a: SO:0001410 ! experimental_feature
12300 relationship: has_part SO:0000695 ! reagent
12304 name: unigene_cluster
12305 def: "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]
12306 comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
12307 synonym: "unigene cluster" RELATED []
12308 is_a: SO:0001457 ! transcribed_cluster
12313 def: "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]
12314 synonym: "Clustered_Regularly_Interspaced_Short_Palindromic_Repeat" EXACT []
12315 synonym: "CRISPR element" EXACT []
12316 xref: http:en.wikipedia.org/wiki/CRISPR
12317 is_a: SO:0000314 ! direct_repeat
12321 name: insulator_binding_site
12322 def: "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
12323 comment: See tracker ID 2060908.
12324 synonym: "insulator binding site" RELATED []
12325 is_a: SO:0001654 ! nucleotide_to_protein_binding_site
12326 relationship: part_of SO:0000627 ! insulator
12330 name: enhancer_binding_site
12331 def: "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
12332 synonym: "enhancer binding site" RELATED []
12333 is_a: SO:0001654 ! nucleotide_to_protein_binding_site
12334 relationship: part_of SO:0000165 ! enhancer
12338 name: contig_collection
12339 def: "A collection of contigs." [SO:ke]
12340 comment: See tracker ID: 2138359.
12341 synonym: "contig collection" EXACT []
12342 is_a: SO:0001085 ! sequence_conflict
12343 is_a: SO:0001260 ! sequence_collection
12344 relationship: has_part SO:0000149 ! contig
12349 def: "A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]
12350 synonym: "large intervening non-coding RNA" EXACT []
12351 synonym: "long intergenic non-coding RNA" EXACT []
12352 is_a: SO:0001877 ! lnc_RNA
12357 def: "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]
12358 synonym: "UTR sequence tag" EXACT []
12359 is_a: SO:0000345 ! EST
12363 name: three_prime_UST
12364 def: "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]
12365 synonym: "3' UST" RELATED []
12366 is_a: SO:0001464 ! UST
12370 name: five_prime_UST
12371 def: "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]
12372 synonym: "5' UST" RELATED []
12373 is_a: SO:0001464 ! UST
12378 def: "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]
12379 synonym: "RACE sequence tag" EXACT []
12380 is_a: SO:0000345 ! EST
12384 name: three_prime_RST
12385 def: "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]
12386 synonym: "3' RST" EXACT []
12387 is_a: SO:0001467 ! RST
12391 name: five_prime_RST
12392 def: "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]
12393 synonym: "5' RST" RELATED []
12394 is_a: SO:0001467 ! RST
12399 def: "A match against an UST sequence." [SO:nlw]
12400 synonym: "UST match" EXACT []
12401 is_a: SO:0000102 ! expressed_sequence_match
12406 def: "A match against an RST sequence." [SO:nlw]
12407 synonym: "RST match" EXACT []
12408 is_a: SO:0000102 ! expressed_sequence_match
12413 def: "A nucleotide match to a primer sequence." [SO:nlw]
12414 synonym: "primer match" EXACT []
12415 is_a: SO:0000347 ! nucleotide_match
12419 name: miRNA_antiguide
12420 def: "A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]
12421 synonym: "miRNA antiguide " EXACT []
12422 synonym: "miRNA passenger strand" EXACT []
12423 synonym: "miRNA star" EXACT []
12424 is_a: SO:0001243 ! miRNA_primary_transcript_region
12425 created_by: kareneilbeck
12426 creation_date: 2009-05-27T03:35:43Z
12430 name: trans_splice_junction
12431 def: "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke]
12432 synonym: "trans-splice junction" EXACT []
12433 is_a: SO:0000699 ! junction
12434 created_by: kareneilbeck
12435 creation_date: 2009-07-13T04:50:49Z
12440 def: "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]
12441 is_a: SO:0000835 ! primary_transcript_region
12442 created_by: kareneilbeck
12443 creation_date: 2009-07-14T11:36:08Z
12447 name: natural_plasmid
12448 def: "A plasmid that occurs naturally." [SO:xp]
12449 synonym: "natural plasmid" EXACT []
12450 is_a: SO:0000155 ! plasmid
12451 is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
12452 relationship: has_quality SO:0000782 ! natural
12453 created_by: kareneilbeck
12454 creation_date: 2009-09-01T03:43:06Z
12458 name: gene_trap_construct
12459 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]
12460 synonym: "gene trap construct" EXACT []
12461 is_a: SO:0000637 ! engineered_plasmid
12462 created_by: kareneilbeck
12463 creation_date: 2009-09-01T03:49:09Z
12467 name: promoter_trap_construct
12468 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]
12469 synonym: "promoter trap construct" EXACT []
12470 is_a: SO:0000637 ! engineered_plasmid
12471 created_by: kareneilbeck
12472 creation_date: 2009-09-01T03:52:01Z
12476 name: enhancer_trap_construct
12477 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]
12478 synonym: "enhancer trap construct" EXACT []
12479 is_a: SO:0000637 ! engineered_plasmid
12480 created_by: kareneilbeck
12481 creation_date: 2009-09-01T03:53:26Z
12486 def: "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]
12487 synonym: "PAC end" EXACT []
12488 is_a: SO:0000150 ! read
12489 relationship: part_of SO:0000154 ! PAC
12490 created_by: kareneilbeck
12491 creation_date: 2009-09-09T05:18:12Z
12496 def: "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]
12497 synonym: "Random Amplification Polymorphic DNA" EXACT []
12498 is_a: SO:0000006 ! PCR_product
12499 created_by: kareneilbeck
12500 creation_date: 2009-09-09T05:26:10Z
12504 name: shadow_enhancer
12505 synonym: "shadow enhancer" EXACT []
12506 is_a: SO:0000165 ! enhancer
12507 created_by: kareneilbeck
12508 creation_date: 2009-09-09T05:29:29Z
12513 def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]
12515 synonym: "single nucleotide variant" EXACT []
12516 is_a: SO:1000002 ! substitution
12517 created_by: kareneilbeck
12518 creation_date: 2009-10-08T11:37:49Z
12522 name: X_element_combinatorial_repeat
12523 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]
12524 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.
12525 synonym: "X element combinatorial repeat" EXACT []
12526 is_a: SO:0000657 ! repeat_region
12527 relationship: part_of SO:0000624 ! telomere
12528 created_by: kareneilbeck
12529 creation_date: 2009-11-10T11:03:37Z
12533 name: Y_prime_element
12534 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]
12535 comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
12536 synonym: "Y' element" EXACT []
12537 is_a: SO:0000657 ! repeat_region
12538 relationship: part_of SO:0000624 ! telomere
12539 created_by: kareneilbeck
12540 creation_date: 2009-11-10T12:08:57Z
12544 name: standard_draft
12545 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]
12546 synonym: "standard draft" EXACT []
12547 is_a: SO:0001499 ! whole_genome_sequence_status
12548 created_by: kareneilbeck
12549 creation_date: 2009-10-23T12:48:32Z
12553 name: high_quality_draft
12554 def: "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]
12555 synonym: "high quality draft" EXACT []
12556 is_a: SO:0001499 ! whole_genome_sequence_status
12557 created_by: kareneilbeck
12558 creation_date: 2009-10-23T12:52:36Z
12562 name: improved_high_quality_draft
12563 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]
12564 synonym: "improved high quality draft" EXACT []
12565 is_a: SO:0001499 ! whole_genome_sequence_status
12566 created_by: kareneilbeck
12567 creation_date: 2009-10-23T12:54:35Z
12571 name: annotation_directed_improved_draft
12572 def: "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]
12573 synonym: "annotation directed improvement" EXACT []
12574 is_a: SO:0001499 ! whole_genome_sequence_status
12575 created_by: kareneilbeck
12576 creation_date: 2009-10-23T12:57:10Z
12580 name: noncontiguous_finished
12581 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]
12582 synonym: "non contiguous finished" EXACT []
12583 is_a: SO:0001499 ! whole_genome_sequence_status
12584 created_by: kareneilbeck
12585 creation_date: 2009-10-23T01:01:07Z
12589 name: finished_genome
12590 def: "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]
12591 synonym: "finished" EXACT []
12592 synonym: "finished genome" EXACT []
12593 is_a: SO:0001499 ! whole_genome_sequence_status
12594 created_by: kareneilbeck
12595 creation_date: 2009-10-23T01:04:43Z
12599 name: intronic_regulatory_region
12600 def: "A regulatory region that is part of an intron." [SO:ke]
12601 synonym: "intronic regulatory region" EXACT []
12602 is_a: SO:0001679 ! transcription_regulatory_region
12603 relationship: part_of SO:0000188 ! intron
12604 created_by: kareneilbeck
12605 creation_date: 2009-11-08T02:48:02Z
12609 name: centromere_DNA_Element_I
12610 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]
12611 comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
12612 synonym: "CDEI" EXACT []
12613 synonym: "Centromere DNA Element I" EXACT []
12614 is_a: SO:0000330 ! conserved_region
12615 relationship: part_of SO:0001794 ! point_centromere
12616 created_by: kareneilbeck
12617 creation_date: 2009-11-09T05:47:23Z
12621 name: centromere_DNA_Element_II
12622 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]
12623 comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
12624 synonym: "CDEII" EXACT []
12625 synonym: "centromere DNA Element II" EXACT []
12626 is_a: SO:0000330 ! conserved_region
12627 relationship: part_of SO:0001794 ! point_centromere
12628 created_by: kareneilbeck
12629 creation_date: 2009-11-09T05:51:26Z
12633 name: centromere_DNA_Element_III
12634 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]
12635 comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
12636 synonym: "CDEIII" EXACT []
12637 synonym: "centromere DNA Element III" EXACT []
12638 is_a: SO:0000330 ! conserved_region
12639 relationship: part_of SO:0001794 ! point_centromere
12640 created_by: kareneilbeck
12641 creation_date: 2009-11-09T05:54:47Z
12645 name: telomeric_repeat
12646 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]
12647 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.
12648 synonym: "telomeric repeat" EXACT []
12649 is_a: SO:0000657 ! repeat_region
12650 relationship: part_of SO:0000624 ! telomere
12651 created_by: kareneilbeck
12652 creation_date: 2009-11-09T06:00:42Z
12657 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]
12658 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.
12659 synonym: "X element" RELATED []
12660 synonym: "X element core sequence" EXACT []
12661 is_a: SO:0000330 ! conserved_region
12662 relationship: part_of SO:0000624 ! telomere
12663 created_by: kareneilbeck
12664 creation_date: 2009-11-10T10:56:54Z
12669 def: "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]
12670 synonym: "YAC end" EXACT []
12671 is_a: SO:0000150 ! read
12672 relationship: part_of SO:0000152 ! YAC
12673 created_by: kareneilbeck
12674 creation_date: 2009-11-19T11:07:18Z
12678 name: whole_genome_sequence_status
12679 def: "The status of whole genome sequence." [DOI:10.1126]
12680 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.
12681 synonym: "whole genome sequence status" EXACT []
12682 is_a: SO:0000905 ! status
12683 created_by: kareneilbeck
12684 creation_date: 2009-10-23T12:47:47Z
12688 name: heritable_phenotypic_marker
12689 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]
12690 synonym: "heritable phenotypic marker" EXACT []
12691 synonym: "phenotypic marker" EXACT []
12692 is_a: SO:0001645 ! genetic_marker
12693 created_by: kareneilbeck
12694 creation_date: 2009-12-07T01:50:55Z
12698 name: peptide_collection
12699 def: "A collection of peptide sequences." [BBOP:nlw]
12700 comment: Term requested via tracker ID: 2910829.
12701 synonym: "peptide collection" EXACT []
12702 synonym: "peptide set" EXACT []
12703 is_a: SO:0001260 ! sequence_collection
12704 relationship: has_part SO:0000104 ! polypeptide
12705 created_by: kareneilbeck
12706 creation_date: 2009-12-11T10:58:58Z
12710 name: high_identity_region
12711 def: "An experimental feature with high sequence identity to another sequence." [SO:ke]
12712 comment: Requested by tracker ID: 2902685.
12713 synonym: "high identity region" EXACT []
12714 is_a: SO:0001410 ! experimental_feature
12715 created_by: kareneilbeck
12716 creation_date: 2009-12-11T11:06:05Z
12720 name: processed_transcript
12721 def: "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]
12722 comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.
12723 synonym: "processed transcript" EXACT []
12724 is_a: SO:0000673 ! transcript
12725 created_by: kareneilbeck
12726 creation_date: 2009-12-21T05:37:14Z
12730 name: assortment_derived_variation
12731 def: "A chromosome variation derived from an event during meiosis." [SO:ke]
12732 synonym: "assortment derived variation" RELATED []
12733 is_a: SO:0000240 ! chromosome_variation
12734 created_by: kareneilbeck
12735 creation_date: 2010-03-02T05:03:18Z
12739 name: reference_genome
12740 def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke]
12741 synonym: "reference genome" RELATED []
12742 is_a: SO:0001026 ! genome
12743 created_by: kareneilbeck
12744 creation_date: 2010-03-03T02:10:03Z
12748 name: variant_genome
12749 def: "A collection of sequences (often chromosomes) of an individual." [SO:ke]
12750 synonym: "variant genome" RELATED []
12751 is_a: SO:0001026 ! genome
12752 created_by: kareneilbeck
12753 creation_date: 2010-03-03T02:11:25Z
12757 name: variant_collection
12758 def: "A collection of one or more sequences of an individual." [SO:ke]
12759 synonym: "variant collection" RELATED []
12760 is_a: SO:0001260 ! sequence_collection
12761 relationship: has_part SO:0001059 ! sequence_alteration
12762 created_by: kareneilbeck
12763 creation_date: 2010-03-03T02:13:28Z
12767 name: alteration_attribute
12768 synonym: "alteration attribute" EXACT []
12769 is_a: SO:0000733 ! feature_attribute
12770 created_by: kareneilbeck
12771 creation_date: 2010-03-04T02:53:23Z
12775 name: chromosomal_variation_attribute
12776 synonym: "chromosomal variation attribute" EXACT []
12777 is_a: SO:0001508 ! alteration_attribute
12778 created_by: kareneilbeck
12779 creation_date: 2010-03-04T02:54:30Z
12783 name: intrachromosomal
12784 is_a: SO:0001509 ! chromosomal_variation_attribute
12785 created_by: kareneilbeck
12786 creation_date: 2010-03-04T02:55:25Z
12790 name: interchromosomal
12791 is_a: SO:0001509 ! chromosomal_variation_attribute
12792 created_by: kareneilbeck
12793 creation_date: 2010-03-04T02:55:43Z
12797 name: insertion_attribute
12798 def: "A quality of a chromosomal insertion,." [SO:ke]
12799 synonym: "insertion attribute" EXACT []
12800 is_a: SO:0001508 ! alteration_attribute
12801 created_by: kareneilbeck
12802 creation_date: 2010-03-04T02:55:56Z
12807 is_a: SO:0001512 ! insertion_attribute
12808 created_by: kareneilbeck
12809 creation_date: 2010-03-04T02:56:37Z
12814 def: "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]
12815 is_a: SO:0001512 ! insertion_attribute
12816 created_by: kareneilbeck
12817 creation_date: 2010-03-04T02:56:49Z
12822 def: "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]
12823 is_a: SO:0001512 ! insertion_attribute
12824 created_by: kareneilbeck
12825 creation_date: 2010-03-04T02:57:40Z
12830 def: "The quality of a duplication where the new region exists independently of the original." [SO:ke]
12831 is_a: SO:0001523 ! duplication_attribute
12832 created_by: kareneilbeck
12833 creation_date: 2010-03-04T02:57:51Z
12837 name: inversion_attribute
12838 synonym: "inversion attribute" EXACT []
12839 is_a: SO:0001508 ! alteration_attribute
12840 created_by: kareneilbeck
12841 creation_date: 2010-03-04T02:58:10Z
12846 is_a: SO:0001517 ! inversion_attribute
12847 created_by: kareneilbeck
12848 creation_date: 2010-03-04T02:58:24Z
12853 is_a: SO:0001517 ! inversion_attribute
12854 created_by: kareneilbeck
12855 creation_date: 2010-03-04T02:58:35Z
12859 name: translocaton_attribute
12860 synonym: "translocation attribute" EXACT []
12861 is_a: SO:0001508 ! alteration_attribute
12862 created_by: kareneilbeck
12863 creation_date: 2010-03-04T02:58:47Z
12868 is_a: SO:0001520 ! translocaton_attribute
12869 created_by: kareneilbeck
12870 creation_date: 2010-03-04T02:59:34Z
12875 is_a: SO:0001520 ! translocaton_attribute
12876 created_by: kareneilbeck
12877 creation_date: 2010-03-04T02:59:51Z
12881 name: duplication_attribute
12882 synonym: "duplication attribute" RELATED []
12883 is_a: SO:0001508 ! alteration_attribute
12884 created_by: kareneilbeck
12885 creation_date: 2010-03-05T01:56:33Z
12889 name: chromosomally_aberrant_genome
12890 synonym: "chromosomally aberrant genome" RELATED []
12891 is_a: SO:0001506 ! variant_genome
12892 created_by: kareneilbeck
12893 creation_date: 2010-03-05T02:21:00Z
12897 name: assembly_error_correction
12898 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]
12899 synonym: "assembly error correction" RELATED []
12900 is_a: SO:0000413 ! sequence_difference
12901 created_by: kareneilbeck
12902 creation_date: 2010-03-09T02:16:31Z
12906 name: base_call_error_correction
12907 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]
12908 synonym: "base call error correction" RELATED []
12909 is_a: SO:0000413 ! sequence_difference
12910 created_by: kareneilbeck
12911 creation_date: 2010-03-09T02:18:07Z
12915 name: peptide_localization_signal
12916 def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]
12918 synonym: "localization signal" RELATED []
12919 synonym: "peptide localization signal" EXACT []
12920 is_a: SO:0000839 ! polypeptide_region
12921 created_by: kareneilbeck
12922 creation_date: 2010-03-11T02:15:05Z
12926 name: nuclear_localization_signal
12927 def: "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]
12928 synonym: "NLS" EXACT []
12929 xref: http://en.wikipedia.org/wiki/Nuclear_localization_signal "wikipedia"
12930 is_a: SO:0001527 ! peptide_localization_signal
12931 created_by: kareneilbeck
12932 creation_date: 2010-03-11T02:16:38Z
12936 name: endosomal_localization_signal
12937 def: "A polypeptide region that targets a polypeptide to the endosome." [SO:ke]
12938 synonym: "endosomal localization signal" EXACT []
12939 is_a: SO:0001527 ! peptide_localization_signal
12940 created_by: kareneilbeck
12941 creation_date: 2010-03-11T02:20:58Z
12945 name: lysosomal_localization_signal
12946 def: "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]
12947 synonym: "lysosomal localization signal" EXACT []
12948 is_a: SO:0001527 ! peptide_localization_signal
12949 created_by: kareneilbeck
12950 creation_date: 2010-03-11T02:24:10Z
12954 name: nuclear_export_signal
12955 def: "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]
12956 synonym: "NES" EXACT []
12957 synonym: "nuclear export signal" EXACT []
12958 xref: http://en.wikipedia.org/wiki/Nuclear_export_signal
12959 is_a: SO:0001527 ! peptide_localization_signal
12960 created_by: kareneilbeck
12961 creation_date: 2010-03-11T02:25:25Z
12965 name: recombination_signal_sequence
12966 def: "A region recognized by a recombinase." [SO:ke]
12967 synonym: "recombination signal sequence" RELATED []
12968 xref: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences "wikipedia"
12969 is_a: SO:0000299 ! specific_recombination_site
12970 created_by: kareneilbeck
12971 creation_date: 2010-03-11T03:16:47Z
12975 name: cryptic_splice_site
12976 def: "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]
12977 synonym: "cryptic splice signal" RELATED []
12978 synonym: "cryptic splice site" EXACT []
12979 is_a: SO:0000162 ! splice_site
12980 created_by: kareneilbeck
12981 creation_date: 2010-03-11T03:25:06Z
12985 name: nuclear_rim_localization_signal
12986 def: "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]
12987 synonym: "nuclear rim localization signal" RELATED []
12988 xref: PMID:16027110
12989 is_a: SO:0001527 ! peptide_localization_signal
12990 created_by: kareneilbeck
12991 creation_date: 2010-03-11T03:31:30Z
12996 def: "A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]
12997 synonym: "P element" RELATED []
12998 is_a: SO:0000182 ! DNA_transposon
12999 created_by: kareneilbeck
13000 creation_date: 2010-03-12T03:40:33Z
13004 name: functional_variant
13005 def: "A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]
13006 synonym: "functional variant" EXACT []
13007 is_a: SO:0001060 ! sequence_variant
13008 created_by: kareneilbeck
13009 creation_date: 2010-03-22T11:30:25Z
13013 name: structural_variant
13014 def: "A sequence variant that changes one or more sequence features." [SO:ke]
13015 synonym: "structural variant" RELATED []
13016 is_a: SO:0001060 ! sequence_variant
13017 created_by: kareneilbeck
13018 creation_date: 2010-03-22T11:31:01Z
13022 name: transcript_function_variant
13023 def: "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]
13024 synonym: "transcript function variant" EXACT []
13025 is_a: SO:0001536 ! functional_variant
13026 created_by: kareneilbeck
13027 creation_date: 2010-03-22T11:32:58Z
13031 name: translational_product_function_variant
13032 def: "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]
13033 synonym: "translational product variant" EXACT []
13034 is_a: SO:0001536 ! functional_variant
13035 created_by: kareneilbeck
13036 creation_date: 2010-03-22T11:46:15Z
13040 name: level_of_transcript_variant
13041 def: "A sequence variant which alters the level of a transcript." [SO:ke]
13042 synonym: "level of transcript variant" EXACT []
13043 is_a: SO:0001538 ! transcript_function_variant
13044 created_by: kareneilbeck
13045 creation_date: 2010-03-22T11:47:07Z
13049 name: decreased_transcript_level_variant
13050 def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]
13051 synonym: "decreased transcript level" EXACT []
13052 is_a: SO:0001540 ! level_of_transcript_variant
13053 created_by: kareneilbeck
13054 creation_date: 2010-03-22T11:47:47Z
13058 name: increased_transcript_level_variant
13059 def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]
13060 synonym: "increased transcript level variant" EXACT []
13061 is_a: SO:0001540 ! level_of_transcript_variant
13062 created_by: kareneilbeck
13063 creation_date: 2010-03-22T11:48:17Z
13067 name: transcript_processing_variant
13068 def: "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]
13069 synonym: "transcript processing variant" EXACT []
13070 is_a: SO:0001538 ! transcript_function_variant
13071 created_by: kareneilbeck
13072 creation_date: 2010-03-22T11:48:48Z
13076 name: editing_variant
13077 def: "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]
13078 synonym: "editing variant" EXACT []
13079 is_a: SO:0001543 ! transcript_processing_variant
13080 created_by: kareneilbeck
13081 creation_date: 2010-03-22T11:49:25Z
13085 name: polyadenylation_variant
13086 def: "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]
13087 synonym: "polyadenylation variant" EXACT []
13088 is_a: SO:0001543 ! transcript_processing_variant
13089 created_by: kareneilbeck
13090 creation_date: 2010-03-22T11:49:40Z
13094 name: transcript_stability_variant
13095 def: "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]
13096 synonym: "transcript stability variant" EXACT []
13097 is_a: SO:0001538 ! transcript_function_variant
13098 created_by: kareneilbeck
13099 creation_date: 2010-03-22T11:50:01Z
13103 name: decreased_transcript_stability_variant
13104 def: "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]
13105 synonym: "decrease transcript stability variant" EXACT []
13106 is_a: SO:0001546 ! transcript_stability_variant
13107 created_by: kareneilbeck
13108 creation_date: 2010-03-22T11:50:23Z
13112 name: increased_transcript_stability_variant
13113 def: "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]
13114 synonym: "increased transcript stability variant" EXACT []
13115 is_a: SO:0001546 ! transcript_stability_variant
13116 created_by: kareneilbeck
13117 creation_date: 2010-03-22T11:50:39Z
13121 name: transcription_variant
13122 def: "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]
13123 synonym: "transcription variant" EXACT []
13124 is_a: SO:0001538 ! transcript_function_variant
13125 created_by: kareneilbeck
13126 creation_date: 2010-03-22T11:51:26Z
13130 name: rate_of_transcription_variant
13131 def: "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]
13132 synonym: "rate of transcription variant" EXACT []
13133 is_a: SO:0001549 ! transcription_variant
13134 created_by: kareneilbeck
13135 creation_date: 2010-03-22T11:51:50Z
13139 name: increased_transcription_rate_variant
13140 def: "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]
13141 synonym: "increased transcription rate variant" EXACT []
13142 is_a: SO:0001550 ! rate_of_transcription_variant
13143 created_by: kareneilbeck
13144 creation_date: 2010-03-22T11:52:17Z
13148 name: decreased_transcription_rate_variant
13149 def: "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]
13150 synonym: "decreased transcription rate variant" EXACT []
13151 is_a: SO:0001550 ! rate_of_transcription_variant
13152 created_by: kareneilbeck
13153 creation_date: 2010-03-22T11:52:43Z
13157 name: translational_product_level_variant
13158 def: "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]
13159 synonym: "translational product level variant" EXACT []
13160 is_a: SO:0001539 ! translational_product_function_variant
13161 created_by: kareneilbeck
13162 creation_date: 2010-03-22T11:53:32Z
13166 name: polypeptide_function_variant
13167 def: "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]
13168 synonym: "polypeptide function variant" EXACT []
13169 is_a: SO:0001539 ! translational_product_function_variant
13170 created_by: kareneilbeck
13171 creation_date: 2010-03-22T11:53:54Z
13175 name: decreased_translational_product_level
13176 def: "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]
13177 synonym: "decrease translational product level" EXACT []
13178 is_a: SO:0001553 ! translational_product_level_variant
13179 created_by: kareneilbeck
13180 creation_date: 2010-03-22T11:54:25Z
13184 name: increased_translational_product_level
13185 def: "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]
13186 synonym: "increase translational product level" EXACT []
13187 is_a: SO:0001553 ! translational_product_level_variant
13188 created_by: kareneilbeck
13189 creation_date: 2010-03-22T11:55:25Z
13193 name: polypeptide_gain_of_function_variant
13194 def: "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]
13195 synonym: "polypeptide gain of function variant" EXACT []
13196 is_a: SO:0001554 ! polypeptide_function_variant
13197 created_by: kareneilbeck
13198 creation_date: 2010-03-22T11:56:12Z
13202 name: polypeptide_localization_variant
13203 def: "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]
13204 synonym: "polypeptide localization variant" EXACT []
13205 is_a: SO:0001554 ! polypeptide_function_variant
13206 created_by: kareneilbeck
13207 creation_date: 2010-03-22T11:56:37Z
13211 name: polypeptide_loss_of_function_variant
13212 def: "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]
13213 synonym: "polypeptide loss of function variant" EXACT []
13214 is_a: SO:0001554 ! polypeptide_function_variant
13215 created_by: kareneilbeck
13216 creation_date: 2010-03-22T11:56:58Z
13220 name: inactive_ligand_binding_site
13221 def: "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]
13222 synonym: "inactive ligand binding site" EXACT []
13223 is_a: SO:0001559 ! polypeptide_loss_of_function_variant
13224 created_by: kareneilbeck
13225 creation_date: 2010-03-22T11:58:00Z
13229 name: polypeptide_partial_loss_of_function
13230 def: "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]
13231 synonym: "polypeptide partial loss of function" EXACT []
13232 is_a: SO:0001559 ! polypeptide_loss_of_function_variant
13233 created_by: kareneilbeck
13234 creation_date: 2010-03-22T11:58:32Z
13238 name: polypeptide_post_translational_processing_variant
13239 def: "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]
13240 synonym: "polypeptide post translational processing variant" EXACT []
13241 is_a: SO:0001554 ! polypeptide_function_variant
13242 created_by: kareneilbeck
13243 creation_date: 2010-03-22T11:59:06Z
13247 name: copy_number_change
13248 def: "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]
13249 synonym: "copy number change" EXACT []
13250 is_a: SO:0001537 ! structural_variant
13251 created_by: kareneilbeck
13252 creation_date: 2010-03-22T02:27:33Z
13257 def: "A sequence variant where the structure of the gene is changed." [SO:ke]
13258 synonym: "gene structure variant" EXACT []
13259 synonym: "snpEff:GENE" EXACT VAR []
13260 synonym: "VAAST:gene_variant" EXACT VAR []
13261 is_a: SO:0001878 ! feature_variant
13262 created_by: kareneilbeck
13263 creation_date: 2010-03-22T02:28:01Z
13268 def: "A sequence variant whereby a two genes have become joined." [SO:ke]
13269 synonym: "gene fusion" EXACT []
13270 is_a: SO:0001564 ! gene_variant
13271 created_by: kareneilbeck
13272 creation_date: 2010-03-22T02:28:28Z
13276 name: regulatory_region_variant
13277 def: "A sequence variant located within a regulatory region." [SO:ke]
13278 comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
13279 synonym: "regulatory region variant" EXACT []
13280 synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13281 is_a: SO:0001878 ! feature_variant
13282 created_by: kareneilbeck
13283 creation_date: 2010-03-22T02:28:48Z
13287 name: stop_retained_variant
13288 def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]
13289 synonym: "snpEff:SYNONYMOUS_STOP" EXACT VAR []
13290 synonym: "stop retained variant" EXACT []
13291 synonym: "VAAST:stop_retained" EXACT VAR []
13292 is_a: SO:0001590 ! terminator_codon_variant
13293 is_a: SO:0001819 ! synonymous_variant
13294 created_by: kareneilbeck
13295 creation_date: 2010-04-19T05:02:30Z
13299 name: splicing_variant
13300 def: "A sequence variant that changes the process of splicing." [SO:ke]
13301 synonym: "splicing variant" EXACT []
13302 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13303 is_a: SO:0001576 ! transcript_variant
13304 created_by: kareneilbeck
13305 creation_date: 2010-03-22T02:29:22Z
13309 name: cryptic_splice_site_variant
13310 def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
13311 synonym: "cryptic splice site activation" EXACT []
13312 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13313 is_a: SO:0001568 ! splicing_variant
13314 created_by: kareneilbeck
13315 creation_date: 2010-03-22T02:29:41Z
13319 name: cryptic_splice_acceptor
13320 def: "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]
13321 synonym: "cryptic splice acceptor" EXACT []
13322 is_a: SO:0001569 ! cryptic_splice_site_variant
13323 created_by: kareneilbeck
13324 creation_date: 2010-03-22T02:30:11Z
13328 name: cryptic_splice_donor
13329 def: "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]
13330 synonym: "cryptic splice donor" EXACT []
13331 is_a: SO:0001569 ! cryptic_splice_site_variant
13332 created_by: kareneilbeck
13333 creation_date: 2010-03-22T02:30:35Z
13337 name: exon_loss_variant
13338 def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke]
13339 synonym: "exon loss" EXACT []
13340 synonym: "snpEff:EXON_DELETED" EXACT VAR []
13341 is_a: SO:0001568 ! splicing_variant
13342 created_by: kareneilbeck
13343 creation_date: 2010-03-22T02:31:09Z
13347 name: intron_gain_variant
13348 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]
13349 synonym: "intron gain" EXACT []
13350 synonym: "intron gain variant" EXACT []
13351 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13352 is_a: SO:0001568 ! splicing_variant
13353 created_by: kareneilbeck
13354 creation_date: 2010-03-22T02:31:25Z
13358 name: splice_acceptor_variant
13359 def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]
13360 synonym: "snpEff:SPLICE_SITE_ACCEPTOR" EXACT VAR []
13361 synonym: "splice acceptor variant" EXACT []
13362 synonym: "VAAST:splice_acceptor_variant" EXACT VAR []
13363 is_a: SO:0001629 ! splice_site_variant
13364 created_by: kareneilbeck
13365 creation_date: 2010-03-22T02:31:52Z
13369 name: splice_donor_variant
13370 def: "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]
13371 synonym: "snpEff:SPLICE_SITE_DONOR" EXACT VAR []
13372 synonym: "splice donor variant" EXACT []
13373 synonym: "VAAST:splice_donor_variant" EXACT VAR []
13374 is_a: SO:0001629 ! splice_site_variant
13375 created_by: kareneilbeck
13376 creation_date: 2010-03-22T02:32:10Z
13380 name: transcript_variant
13381 def: "A sequence variant that changes the structure of the transcript." [SO:ke]
13382 synonym: "snpEff:TRANSCRIPT" EXACT VAR []
13383 synonym: "transcript variant" EXACT []
13384 synonym: "VAAST:transcript_variant" EXACT VAR []
13385 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13386 is_a: SO:0001564 ! gene_variant
13387 created_by: kareneilbeck
13388 creation_date: 2010-03-22T02:32:41Z
13392 name: complex_transcript_variant
13393 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]
13394 comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
13395 synonym: "complex transcript variant" EXACT []
13396 synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13397 synonym: "complext change in transcript" EXACT []
13398 is_a: SO:0001576 ! transcript_variant
13399 created_by: kareneilbeck
13400 creation_date: 2010-03-22T02:33:03Z
13405 def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]
13406 comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
13407 synonym: "ANNOVAR:stoploss" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13408 synonym: "snpEff:STOP_LOST" EXACT VAR []
13409 synonym: "stop codon lost" EXACT []
13410 synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13411 synonym: "VAAST:stop_lost" EXACT VAR []
13412 is_a: SO:0001590 ! terminator_codon_variant
13413 is_a: SO:0001907 ! feature_elongation
13414 is_a: SO:0001992 ! nonsynonymous_variant
13415 created_by: kareneilbeck
13416 creation_date: 2010-03-23T03:46:42Z
13420 name: transcript_sequence_variant
13421 synonym: "transcript sequence variant" EXACT []
13426 name: coding_sequence_variant
13428 def: "A sequence variant that changes the coding sequence." [SO:ke]
13429 synonym: "coding sequence variant" EXACT []
13430 synonym: "coding variant" EXACT []
13431 synonym: "codon variant" EXACT []
13432 synonym: "codon_variant" EXACT []
13433 synonym: "snpEff:CDS" EXACT VAR []
13434 synonym: "snpEff:CODON_CHANGE" RELATED VAR []
13435 synonym: "VAAST:coding_sequence_variant" EXACT VAR []
13436 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13437 is_a: SO:0001791 ! exon_variant
13438 is_a: SO:0001968 ! coding_transcript_variant
13439 created_by: kareneilbeck
13440 creation_date: 2010-03-22T02:34:36Z
13444 name: initiator_codon_variant
13445 def: "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]
13446 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.
13447 synonym: "initiatior codon variant" EXACT []
13448 synonym: "initiator codon change" EXACT []
13449 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13450 xref: loinc:LA6695-6 "Initiating Methionine"
13451 is_a: SO:0001580 ! coding_sequence_variant
13452 created_by: kareneilbeck
13453 creation_date: 2010-03-22T02:35:18Z
13457 name: missense_variant
13460 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]
13461 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.
13462 synonym: "ANNOVAR:nonsynonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13463 synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13464 synonym: "missense codon" EXACT []
13465 synonym: "snpEff:NON_SYSNONYMOUS_CODING" EXACT VAR []
13466 synonym: "VAAST:non_synonymous_codon" RELATED VAR []
13467 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13468 xref: http://en.wikipedia.org/wiki/Missense_mutation
13469 xref: loinc:LA6698-0 "Missense"
13470 is_a: SO:0001992 ! nonsynonymous_variant
13471 created_by: kareneilbeck
13472 creation_date: 2010-03-22T02:35:49Z
13476 name: conservative_missense_variant
13477 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]
13478 synonym: "conservative missense codon" EXACT []
13479 synonym: "conservative missense variant" EXACT []
13480 synonym: "neutral missense codon" RELATED []
13481 synonym: "quiet missense codon" RELATED []
13482 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13483 is_a: SO:0001583 ! missense_variant
13484 created_by: kareneilbeck
13485 creation_date: 2010-03-22T02:36:40Z
13489 name: non_conservative_missense_variant
13490 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]
13491 synonym: "non conservative missense codon" EXACT []
13492 synonym: "non conservative missense variant" EXACT []
13493 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13494 is_a: SO:0001583 ! missense_variant
13495 created_by: kareneilbeck
13496 creation_date: 2010-03-22T02:37:16Z
13501 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]
13502 comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
13503 synonym: "ANNOVAR:stopgain" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13504 synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13505 synonym: "nonsense codon" EXACT []
13506 synonym: "snpEFF:STOP_GAINED" EXACT VAR []
13507 synonym: "stop codon gained" RELATED []
13508 synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13509 synonym: "VAAST:stop_gained" EXACT VAR []
13510 xref: loinc:LA6699-8 "Nonsense"
13511 is_a: SO:0001906 ! feature_truncation
13512 is_a: SO:0001992 ! nonsynonymous_variant
13513 created_by: kareneilbeck
13514 creation_date: 2010-03-22T02:37:52Z
13518 name: frameshift_variant
13519 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]
13520 comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
13521 synonym: "ANNOVAR:frameshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13522 synonym: "frameshift variant" EXACT []
13523 synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13524 synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13525 synonym: "snpEff:FRAME_SHIFT" EXACT VAR []
13526 synonym: "VAAST:frameshift_variant" EXACT VAR []
13527 xref: loinc:LA6694-9 "Frameshift"
13528 is_a: SO:0001818 ! protein_altering_variant
13529 created_by: kareneilbeck
13530 creation_date: 2010-03-22T02:40:19Z
13534 name: terminator_codon_variant
13536 def: "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]
13537 comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon.
13538 synonym: "terminal codon variant" EXACT []
13539 synonym: "terminal_codon_variant" EXACT []
13540 synonym: "terminator codon variant" EXACT []
13541 xref: loinc:LA6700-2 "Stop Codon Mutation"
13542 is_a: SO:0001580 ! coding_sequence_variant
13543 created_by: kareneilbeck
13544 creation_date: 2010-03-22T02:40:37Z
13548 name: frame_restoring_variant
13549 def: "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
13550 synonym: "frame restoring variant" EXACT []
13551 is_a: SO:0001589 ! frameshift_variant
13552 created_by: kareneilbeck
13553 creation_date: 2010-03-22T02:41:09Z
13557 name: minus_1_frameshift_variant
13558 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]
13559 synonym: "-1 frameshift variant" EXACT []
13560 synonym: "minus 1 frameshift variant" EXACT []
13561 is_a: SO:0001589 ! frameshift_variant
13562 created_by: kareneilbeck
13563 creation_date: 2010-03-22T02:41:30Z
13567 name: minus_2_frameshift_variant
13568 synonym: "-2 frameshift variant" EXACT []
13569 synonym: "minus 2 frameshift variant" EXACT []
13570 is_a: SO:0001589 ! frameshift_variant
13571 created_by: kareneilbeck
13572 creation_date: 2010-03-22T02:41:52Z
13576 name: plus_1_frameshift_variant
13577 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]
13578 synonym: "+1 frameshift variant" EXACT []
13579 synonym: "plus 1 frameshift variant" EXACT []
13580 is_a: SO:0001589 ! frameshift_variant
13581 created_by: kareneilbeck
13582 creation_date: 2010-03-22T02:42:06Z
13586 name: plus_2_frameshift_variant
13587 synonym: "+2 frameshift variant" EXACT []
13588 synonym: "plus 2 frameshift variant" EXACT []
13589 is_a: SO:0001589 ! frameshift_variant
13590 created_by: kareneilbeck
13591 creation_date: 2010-03-22T02:42:23Z
13595 name: transcript_secondary_structure_variant
13596 def: "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]
13597 synonym: "transcript secondary structure variant" EXACT []
13598 is_a: SO:0001576 ! transcript_variant
13599 created_by: kareneilbeck
13600 creation_date: 2010-03-22T02:43:18Z
13604 name: compensatory_transcript_secondary_structure_variant
13605 def: "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]
13606 synonym: "compensatory transcript secondary structure variant" EXACT []
13607 is_a: SO:0001596 ! transcript_secondary_structure_variant
13608 created_by: kareneilbeck
13609 creation_date: 2010-03-22T02:43:54Z
13613 name: translational_product_structure_variant
13614 def: "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]
13615 synonym: "translational product structure variant" EXACT []
13616 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13617 is_a: SO:0001564 ! gene_variant
13618 created_by: kareneilbeck
13619 creation_date: 2010-03-22T02:44:17Z
13623 name: 3D_polypeptide_structure_variant
13624 def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke]
13625 synonym: "3D polypeptide structure variant" EXACT []
13626 is_a: SO:0001539 ! translational_product_function_variant
13627 created_by: kareneilbeck
13628 creation_date: 2010-03-22T02:44:46Z
13632 name: complex_3D_structural_variant
13633 def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke]
13634 synonym: "complex 3D structural variant" EXACT []
13635 is_a: SO:0001599 ! 3D_polypeptide_structure_variant
13636 created_by: kareneilbeck
13637 creation_date: 2010-03-22T02:45:13Z
13641 name: conformational_change_variant
13642 def: "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]
13643 synonym: "conformational change variant" EXACT []
13644 is_a: SO:0001599 ! 3D_polypeptide_structure_variant
13645 created_by: kareneilbeck
13646 creation_date: 2010-03-22T02:45:48Z
13650 name: complex_change_of_translational_product_variant
13651 synonym: "complex change of translational product variant" EXACT []
13652 is_a: SO:0001539 ! translational_product_function_variant
13653 created_by: kareneilbeck
13654 creation_date: 2010-03-22T02:46:54Z
13658 name: polypeptide_sequence_variant
13659 def: "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]
13660 synonym: "polypeptide sequence variant" EXACT []
13661 is_a: SO:0001598 ! translational_product_structure_variant
13662 created_by: kareneilbeck
13663 creation_date: 2010-03-22T02:47:13Z
13667 name: amino_acid_deletion
13668 def: "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]
13669 synonym: "amino acid deletion" EXACT []
13670 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13671 is_a: SO:0001603 ! polypeptide_sequence_variant
13672 created_by: kareneilbeck
13673 creation_date: 2010-03-22T02:47:36Z
13677 name: amino_acid_insertion
13678 def: "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]
13679 synonym: "amino acid insertion" EXACT []
13680 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13681 is_a: SO:0001603 ! polypeptide_sequence_variant
13682 created_by: kareneilbeck
13683 creation_date: 2010-03-22T02:47:56Z
13687 name: amino_acid_substitution
13688 def: "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]
13689 synonym: "amino acid substitution" EXACT []
13690 synonym: "VAAST:amino_acid_substitution" EXACT VAR []
13691 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13692 is_a: SO:0001603 ! polypeptide_sequence_variant
13693 created_by: kareneilbeck
13694 creation_date: 2010-03-22T02:48:17Z
13698 name: conservative_amino_acid_substitution
13699 def: "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]
13700 synonym: "conservative amino acid substitution" EXACT []
13701 is_a: SO:0001606 ! amino_acid_substitution
13702 created_by: kareneilbeck
13703 creation_date: 2010-03-22T02:48:57Z
13707 name: non_conservative_amino_acid_substitution
13708 def: "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]
13709 synonym: "non conservative amino acid substitution" EXACT []
13710 is_a: SO:0001606 ! amino_acid_substitution
13711 created_by: kareneilbeck
13712 creation_date: 2010-03-22T02:49:23Z
13716 name: elongated_polypeptide
13717 def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]
13718 synonym: "elongated polypeptide" EXACT []
13719 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13720 is_a: SO:0001603 ! polypeptide_sequence_variant
13721 created_by: kareneilbeck
13722 creation_date: 2010-03-22T02:49:52Z
13726 name: elongated_polypeptide_C_terminal
13727 def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
13728 synonym: "elongated polypeptide C terminal" EXACT []
13729 is_a: SO:0001609 ! elongated_polypeptide
13730 created_by: kareneilbeck
13731 creation_date: 2010-03-22T02:50:20Z
13735 name: elongated_polypeptide_N_terminal
13736 def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
13737 synonym: "elongated polypeptide N terminal" EXACT []
13738 is_a: SO:0001609 ! elongated_polypeptide
13739 created_by: kareneilbeck
13740 creation_date: 2010-03-22T02:50:31Z
13744 name: elongated_in_frame_polypeptide_C_terminal
13745 def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
13746 synonym: "elongated in frame polypeptide C terminal" EXACT []
13747 is_a: SO:0001610 ! elongated_polypeptide_C_terminal
13748 created_by: kareneilbeck
13749 creation_date: 2010-03-22T02:51:05Z
13753 name: elongated_out_of_frame_polypeptide_C_terminal
13754 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]
13755 synonym: "elongated polypeptide out of frame C terminal" EXACT []
13756 is_a: SO:0001610 ! elongated_polypeptide_C_terminal
13757 created_by: kareneilbeck
13758 creation_date: 2010-03-22T02:51:20Z
13762 name: elongated_in_frame_polypeptide_N_terminal_elongation
13763 def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
13764 synonym: "elongated in frame polypeptide N terminal" EXACT []
13765 is_a: SO:0001611 ! elongated_polypeptide_N_terminal
13766 created_by: kareneilbeck
13767 creation_date: 2010-03-22T02:51:49Z
13771 name: elongated_out_of_frame_polypeptide_N_terminal
13772 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]
13773 synonym: "elongated out of frame N terminal" EXACT []
13774 is_a: SO:0001611 ! elongated_polypeptide_N_terminal
13775 created_by: kareneilbeck
13776 creation_date: 2010-03-22T02:52:05Z
13780 name: polypeptide_fusion
13781 def: "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]
13782 synonym: "polypeptide fusion" EXACT []
13783 is_a: SO:0001603 ! polypeptide_sequence_variant
13784 created_by: kareneilbeck
13785 creation_date: 2010-03-22T02:52:43Z
13789 name: polypeptide_truncation
13790 def: "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]
13791 synonym: "polypeptide truncation" EXACT []
13792 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
13793 is_a: SO:0001603 ! polypeptide_sequence_variant
13794 created_by: kareneilbeck
13795 creation_date: 2010-03-22T02:53:07Z
13799 name: inactive_catalytic_site
13800 def: "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]
13801 synonym: "inactive catalytic site" EXACT []
13802 is_a: SO:0001560 ! inactive_ligand_binding_site
13803 created_by: kareneilbeck
13804 creation_date: 2010-03-22T03:06:14Z
13808 name: non_coding_transcript_variant
13809 def: "A transcript variant of a non coding RNA gene." [SO:ke]
13810 comment: Within non-coding gene - Located within a gene that does not code for a protein.
13811 synonym: "ANNOVAR:ncRNA" RELATED VAR [http:http://www.openbioinformatics.org/annovar/annovar_download.html]
13812 synonym: "nc transcript variant" EXACT []
13813 synonym: "non coding transcript variant" EXACT []
13814 synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html]
13815 is_a: SO:0001576 ! transcript_variant
13816 created_by: kareneilbeck
13817 creation_date: 2010-03-23T11:16:23Z
13821 name: mature_miRNA_variant
13822 def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke]
13823 comment: EBI term: Within mature miRNA - Located within a microRNA.
13824 synonym: "mature miRNA variant" EXACT []
13825 synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13826 is_a: SO:0001619 ! non_coding_transcript_variant
13827 created_by: kareneilbeck
13828 creation_date: 2010-03-23T11:16:58Z
13832 name: NMD_transcript_variant
13833 def: "A variant in a transcript that is the target of NMD." [SO:ke]
13834 synonym: "NMD transcript variant" EXACT []
13835 synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13836 is_a: SO:0001576 ! transcript_variant
13837 created_by: kareneilbeck
13838 creation_date: 2010-03-23T11:20:40Z
13843 def: "A transcript variant that is located within the UTR." [SO:ke]
13844 synonym: "UTR variant" EXACT []
13845 synonym: "UTR_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13846 is_a: SO:0001791 ! exon_variant
13847 is_a: SO:0001968 ! coding_transcript_variant
13848 created_by: kareneilbeck
13849 creation_date: 2010-03-23T11:22:58Z
13853 name: 5_prime_UTR_variant
13854 def: "A UTR variant of the 5' UTR." [SO:ke]
13855 comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).
13856 synonym: "5'UTR variant" EXACT []
13857 synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13858 synonym: "ANNOVAR:UTR5" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13859 synonym: "five prime UTR variant" EXACT []
13860 synonym: "snpEff:UTR_5_PRIME" EXACT VAR []
13861 synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13862 synonym: "VAAST:five_prime_UTR_variant" EXACT VAR []
13863 is_a: SO:0001622 ! UTR_variant
13864 created_by: kareneilbeck
13865 creation_date: 2010-03-23T11:23:29Z
13869 name: 3_prime_UTR_variant
13870 def: "A UTR variant of the 3' UTR." [SO:ke]
13871 comment: EBI term 3prime UTR variations - In 3prime UTR.
13872 synonym: "3'UTR variant" EXACT []
13873 synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13874 synonym: "ANNOVAR:UTR3" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13875 synonym: "snpEff:UTR_3_PRIME" EXACT VAR []
13876 synonym: "three prime UTR variant" EXACT []
13877 synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13878 synonym: "VAAST:three_prime_UTR_variant" EXACT VAR []
13879 is_a: SO:0001622 ! UTR_variant
13880 created_by: kareneilbeck
13881 creation_date: 2010-03-23T11:23:54Z
13885 name: incomplete_terminal_codon_variant
13886 def: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]
13887 comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
13888 synonym: "incomplete terminal codon variant" EXACT []
13889 synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13890 is_a: SO:0001590 ! terminator_codon_variant
13891 is_a: SO:0001650 ! inframe_variant
13892 created_by: kareneilbeck
13893 creation_date: 2010-03-23T03:51:15Z
13897 name: intron_variant
13898 def: "A transcript variant occurring within an intron." [SO:ke]
13899 comment: EBI term: Intronic variations - In intron.
13900 synonym: "ANNOVAR:intronic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13901 synonym: "intron variant" EXACT []
13902 synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13903 synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13904 synonym: "snpEff:INTRON" EXACT VAR []
13905 synonym: "VAAST:intron_variant" EXACT VAR []
13906 is_a: SO:0001576 ! transcript_variant
13907 created_by: kareneilbeck
13908 creation_date: 2010-03-23T03:52:38Z
13912 name: intergenic_variant
13913 def: "A sequence variant located in the intergenic region, between genes." [SO:ke]
13914 comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
13915 synonym: "ANNOVAR:intergenic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13916 synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13917 synonym: "intergenic variant" EXACT []
13918 synonym: "snpEff:INTERGENIC" EXACT VAR []
13919 is_a: SO:0001878 ! feature_variant
13920 created_by: kareneilbeck
13921 creation_date: 2010-03-23T05:07:37Z
13925 name: splice_site_variant
13926 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]
13927 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.
13928 synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13929 synonym: "splice site variant" EXACT []
13930 is_a: SO:0001568 ! splicing_variant
13931 is_a: SO:0001627 ! intron_variant
13932 created_by: kareneilbeck
13933 creation_date: 2010-03-24T09:42:00Z
13937 name: splice_region_variant
13938 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]
13939 comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
13940 synonym: "ANNOVAR:splicing" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13941 synonym: "splice region variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13942 synonym: "VAAST:splice_region_variant" EXACT VAR []
13943 is_a: SO:0001568 ! splicing_variant
13944 created_by: kareneilbeck
13945 creation_date: 2010-03-24T09:46:02Z
13949 name: upstream_gene_variant
13950 def: "A sequence variant located 5' of a gene." [SO:ke]
13951 comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
13952 synonym: "ANNOVAR:upstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13953 synonym: "snpEff:UPSTREAM" EXACT VAR []
13954 synonym: "upstream gene variant" EXACT []
13955 is_a: SO:0001628 ! intergenic_variant
13956 created_by: kareneilbeck
13957 creation_date: 2010-03-24T09:49:13Z
13961 name: downstream_gene_variant
13962 def: "A sequence variant located 3' of a gene." [SO:ke]
13963 comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
13964 synonym: "ANNOVAR:downstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
13965 synonym: "downstream gene variant" EXACT []
13966 synonym: "snpEff:DOWNSTREAM" EXACT VAR []
13967 is_a: SO:0001628 ! intergenic_variant
13968 created_by: kareneilbeck
13969 creation_date: 2010-03-24T09:49:38Z
13973 name: 5KB_downstream_variant
13974 def: "A sequence variant located within 5 KB of the end of a gene." [SO:ke]
13975 comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
13976 synonym: "5KB downstream variant" EXACT []
13977 synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
13978 synonym: "within 5KB downstream" RELATED []
13979 is_a: SO:0001632 ! downstream_gene_variant
13980 created_by: kareneilbeck
13981 creation_date: 2010-03-24T09:50:16Z
13985 name: 500B_downstream_variant
13986 def: "A sequence variant located within a half KB of the end of a gene." [SO:ke]
13987 synonym: "500B downstream variant" EXACT []
13988 synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
13989 is_a: SO:0001633 ! 5KB_downstream_variant
13990 created_by: kareneilbeck
13991 creation_date: 2010-03-24T09:50:42Z
13995 name: 5KB_upstream_variant
13996 def: "A sequence variant located within 5KB 5' of a gene." [SO:ke]
13997 comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
13998 synonym: "5kb upstream variant" EXACT []
13999 synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
14000 is_a: SO:0001631 ! upstream_gene_variant
14001 created_by: kareneilbeck
14002 creation_date: 2010-03-24T09:51:06Z
14006 name: 2KB_upstream_variant
14007 def: "A sequence variant located within 2KB 5' of a gene." [SO:ke]
14008 synonym: "2KB upstream variant" EXACT []
14009 synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
14010 is_a: SO:0001635 ! 5KB_upstream_variant
14011 created_by: kareneilbeck
14012 creation_date: 2010-03-24T09:51:22Z
14017 def: "A gene that encodes for ribosomal RNA." [SO:ke]
14018 synonym: "rDNA" EXACT []
14019 synonym: "rRNA gene" EXACT []
14020 is_a: SO:0001263 ! ncRNA_gene
14021 created_by: kareneilbeck
14022 creation_date: 2010-04-21T10:10:32Z
14027 def: "A gene that encodes for an piwi associated RNA." [SO:ke]
14028 synonym: "piRNA gene" EXACT []
14029 is_a: SO:0001263 ! ncRNA_gene
14030 created_by: kareneilbeck
14031 creation_date: 2010-04-21T10:11:36Z
14035 name: RNase_P_RNA_gene
14036 def: "A gene that encodes an RNase P RNA." [SO:ke]
14037 synonym: "RNase P RNA gene" EXACT []
14038 is_a: SO:0001263 ! ncRNA_gene
14039 created_by: kareneilbeck
14040 creation_date: 2010-04-21T10:13:23Z
14044 name: RNase_MRP_RNA_gene
14045 def: "A gene that encodes a RNase_MRP_RNA." [SO:ke]
14046 synonym: "RNase MRP RNA gene" RELATED []
14047 is_a: SO:0001263 ! ncRNA_gene
14048 created_by: kareneilbeck
14049 creation_date: 2010-04-21T10:13:58Z
14054 def: "A gene that encodes large intervening non-coding RNA." [SO:ke]
14055 synonym: "lincRNA gene" EXACT []
14056 is_a: SO:0001263 ! ncRNA_gene
14057 created_by: kareneilbeck
14058 creation_date: 2010-04-21T10:14:24Z
14062 name: mathematically_defined_repeat
14063 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]
14064 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.).
14065 synonym: "mathematically defined repeat" EXACT []
14066 is_a: SO:0001410 ! experimental_feature
14067 created_by: kareneilbeck
14068 creation_date: 2010-05-03T11:50:14Z
14072 name: telomerase_RNA_gene
14073 def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]
14074 synonym: "Telomerase RNA component" EXACT []
14075 synonym: "telomerase RNA gene" EXACT []
14076 synonym: "TERC" EXACT []
14077 xref: http:http://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia"
14078 is_a: SO:0001263 ! ncRNA_gene
14079 created_by: kareneilbeck
14080 creation_date: 2010-05-18T05:26:38Z
14084 name: targeting_vector
14085 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]
14086 synonym: "targeting vector" RELATED []
14087 is_a: SO:0000440 ! vector_replicon
14088 is_a: SO:0000804 ! engineered_region
14089 relationship: has_part SO:0000853 ! homologous_region
14090 relationship: has_quality SO:0000783 ! engineered
14091 created_by: kareneilbeck
14092 creation_date: 2010-05-28T02:05:25Z
14096 name: genetic_marker
14097 def: "A measurable sequence feature that varies within a population." [SO:db]
14098 synonym: "genetic marker" RELATED []
14099 is_a: SO:0001411 ! biological_region
14100 created_by: kareneilbeck
14101 creation_date: 2010-05-28T02:33:07Z
14106 def: "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]
14107 synonym: "DArT marker" EXACT []
14108 is_a: SO:0001645 ! genetic_marker
14109 created_by: kareneilbeck
14110 creation_date: 2010-05-28T02:34:43Z
14114 name: kozak_sequence
14115 def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]
14117 synonym: "kozak consensus" EXACT []
14118 synonym: "kozak consensus sequence" EXACT []
14119 synonym: "kozak sequence" EXACT []
14120 xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia"
14121 is_a: SO:0000139 ! ribosome_entry_site
14122 created_by: kareneilbeck
14123 creation_date: 2010-06-07T03:12:20Z
14127 name: nested_transposon
14128 def: "A transposon that is disrupted by the insertion of another element." [SO:ke]
14129 synonym: "nested transposon" EXACT []
14130 is_a: SO:0000101 ! transposable_element
14131 created_by: kareneilbeck
14132 creation_date: 2010-06-23T03:22:57Z
14136 name: nested_repeat
14137 def: "A repeat that is disrupted by the insertion of another element." [SO:ke]
14138 synonym: "nested repeat" RELATED []
14139 is_a: SO:0000657 ! repeat_region
14140 created_by: kareneilbeck
14141 creation_date: 2010-06-23T03:24:55Z
14145 name: inframe_variant
14146 def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]
14147 synonym: "ANNOVAR:nonframeshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
14148 synonym: "cds-indel" EXACT dbsnp []
14149 synonym: "inframe variant" EXACT []
14150 synonym: "VAAST:inframe_variant" EXACT VAR []
14151 is_a: SO:0001818 ! protein_altering_variant
14152 created_by: kareneilbeck
14153 creation_date: 2010-07-19T01:24:44Z
14157 name: retinoic_acid_responsive_element
14158 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]
14159 synonym: "RARE" EXACT []
14160 synonym: "retinoic acid responsive element" EXACT []
14161 is_a: SO:0000713 ! DNA_motif
14162 relationship: part_of SO:0000167 ! promoter
14163 created_by: kareneilbeck
14164 creation_date: 2010-08-03T10:46:12Z
14168 name: nucleotide_to_protein_binding_site
14169 def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
14171 synonym: "nucleotide to protein binding site" RELATED []
14172 is_a: SO:0000410 ! protein_binding_site
14173 created_by: kareneilbeck
14174 creation_date: 2010-08-03T12:26:05Z
14178 name: nucleotide_binding_site
14179 def: "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]
14180 comment: See GO:0000166 : nucleotide binding.
14181 synonym: "np_bind" EXACT BS [uniprot:feature]
14182 synonym: "nucleotide binding site" EXACT []
14183 is_a: SO:0000409 ! binding_site
14184 created_by: kareneilbeck
14185 creation_date: 2010-08-03T12:30:04Z
14189 name: metal_binding_site
14190 def: "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]
14191 comment: See GO:0046872 : metal ion binding.
14192 synonym: "metal binding site" RELATED []
14193 is_a: SO:0000409 ! binding_site
14194 created_by: kareneilbeck
14195 creation_date: 2010-08-03T12:31:42Z
14199 name: ligand_binding_site
14200 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]
14201 synonym: "ligand binding site" EXACT []
14202 is_a: SO:0000409 ! binding_site
14203 created_by: kareneilbeck
14204 creation_date: 2010-08-03T12:32:58Z
14208 name: nested_tandem_repeat
14209 def: "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]
14210 comment: Tracker ID: 3052459.
14211 synonym: "nested tandem repeat" EXACT []
14212 synonym: "NTR" EXACT []
14213 is_a: SO:0001649 ! nested_repeat
14214 created_by: kareneilbeck
14215 creation_date: 2010-08-26T09:36:16Z
14219 name: promoter_element
14220 synonym: "promoter element" EXACT []
14221 is_a: SO:0000713 ! DNA_motif
14222 relationship: overlaps SO:0000235 ! TF_binding_site
14223 created_by: kareneilbeck
14224 creation_date: 2010-10-01T11:48:32Z
14228 name: core_promoter_element
14229 synonym: "core promoter element" EXACT []
14230 synonym: "general transcription factor binding site" RELATED []
14231 is_a: SO:0001659 ! promoter_element
14232 created_by: kareneilbeck
14233 creation_date: 2010-10-01T11:49:03Z
14237 name: RNA_polymerase_II_TATA_box
14238 def: "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]
14239 synonym: "RNA polymerase II TATA box" EXACT []
14240 is_a: SO:0000174 ! TATA_box
14241 relationship: part_of SO:0001669 ! RNApol_II_core_promoter
14242 created_by: kareneilbeck
14243 creation_date: 2010-10-01T02:42:12Z
14247 name: RNA_polymerase_III_TATA_box
14248 def: "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]
14249 synonym: "RNA polymerase III TATA box" EXACT []
14250 is_a: SO:0000174 ! TATA_box
14251 relationship: part_of SO:0000171 ! RNApol_III_promoter
14252 created_by: kareneilbeck
14253 creation_date: 2010-10-01T02:43:16Z
14258 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]
14259 synonym: "BREd" EXACT []
14260 synonym: "BREd motif" RELATED []
14261 is_a: SO:0001660 ! core_promoter_element
14262 relationship: part_of SO:0001669 ! RNApol_II_core_promoter
14263 created_by: kareneilbeck
14264 creation_date: 2010-10-01T02:49:55Z
14269 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]
14270 synonym: "downstream core element" RELATED []
14271 is_a: SO:0001660 ! core_promoter_element
14272 relationship: part_of SO:0001669 ! RNApol_II_core_promoter
14273 created_by: kareneilbeck
14274 creation_date: 2010-10-01T02:56:41Z
14279 def: "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]
14280 synonym: "DCE SI" RELATED []
14281 is_a: SO:0000713 ! DNA_motif
14282 relationship: part_of SO:0001664 ! DCE
14283 created_by: kareneilbeck
14284 creation_date: 2010-10-01T03:00:10Z
14289 def: "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]
14290 synonym: "DCE SII" EXACT []
14291 is_a: SO:0000713 ! DNA_motif
14292 relationship: part_of SO:0001664 ! DCE
14293 created_by: kareneilbeck
14294 creation_date: 2010-10-01T03:00:30Z
14299 def: "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]
14300 synonym: "DCE SIII" EXACT []
14301 is_a: SO:0000713 ! DNA_motif
14302 relationship: part_of SO:0001664 ! DCE
14303 created_by: kareneilbeck
14304 creation_date: 2010-10-01T03:00:44Z
14308 name: proximal_promoter_element
14309 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]
14310 synonym: "proximal promoter element" RELATED []
14311 synonym: "specific transcription factor binding site" RELATED []
14312 is_a: SO:0001678 ! regulatory_promoter_element
14313 created_by: kareneilbeck
14314 creation_date: 2010-10-01T03:10:23Z
14318 name: RNApol_II_core_promoter
14319 def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]
14320 synonym: "RNApol II core promoter" EXACT []
14321 is_a: SO:0000170 ! RNApol_II_promoter
14322 created_by: kareneilbeck
14323 creation_date: 2010-10-01T03:13:41Z
14327 name: distal_promoter_element
14328 synonym: "distal promoter element" RELATED []
14329 is_a: SO:0001678 ! regulatory_promoter_element
14330 created_by: kareneilbeck
14331 creation_date: 2010-10-01T03:21:08Z
14335 name: bacterial_RNApol_promoter_sigma_70
14336 synonym: "bacterial RNA polymerase promoter sigma 70" EXACT []
14337 is_a: SO:0000613 ! bacterial_RNApol_promoter
14338 created_by: kareneilbeck
14339 creation_date: 2010-10-06T01:41:34Z
14343 name: bacterial_RNApol_promoter_sigma54
14344 synonym: "bacterial RNA polymerase promoter sigma54" EXACT []
14345 is_a: SO:0000613 ! bacterial_RNApol_promoter
14346 created_by: kareneilbeck
14347 creation_date: 2010-10-06T01:42:37Z
14351 name: minus_12_signal
14352 def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]
14353 synonym: "minus 12 signal" EXACT []
14354 is_a: SO:0000713 ! DNA_motif
14355 relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54
14356 created_by: kareneilbeck
14357 creation_date: 2010-10-06T01:44:57Z
14361 name: minus_24_signal
14362 def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]
14363 synonym: "minus 24 signal" RELATED []
14364 is_a: SO:0000713 ! DNA_motif
14365 relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54
14366 created_by: kareneilbeck
14367 creation_date: 2010-10-06T01:45:24Z
14372 def: "An A box within an RNA polymerase III type 1 promoter." [SO:ke]
14373 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.
14374 synonym: "A box type 1" RELATED []
14375 is_a: SO:0000619 ! A_box
14376 relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
14377 created_by: kareneilbeck
14378 creation_date: 2010-10-06T05:43:43Z
14383 def: "An A box within an RNA polymerase III type 2 promoter." [SO:ke]
14384 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.
14385 synonym: "A box type 2" RELATED []
14386 is_a: SO:0000619 ! A_box
14387 relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2
14388 created_by: kareneilbeck
14389 creation_date: 2010-10-06T05:44:18Z
14393 name: intermediate_element
14394 def: "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]
14395 synonym: "IE" EXACT []
14396 synonym: "intermediate element" RELATED []
14397 is_a: SO:0001660 ! core_promoter_element
14398 relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
14399 created_by: kareneilbeck
14400 creation_date: 2010-10-06T05:52:03Z
14404 name: regulatory_promoter_element
14405 def: "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]
14406 synonym: "regulatory promoter element" RELATED []
14407 is_a: SO:0001659 ! promoter_element
14408 created_by: kareneilbeck
14409 creation_date: 2010-10-07T04:39:48Z
14413 name: transcription_regulatory_region
14414 def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke]
14416 synonym: "transcription regulatory region" EXACT []
14417 is_a: SO:0005836 ! regulatory_region
14418 created_by: kareneilbeck
14419 creation_date: 2010-10-12T03:49:35Z
14423 name: translation_regulatory_region
14424 def: "A regulatory region that is involved in the control of the process of translation." [SO:ke]
14425 synonym: "translation regulatory region" EXACT []
14426 is_a: SO:0005836 ! regulatory_region
14427 created_by: kareneilbeck
14428 creation_date: 2010-10-12T03:52:45Z
14432 name: recombination_regulatory_region
14433 def: "A regulatory region that is involved in the control of the process of recombination." [SO:ke]
14434 synonym: "recombination regulatory region" EXACT []
14435 is_a: SO:0005836 ! regulatory_region
14436 created_by: kareneilbeck
14437 creation_date: 2010-10-12T03:53:35Z
14441 name: replication_regulatory_region
14442 def: "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]
14443 synonym: "replication regulatory region" RELATED []
14444 is_a: SO:0005836 ! regulatory_region
14445 created_by: kareneilbeck
14446 creation_date: 2010-10-12T03:54:09Z
14450 name: sequence_motif
14451 def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]
14453 synonym: "sequence motif" RELATED []
14454 xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia"
14455 is_a: SO:0001411 ! biological_region
14456 created_by: kareneilbeck
14457 creation_date: 2010-10-14T04:13:22Z
14461 name: experimental_feature_attribute
14462 def: "An attribute of an experimentally derived feature." [SO:ke]
14463 synonym: "experimental feature attribute" RELATED []
14464 is_a: SO:0000733 ! feature_attribute
14465 created_by: kareneilbeck
14466 creation_date: 2010-10-28T02:22:23Z
14471 def: "The score of an experimentally derived feature such as a p-value." [SO:ke]
14472 is_a: SO:0001684 ! experimental_feature_attribute
14473 created_by: kareneilbeck
14474 creation_date: 2010-10-28T02:23:16Z
14478 name: quality_value
14479 def: "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]
14480 synonym: "quality value" RELATED []
14481 is_a: SO:0001684 ! experimental_feature_attribute
14482 created_by: kareneilbeck
14483 creation_date: 2010-10-28T02:24:11Z
14487 name: restriction_enzyme_recognition_site
14488 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]
14489 synonym: "restriction endonuclease recognition site" EXACT []
14490 synonym: "restriction enzyme recognition site" EXACT []
14491 is_a: SO:0001954 ! restriction_enzyme_region
14492 created_by: kareneilbeck
14493 creation_date: 2010-10-29T12:29:57Z
14497 name: restriction_enzyme_cleavage_junction
14498 def: "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]
14499 synonym: "restriction enzyme cleavage junction" EXACT []
14500 is_a: SO:0000699 ! junction
14501 created_by: kareneilbeck
14502 creation_date: 2010-10-29T12:35:02Z
14506 name: five_prime_restriction_enzyme_junction
14507 def: "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]
14508 synonym: "5' restriction enzyme junction" EXACT []
14509 is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site
14510 relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
14511 created_by: kareneilbeck
14512 creation_date: 2010-10-29T12:36:24Z
14516 name: three_prime_restriction_enzyme_junction
14517 synonym: "3' restriction enzyme junction" EXACT []
14518 is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site
14519 relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
14520 created_by: kareneilbeck
14521 creation_date: 2010-10-29T12:37:52Z
14525 name: blunt_end_restriction_enzyme_cleavage_site
14526 synonym: "blunt end restriction enzyme cleavage site" EXACT []
14527 is_a: SO:0001687 ! restriction_enzyme_recognition_site
14528 created_by: kareneilbeck
14529 creation_date: 2010-10-29T12:39:53Z
14533 name: sticky_end_restriction_enzyme_cleavage_site
14534 synonym: "sticky end restriction enzyme cleavage site" RELATED []
14535 is_a: SO:0001687 ! restriction_enzyme_recognition_site
14536 created_by: kareneilbeck
14537 creation_date: 2010-10-29T12:40:50Z
14541 name: blunt_end_restriction_enzyme_cleavage_junction
14542 def: "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]
14543 synonym: "blunt end restriction enzyme cleavage site" RELATED []
14544 is_a: SO:0001688 ! restriction_enzyme_cleavage_junction
14545 relationship: part_of SO:0001691 ! blunt_end_restriction_enzyme_cleavage_site
14546 created_by: kareneilbeck
14547 creation_date: 2010-10-29T12:43:14Z
14551 name: single_strand_restriction_enzyme_cleavage_site
14552 def: "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]
14553 synonym: "single strand restriction enzyme cleavage site" RELATED []
14554 is_a: SO:0001688 ! restriction_enzyme_cleavage_junction
14555 created_by: kareneilbeck
14556 creation_date: 2010-10-29T12:44:48Z
14560 name: restriction_enzyme_single_strand_overhang
14561 def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]
14562 synonym: "single strand overhang" EXACT []
14563 synonym: "sticky end" RELATED []
14564 is_a: SO:0001954 ! restriction_enzyme_region
14565 relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
14566 created_by: kareneilbeck
14567 creation_date: 2010-10-29T12:48:35Z
14571 name: experimentally_defined_binding_region
14572 def: "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]
14573 synonym: "experimentally defined binding region" RELATED []
14574 is_a: SO:0001410 ! experimental_feature
14575 created_by: kareneilbeck
14576 creation_date: 2010-11-02T11:39:59Z
14580 name: ChIP_seq_region
14581 def: "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]
14582 synonym: "ChIP seq region" RELATED []
14583 is_a: SO:0001696 ! experimentally_defined_binding_region
14584 relationship: contains SO:0000410 ! protein_binding_site
14585 created_by: kareneilbeck
14586 creation_date: 2010-11-02T11:43:07Z
14591 def: "\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]
14592 synonym: "allele specific primer extension primer" EXACT []
14593 synonym: "ASPE primer" EXACT []
14594 is_a: SO:0000112 ! primer
14595 created_by: kareneilbeck
14596 creation_date: 2010-11-11T03:25:21Z
14601 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]
14602 synonym: "dCAPS primer" EXACT []
14603 synonym: "derived cleaved amplified polymorphic primer" EXACT []
14604 is_a: SO:0000112 ! primer
14605 created_by: kareneilbeck
14606 creation_date: 2010-11-11T03:27:09Z
14610 name: histone_modification
14611 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]
14612 synonym: "histone modification" EXACT []
14613 synonym: "histone modification site" RELATED []
14614 is_a: SO:0001089 ! post_translationally_modified_region
14615 is_a: SO:0001720 ! epigenetically_modified_region
14616 relationship: has_quality SO:0000133 ! epigenetically_modified
14617 created_by: kareneilbeck
14618 creation_date: 2010-03-31T10:22:08Z
14622 name: histone_methylation_site
14623 def: "A histone modification site where the modification is the methylation of the residue." [SO:ke]
14624 synonym: "histone methylation" EXACT []
14625 synonym: "histone methylation site" EXACT []
14626 is_a: SO:0001700 ! histone_modification
14627 created_by: kareneilbeck
14628 creation_date: 2010-03-31T10:23:02Z
14632 name: histone_acetylation_site
14633 def: "A histone modification where the modification is the acylation of the residue." [SO:ke]
14634 synonym: "histone acetylation" EXACT []
14635 synonym: "histone acetylation site" EXACT []
14636 is_a: SO:0001700 ! histone_modification
14637 created_by: kareneilbeck
14638 creation_date: 2010-03-31T10:23:27Z
14642 name: H3K9_acetylation_site
14643 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]
14644 synonym: "H3K9 acetylation site" EXACT []
14645 synonym: "H3K9Ac" RELATED []
14646 is_a: SO:0001973 ! histone_3_acetylation_site
14647 created_by: kareneilbeck
14648 creation_date: 2010-03-31T10:25:05Z
14652 name: H3K14_acetylation_site
14653 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]
14654 synonym: "H3K14 acetylation site" EXACT []
14655 synonym: "H3K14Ac" RELATED []
14656 is_a: SO:0001973 ! histone_3_acetylation_site
14657 created_by: kareneilbeck
14658 creation_date: 2010-03-31T10:25:53Z
14662 name: H3K4_monomethylation_site
14663 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]
14664 synonym: "H3K4 mono-methylation site" EXACT []
14665 synonym: "H3K4me1" RELATED []
14666 is_a: SO:0001734 ! H3K4_methylation_site
14667 created_by: kareneilbeck
14668 creation_date: 2010-03-31T10:28:14Z
14672 name: H3K4_trimethylation
14673 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]
14674 synonym: "H3K4 tri-methylation" EXACT []
14675 synonym: "H3K4me3" RELATED []
14676 is_a: SO:0001734 ! H3K4_methylation_site
14677 created_by: kareneilbeck
14678 creation_date: 2010-03-31T10:29:12Z
14682 name: H3K9_trimethylation_site
14683 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]
14684 synonym: "H3K9 tri-methylation site" EXACT []
14685 synonym: "H3K9Me3" RELATED []
14686 is_a: SO:0001736 ! H3K9_methylation_site
14687 created_by: kareneilbeck
14688 creation_date: 2010-03-31T10:30:34Z
14692 name: H3K27_monomethylation_site
14693 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]
14694 synonym: "H2K27 mono-methylation site" EXACT []
14695 synonym: "H2K27Me1" RELATED []
14696 is_a: SO:0001732 ! H3K27_methylation_site
14697 created_by: kareneilbeck
14698 creation_date: 2010-03-31T10:31:54Z
14702 name: H3K27_trimethylation_site
14703 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]
14704 synonym: "H3K27 tri-methylation site" EXACT []
14705 synonym: "H3K27Me3" RELATED []
14706 is_a: SO:0001732 ! H3K27_methylation_site
14707 created_by: kareneilbeck
14708 creation_date: 2010-03-31T10:32:41Z
14712 name: H3K79_monomethylation_site
14713 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]
14714 synonym: "H3K79 mono-methylation site" EXACT []
14715 synonym: "H3K79me1" RELATED []
14716 is_a: SO:0001735 ! H3K79_methylation_site
14717 created_by: kareneilbeck
14718 creation_date: 2010-03-31T10:33:42Z
14722 name: H3K79_dimethylation_site
14723 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]
14724 synonym: "H3K79 di-methylation site" EXACT []
14725 synonym: "H3K79Me2" RELATED []
14726 is_a: SO:0001735 ! H3K79_methylation_site
14727 created_by: kareneilbeck
14728 creation_date: 2010-03-31T10:34:39Z
14732 name: H3K79_trimethylation_site
14733 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]
14734 synonym: "H3K79 tri-methylation site" EXACT []
14735 synonym: "H3K79Me3" RELATED []
14736 is_a: SO:0001735 ! H3K79_methylation_site
14737 created_by: kareneilbeck
14738 creation_date: 2010-03-31T10:35:30Z
14742 name: H4K20_monomethylation_site
14743 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]
14744 synonym: "H4K20 mono-methylation site" EXACT []
14745 synonym: "H4K20Me1" RELATED []
14746 is_a: SO:0001701 ! histone_methylation_site
14747 created_by: kareneilbeck
14748 creation_date: 2010-03-31T10:36:43Z
14752 name: H2BK5_monomethylation_site
14753 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]
14754 synonym: "H2BK5 mono-methylation site" EXACT []
14755 is_a: SO:0001701 ! histone_methylation_site
14756 created_by: kareneilbeck
14757 creation_date: 2010-03-31T10:38:12Z
14762 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]
14763 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.
14764 synonym: "interferon stimulated response element" EXACT []
14765 is_a: SO:0001055 ! transcriptional_cis_regulatory_region
14766 created_by: kareneilbeck
14767 creation_date: 2010-04-05T11:15:08Z
14771 name: histone_ubiqitination_site
14772 def: "A histone modification site where ubiquitin may be added." [SO:ke]
14773 synonym: "histone ubiquitination site" RELATED []
14774 is_a: SO:0001700 ! histone_modification
14775 created_by: kareneilbeck
14776 creation_date: 2010-04-13T10:12:18Z
14780 name: H2B_ubiquitination_site
14781 def: "A histone modification site on H2B where ubiquitin may be added." [SO:ke]
14782 synonym: "H2BUbiq" RELATED []
14783 is_a: SO:0001716 ! histone_ubiqitination_site
14784 created_by: kareneilbeck
14785 creation_date: 2010-04-13T10:13:28Z
14789 name: H3K18_acetylation_site
14790 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]
14791 synonym: "H3K18 acetylation site" EXACT []
14792 synonym: "H3K18Ac" RELATED []
14793 is_a: SO:0001973 ! histone_3_acetylation_site
14794 created_by: kareneilbeck
14795 creation_date: 2010-04-13T10:39:35Z
14799 name: H3K23_acylation_site
14800 def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
14801 synonym: "H3K23 acylation site" RELATED []
14802 synonym: "H3K23Ac" RELATED []
14803 is_a: SO:0001973 ! histone_3_acetylation_site
14804 created_by: kareneilbeck
14805 creation_date: 2010-04-13T10:42:45Z
14809 name: epigenetically_modified_region
14810 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]
14812 synonym: "epigenetically modified region" RELATED []
14813 is_a: SO:0001411 ! biological_region
14814 relationship: has_quality SO:0000133 ! epigenetically_modified
14815 created_by: kareneilbeck
14816 creation_date: 2010-03-27T12:02:29Z
14820 name: H3K27_acylation_site
14821 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]
14822 synonym: "H3K27 acylation site" EXACT []
14823 synonym: "H3K27Ac" RELATED []
14824 is_a: SO:0001973 ! histone_3_acetylation_site
14825 created_by: kareneilbeck
14826 creation_date: 2010-04-13T10:44:09Z
14830 name: H3K36_monomethylation_site
14831 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]
14832 synonym: "H3K36 mono-methylation site" EXACT []
14833 synonym: "H3K36<Me1" RELATED []
14834 is_a: SO:0001733 ! H3K36_methylation_site
14835 created_by: kareneilbeck
14836 creation_date: 2010-04-13T10:46:32Z
14840 name: H3K36_dimethylation_site
14841 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]
14842 synonym: "H3K36 di-methylation site" EXACT []
14843 synonym: "H3K36Me2" RELATED []
14844 is_a: SO:0001733 ! H3K36_methylation_site
14845 created_by: kareneilbeck
14846 creation_date: 2010-04-13T10:59:35Z
14850 name: H3K36_trimethylation_site
14851 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]
14852 synonym: "H3K36 tri-methylation site" EXACT []
14853 synonym: "H3K36Me3" RELATED []
14854 is_a: SO:0001733 ! H3K36_methylation_site
14855 created_by: kareneilbeck
14856 creation_date: 2010-04-13T11:01:58Z
14860 name: H3K4_dimethylation_site
14861 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]
14862 synonym: "H3K4 di-methylation site" EXACT []
14863 synonym: "H3K4Me2" RELATED []
14864 is_a: SO:0001734 ! H3K4_methylation_site
14865 created_by: kareneilbeck
14866 creation_date: 2010-04-13T11:03:15Z
14870 name: H3K27_dimethylation_site
14871 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]
14872 synonym: "H3K27 di-methylation site" EXACT []
14873 synonym: "H3K27Me2" RELATED []
14874 is_a: SO:0001732 ! H3K27_methylation_site
14875 created_by: kareneilbeck
14876 creation_date: 2010-04-13T01:45:41Z
14880 name: H3K9_monomethylation_site
14881 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]
14882 synonym: "H3K9 mono-methylation site" EXACT []
14883 synonym: "H3K9Me1" RELATED []
14884 is_a: SO:0001736 ! H3K9_methylation_site
14885 created_by: kareneilbeck
14886 creation_date: 2010-04-13T11:06:17Z
14890 name: H3K9_dimethylation_site
14891 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]
14892 synonym: "H3K9 di-methylation site" EXACT []
14893 synonym: "H3K9Me2" RELATED []
14894 is_a: SO:0001736 ! H3K9_methylation_site
14895 created_by: kareneilbeck
14896 creation_date: 2010-04-13T11:08:19Z
14900 name: H4K16_acylation_site
14901 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]
14902 synonym: "H4K16 acylation_site" RELATED []
14903 synonym: "H4K16Ac" RELATED []
14904 is_a: SO:0001972 ! histone_4_acylation_site
14905 created_by: kareneilbeck
14906 creation_date: 2010-04-13T11:09:41Z
14910 name: H4K5_acylation_site
14911 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]
14912 synonym: "H4K5 acylation site" RELATED []
14913 synonym: "H4K5Ac" RELATED []
14914 is_a: SO:0001972 ! histone_4_acylation_site
14915 created_by: kareneilbeck
14916 creation_date: 2010-04-13T11:13:00Z
14920 name: H4K8_acylation_site
14921 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]
14922 synonym: "H4K8 acylation site" RELATED []
14923 synonym: "H4K8Ac" RELATED []
14924 is_a: SO:0001972 ! histone_4_acylation_site
14925 created_by: kareneilbeck
14926 creation_date: 2010-04-13T11:14:24Z
14930 name: H3K27_methylation_site
14931 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]
14932 synonym: "H3K27 methylation site" EXACT []
14933 is_a: SO:0001701 ! histone_methylation_site
14934 created_by: kareneilbeck
14935 creation_date: 2010-04-13T11:26:22Z
14939 name: H3K36_methylation_site
14940 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]
14941 synonym: "H3K36 methylation site" EXACT []
14942 is_a: SO:0001701 ! histone_methylation_site
14943 created_by: kareneilbeck
14944 creation_date: 2010-04-13T11:27:28Z
14948 name: H3K4_methylation_site
14949 def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]
14950 synonym: "H3K4 methylation site" EXACT []
14951 is_a: SO:0001701 ! histone_methylation_site
14952 created_by: kareneilbeck
14953 creation_date: 2010-04-13T11:28:14Z
14957 name: H3K79_methylation_site
14958 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]
14959 synonym: "H3K79 methylation site" EXACT []
14960 is_a: SO:0001701 ! histone_methylation_site
14961 created_by: kareneilbeck
14962 creation_date: 2010-04-13T11:29:16Z
14966 name: H3K9_methylation_site
14967 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]
14968 synonym: "H3K9 methylation site" EXACT []
14969 is_a: SO:0001701 ! histone_methylation_site
14970 created_by: kareneilbeck
14971 creation_date: 2010-04-13T11:31:37Z
14975 name: histone_acylation_region
14976 def: "A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]
14977 synonym: "histone acylation region" RELATED []
14978 is_a: SO:0001700 ! histone_modification
14979 created_by: kareneilbeck
14980 creation_date: 2010-04-13T01:58:21Z
14984 name: H4K_acylation_region
14985 def: "A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]
14986 synonym: "H4K acylation region" EXACT []
14987 synonym: "H4KAc" RELATED []
14988 is_a: SO:0001737 ! histone_acylation_region
14989 created_by: kareneilbeck
14990 creation_date: 2010-04-13T02:00:06Z
14994 name: gene_with_non_canonical_start_codon
14995 def: "A gene with a start codon other than AUG." [SO:xp]
14996 comment: Requested by flybase, Dec 2010.
14997 synonym: "gene with non canonical start codon" EXACT []
14998 is_a: SO:0000704 ! gene
14999 relationship: contains SO:0000680 ! non_canonical_start_codon
15000 created_by: kareneilbeck
15001 creation_date: 2011-01-10T01:30:31Z
15005 name: gene_with_start_codon_CUG
15006 def: "A gene with a translational start codon of CUG." [SO:mc]
15007 comment: Requested by flybase, Dec 2010.
15008 synonym: "gene with start codon CUG" EXACT []
15009 is_a: SO:0001739 ! gene_with_non_canonical_start_codon
15010 created_by: kareneilbeck
15011 creation_date: 2011-01-10T01:32:35Z
15015 name: pseudogenic_gene_segment
15016 def: "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]
15017 synonym: "pseudogenic gene segment" EXACT []
15018 is_a: SO:3000000 ! gene_segment
15019 created_by: batchelorc
15020 creation_date: 2011-02-15T05:07:52Z
15024 name: copy_number_gain
15025 def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]
15027 synonym: "copy number gain" EXACT []
15028 synonym: "gain" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
15029 is_a: SO:0001019 ! copy_number_variation
15030 created_by: kareneilbeck
15031 creation_date: 2011-02-28T01:54:09Z
15035 name: copy_number_loss
15036 def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]
15038 synonym: "copy number loss" EXACT []
15039 synonym: "loss" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
15040 is_a: SO:0001019 ! copy_number_variation
15041 created_by: kareneilbeck
15042 creation_date: 2011-02-28T01:55:02Z
15047 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]
15049 synonym: "uniparental disomy" EXACT []
15050 synonym: "UPD" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
15051 xref: http:http://en.wikipedia.org/wiki/Uniparental_disomy "wikipedia"
15052 is_a: SO:0001059 ! sequence_alteration
15053 created_by: kareneilbeck
15054 creation_date: 2011-02-28T02:01:05Z
15058 name: maternal_uniparental_disomy
15059 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]
15060 synonym: "maternal uniparental disomy" EXACT []
15061 is_a: SO:0001744 ! UPD
15062 created_by: kareneilbeck
15063 creation_date: 2011-02-28T02:03:01Z
15067 name: paternal_uniparental_disomy
15068 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]
15069 synonym: "paternal uniparental disomy" EXACT []
15070 is_a: SO:0001744 ! UPD
15071 created_by: kareneilbeck
15072 creation_date: 2011-02-28T02:03:30Z
15076 name: open_chromatin_region
15077 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]
15078 comment: Requested by John Calley 3125900.
15079 synonym: "open chromatin region" EXACT []
15080 is_a: SO:0001411 ! biological_region
15081 created_by: kareneilbeck
15082 creation_date: 2011-02-28T02:21:52Z
15086 name: SL3_acceptor_site
15087 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]
15088 synonym: "SL3 acceptor site" EXACT []
15089 is_a: SO:0000709 ! SL2_acceptor_site
15090 created_by: kareneilbeck
15091 creation_date: 2011-02-28T02:58:40Z
15095 name: SL4_acceptor_site
15096 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]
15097 synonym: "SL4 acceptor site" EXACT []
15098 is_a: SO:0000709 ! SL2_acceptor_site
15099 created_by: kareneilbeck
15100 creation_date: 2011-02-28T03:08:47Z
15104 name: SL5_acceptor_site
15105 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]
15106 synonym: "SL5 acceptor site" EXACT []
15107 is_a: SO:0000709 ! SL2_acceptor_site
15108 created_by: kareneilbeck
15109 creation_date: 2011-02-28T03:09:36Z
15113 name: SL6_acceptor_site
15114 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]
15115 synonym: "SL6 acceptor site" EXACT []
15116 is_a: SO:0000709 ! SL2_acceptor_site
15117 created_by: kareneilbeck
15118 creation_date: 2011-02-28T03:10:14Z
15122 name: SL7_acceptor_site
15123 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]
15124 synonym: "SL37 acceptor site" EXACT []
15125 is_a: SO:0000709 ! SL2_acceptor_site
15126 created_by: kareneilbeck
15127 creation_date: 2011-02-28T03:13:20Z
15131 name: SL8_acceptor_site
15132 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]
15133 synonym: "SL8 acceptor site" EXACT []
15134 is_a: SO:0000709 ! SL2_acceptor_site
15135 created_by: kareneilbeck
15136 creation_date: 2011-02-28T03:15:26Z
15140 name: SL9_acceptor_site
15141 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]
15142 synonym: "SL9 acceptor site" EXACT []
15143 is_a: SO:0000709 ! SL2_acceptor_site
15144 created_by: kareneilbeck
15145 creation_date: 2011-02-28T03:15:57Z
15149 name: SL10_acceptor_site
15150 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]
15151 synonym: "SL10 acceptor site" EXACT []
15152 is_a: SO:0000709 ! SL2_acceptor_site
15153 created_by: kareneilbeck
15154 creation_date: 2011-02-28T03:16:31Z
15158 name: SL11_acceptor_site
15159 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]
15160 synonym: "SL11 acceptor site" EXACT []
15161 is_a: SO:0000709 ! SL2_acceptor_site
15162 created_by: kareneilbeck
15163 creation_date: 2011-02-28T03:16:54Z
15167 name: SL12_acceptor_site
15168 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]
15169 synonym: "SL12 acceptor site" EXACT []
15170 is_a: SO:0000709 ! SL2_acceptor_site
15171 created_by: kareneilbeck
15172 creation_date: 2011-02-28T03:17:23Z
15176 name: duplicated_pseudogene
15177 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]
15178 synonym: "duplicated pseudogene" RELATED []
15179 is_a: SO:0001760 ! non_processed_pseudogene
15180 created_by: kareneilbeck
15181 creation_date: 2011-03-09T09:58:04Z
15185 name: unitary_pseudogene
15186 def: "A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]
15187 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.
15188 synonym: "disabled gene" RELATED []
15189 synonym: "unitary pseudogene" RELATED []
15190 is_a: SO:0001760 ! non_processed_pseudogene
15191 created_by: kareneilbeck
15192 creation_date: 2011-03-09T10:04:04Z
15196 name: non_processed_pseudogene
15197 def: "A pseudogene that arose from a means other than retrotransposition." [SO:ke]
15198 synonym: "non processed pseudogene" RELATED []
15199 is_a: SO:0000336 ! pseudogene
15200 created_by: kareneilbeck
15201 creation_date: 2011-03-09T10:54:47Z
15205 name: variant_quality
15206 def: "A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]
15207 synonym: "variant quality" EXACT []
15208 is_a: SO:0000400 ! sequence_attribute
15209 created_by: kareneilbeck
15210 creation_date: 2011-03-15T03:40:35Z
15214 name: variant_origin
15215 def: "A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]
15216 synonym: "variant origin" EXACT []
15217 is_a: SO:0001761 ! variant_quality
15218 created_by: kareneilbeck
15219 creation_date: 2011-03-15T03:42:13Z
15223 name: variant_frequency
15224 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]
15225 synonym: "variant frequency" EXACT []
15226 is_a: SO:0001761 ! variant_quality
15227 created_by: kareneilbeck
15228 creation_date: 2011-03-15T03:44:39Z
15232 name: unique_variant
15233 def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]
15234 synonym: "unique variant" EXACT []
15235 is_a: SO:0001763 ! variant_frequency
15236 created_by: kareneilbeck
15237 creation_date: 2011-03-15T03:47:20Z
15242 synonym: "rare variant" EXACT []
15243 is_a: SO:0001763 ! variant_frequency
15244 created_by: kareneilbeck
15245 creation_date: 2011-03-15T03:48:29Z
15249 name: polymorphic_variant
15250 synonym: "polymorphic variant" EXACT []
15251 is_a: SO:0001763 ! variant_frequency
15252 created_by: kareneilbeck
15253 creation_date: 2011-03-15T03:48:51Z
15257 name: common_variant
15258 synonym: "common variant" EXACT []
15259 is_a: SO:0001763 ! variant_frequency
15260 created_by: kareneilbeck
15261 creation_date: 2011-03-15T03:50:36Z
15265 name: fixed_variant
15266 synonym: "fixed variant" EXACT []
15267 is_a: SO:0001763 ! variant_frequency
15268 created_by: kareneilbeck
15269 creation_date: 2011-03-15T03:50:53Z
15273 name: variant_phenotype
15274 def: "A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]
15275 synonym: "variant phenotype" EXACT []
15276 is_a: SO:0001761 ! variant_quality
15277 created_by: kareneilbeck
15278 creation_date: 2011-03-15T03:53:15Z
15282 name: benign_variant
15283 synonym: "benign variant" EXACT []
15284 is_a: SO:0001769 ! variant_phenotype
15285 created_by: kareneilbeck
15286 creation_date: 2011-03-15T03:55:40Z
15290 name: disease_associated_variant
15291 synonym: "disease associated variant" EXACT []
15292 is_a: SO:0001769 ! variant_phenotype
15293 created_by: kareneilbeck
15294 creation_date: 2011-03-15T04:05:16Z
15298 name: disease_causing_variant
15299 synonym: "disease causing variant" EXACT []
15300 is_a: SO:0001769 ! variant_phenotype
15301 created_by: kareneilbeck
15302 creation_date: 2011-03-15T04:05:46Z
15306 name: lethal_variant
15307 synonym: "lethal variant" EXACT []
15308 is_a: SO:0001536 ! functional_variant
15309 created_by: kareneilbeck
15310 creation_date: 2011-03-15T04:06:22Z
15314 name: quantitative_variant
15315 synonym: "quantitative variant" EXACT []
15316 is_a: SO:0001769 ! variant_phenotype
15317 created_by: kareneilbeck
15318 creation_date: 2011-03-15T04:28:13Z
15322 name: maternal_variant
15323 synonym: "maternal variant" EXACT []
15324 is_a: SO:0001762 ! variant_origin
15325 created_by: kareneilbeck
15326 creation_date: 2011-03-15T04:30:23Z
15330 name: paternal_variant
15331 synonym: "paternal variant" EXACT []
15332 is_a: SO:0001762 ! variant_origin
15333 created_by: kareneilbeck
15334 creation_date: 2011-03-15T04:30:47Z
15338 name: somatic_variant
15339 synonym: "somatic variant" EXACT []
15340 is_a: SO:0001762 ! variant_origin
15341 created_by: kareneilbeck
15342 creation_date: 2011-03-15T04:31:12Z
15346 name: germline_variant
15347 synonym: "germline variant" EXACT []
15348 is_a: SO:0001762 ! variant_origin
15349 created_by: kareneilbeck
15350 creation_date: 2011-03-15T04:31:46Z
15354 name: pedigree_specific_variant
15355 synonym: "pedigree specific variant" EXACT []
15356 is_a: SO:0001762 ! variant_origin
15357 created_by: kareneilbeck
15358 creation_date: 2011-03-15T04:32:18Z
15362 name: population_specific_variant
15363 synonym: "population specific variant" EXACT []
15364 is_a: SO:0001762 ! variant_origin
15365 created_by: kareneilbeck
15366 creation_date: 2011-03-15T04:33:05Z
15370 name: de_novo_variant
15371 synonym: "de novo variant" EXACT []
15372 is_a: SO:0001762 ! variant_origin
15373 created_by: kareneilbeck
15374 creation_date: 2011-03-15T04:33:34Z
15378 name: TF_binding_site_variant
15379 def: "A sequence variant located within a transcription factor binding site." [EBI:fc]
15380 synonym: "TF binding site variant" EXACT []
15381 is_a: SO:0001566 ! regulatory_region_variant
15382 created_by: kareneilbeck
15383 creation_date: 2011-03-17T10:59:20Z
15387 name: complex_structural_alteration
15389 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]
15391 synonym: "complex" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
15392 synonym: "complex chromosomal mutation" EXACT []
15393 synonym: "complex_chromosomal_mutation" EXACT []
15394 is_a: SO:0001785 ! structural_alteration
15395 is_a: SO:1000183 ! chromosome_structure_variation
15396 created_by: kareneilbeck
15397 creation_date: 2011-03-23T03:21:19Z
15401 name: structural_alteration
15403 synonym: "structural alteration" EXACT []
15404 is_a: SO:0001059 ! sequence_alteration
15405 created_by: kareneilbeck
15406 creation_date: 2011-03-25T02:27:41Z
15410 name: loss_of_heterozygosity
15411 def: "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke]
15413 synonym: "LOH" EXACT []
15414 synonym: "loss of heterozygosity" EXACT []
15415 is_a: SO:0001536 ! functional_variant
15416 created_by: kareneilbeck
15417 creation_date: 2011-03-25T02:32:58Z
15421 name: splice_donor_5th_base_variant
15422 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]
15423 synonym: "splice donor 5th base variant" EXACT []
15424 is_a: SO:0001629 ! splice_site_variant
15425 created_by: kareneilbeck
15426 creation_date: 2011-04-05T04:16:28Z
15431 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]
15432 synonym: "U-box" EXACT []
15433 is_a: SO:0000330 ! conserved_region
15434 relationship: part_of SO:0000186 ! LTR_retrotransposon
15435 created_by: kareneilbeck
15436 creation_date: 2011-04-08T10:39:14Z
15440 name: mating_type_region
15441 def: "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]
15442 synonym: "mating type region" EXACT []
15443 xref: http://en.wikipedia.org/wiki/Mating-type_region
15444 is_a: SO:0005855 ! gene_group
15445 created_by: kareneilbeck
15446 creation_date: 2011-04-08T11:14:07Z
15450 name: paired_end_fragment
15451 def: "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]
15453 synonym: "paired end fragment" EXACT []
15454 is_a: SO:0000143 ! assembly_component
15455 created_by: kareneilbeck
15456 creation_date: 2011-04-14T01:48:20Z
15461 def: "A sequence variant that changes exon sequence." [SO:ke]
15462 synonym: "ANNOVAR:exonic" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
15463 synonym: "exon variant" EXACT []
15464 synonym: "snpEff:EXON" EXACT VAR []
15465 synonym: "VAAST:exon_variant" EXACT VAR []
15466 is_a: SO:0001576 ! transcript_variant
15467 created_by: kareneilbeck
15468 creation_date: 2011-05-06T01:51:17Z
15472 name: non_coding_transcript_exon_variant
15473 def: "A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]
15474 synonym: "non coding transcript exon variant" EXACT []
15475 is_a: SO:0001619 ! non_coding_transcript_variant
15476 is_a: SO:0001791 ! exon_variant
15477 created_by: kareneilbeck
15478 creation_date: 2011-05-06T01:51:59Z
15483 def: "A read from an end of the clone sequence." [SO:ke]
15484 synonym: "clone end" EXACT []
15485 is_a: SO:0000150 ! read
15486 relationship: part_of SO:0000151 ! clone
15487 created_by: kareneilbeck
15488 creation_date: 2011-05-13T11:32:27Z
15492 name: point_centromere
15493 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]
15494 synonym: "point centromere" EXACT []
15495 is_a: SO:0000577 ! centromere
15496 created_by: kareneilbeck
15497 creation_date: 2011-05-31T12:42:35Z
15501 name: regional_centromere
15502 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]
15503 synonym: "regional centromere" EXACT []
15504 is_a: SO:0000577 ! centromere
15505 created_by: kareneilbeck
15506 creation_date: 2011-05-31T12:43:07Z
15510 name: regional_centromere_central_core
15511 def: "A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]
15512 synonym: "regional centromere central core" EXACT []
15513 is_a: SO:0000330 ! conserved_region
15514 relationship: part_of SO:0001795 ! regional_centromere
15515 created_by: kareneilbeck
15516 creation_date: 2011-05-31T12:56:30Z
15520 name: centromeric_repeat
15521 def: "A repeat region found within the modular centromere." [SO:ke]
15522 synonym: "centromeric repeat" EXACT []
15523 is_a: SO:0000657 ! repeat_region
15524 created_by: kareneilbeck
15525 creation_date: 2011-05-31T12:59:27Z
15529 name: regional_centromere_inner_repeat_region
15530 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]
15531 synonym: "lmr repeat" EXACT []
15532 synonym: "lmr1L" EXACT []
15533 synonym: "lmr1R" EXACT []
15534 synonym: "regional centromere inner repeat region" EXACT []
15535 is_a: SO:0001797 ! centromeric_repeat
15536 relationship: part_of SO:0001796 ! regional_centromere_central_core
15537 created_by: kareneilbeck
15538 creation_date: 2011-05-31T01:01:08Z
15542 name: regional_centromere_outer_repeat_region
15543 def: "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]
15544 synonym: "regional centromere outer repeat region" EXACT []
15545 is_a: SO:0001797 ! centromeric_repeat
15546 relationship: part_of SO:0001795 ! regional_centromere
15547 created_by: kareneilbeck
15548 creation_date: 2011-05-31T01:03:23Z
15553 def: "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]
15554 synonym: "trans acting small interfering RNA" RELATED []
15555 is_a: SO:0000655 ! ncRNA
15556 relationship: derives_from SO:0001801 ! tasiRNA_primary_transcript
15557 created_by: kareneilbeck
15558 creation_date: 2011-05-31T03:24:06Z
15562 name: tasiRNA_primary_transcript
15563 def: "A primary transcript encoding a tasiRNA." [PMID:16145017]
15564 synonym: "tasiRNA primary transcript" EXACT []
15565 is_a: SO:0000483 ! nc_primary_transcript
15566 created_by: kareneilbeck
15567 creation_date: 2011-05-31T03:27:35Z
15571 name: increased_polyadenylation_variant
15572 def: "A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]
15573 comment: Term requested by M. Dumontier, June 1 2011.
15574 synonym: "increased polyadenylation variant" EXACT []
15575 is_a: SO:0001545 ! polyadenylation_variant
15576 created_by: kareneilbeck
15577 creation_date: 2011-06-01T10:53:12Z
15581 name: decreased_polyadenylation_variant
15582 def: "A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]
15583 comment: Term requested by M. Dumontier, June 1 2011.
15584 synonym: "decreased polyadenylation variant" EXACT []
15585 is_a: SO:0001545 ! polyadenylation_variant
15586 created_by: kareneilbeck
15587 creation_date: 2011-06-01T10:53:40Z
15592 def: "A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]
15593 comment: Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence.
15594 synonym: "DDB box" EXACT []
15595 synonym: "DDB-box" EXACT []
15596 is_a: SO:0001093 ! protein_protein_contact
15597 created_by: kareneilbeck
15598 creation_date: 2011-06-17T12:10:44Z
15602 name: destruction_box
15603 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]
15604 synonym: "D-box" EXACT []
15605 synonym: "destruction box" EXACT []
15606 is_a: SO:0100017 ! polypeptide_conserved_motif
15607 created_by: kareneilbeck
15608 creation_date: 2011-06-17T12:16:02Z
15612 name: ER_retention_signal
15613 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]
15614 synonym: "endoplasmic reticulum retention signal" EXACT []
15615 synonym: "ER retention signal" EXACT []
15616 is_a: SO:0001527 ! peptide_localization_signal
15617 created_by: kareneilbeck
15618 creation_date: 2011-06-17T12:19:49Z
15623 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]
15624 synonym: "KEN box" EXACT []
15625 is_a: SO:0100017 ! polypeptide_conserved_motif
15626 created_by: kareneilbeck
15627 creation_date: 2011-06-17T12:24:14Z
15631 name: mitochondrial_targeting_signal
15632 def: "A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]
15633 synonym: "mitochondrial signal sequence" EXACT []
15634 synonym: "mitochondrial targeting signal" EXACT []
15635 synonym: "MTS" EXACT []
15636 is_a: SO:0001527 ! peptide_localization_signal
15637 created_by: kareneilbeck
15638 creation_date: 2011-06-17T12:26:35Z
15642 name: signal_anchor
15643 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]
15644 synonym: "signal anchor" EXACT []
15645 synonym: "uncleaved signal peptide" EXACT []
15646 is_a: SO:0000418 ! signal_peptide
15647 created_by: kareneilbeck
15648 creation_date: 2011-06-17T12:28:53Z
15653 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]
15654 synonym: "PIP box" EXACT []
15655 is_a: SO:0001093 ! protein_protein_contact
15656 created_by: kareneilbeck
15657 creation_date: 2011-06-17T12:33:25Z
15661 name: phosphorylation_site
15662 def: "A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]
15663 synonym: "phosphorylation site" EXACT []
15664 is_a: SO:0001089 ! post_translationally_modified_region
15665 created_by: kareneilbeck
15666 creation_date: 2011-06-17T12:36:20Z
15670 name: transmembrane_helix
15671 def: "A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]
15672 synonym: "transmembrane helix" EXACT []
15673 is_a: SO:0001114 ! peptide_helix
15674 relationship: part_of SO:0001077 ! transmembrane_polypeptide_region
15675 created_by: kareneilbeck
15676 creation_date: 2011-06-17T12:39:46Z
15680 name: vacuolar_sorting_signal
15681 def: "A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]
15682 synonym: "vacuolar sorting signal" EXACT []
15683 is_a: SO:0001527 ! peptide_localization_signal
15684 created_by: kareneilbeck
15685 creation_date: 2011-06-17T12:42:48Z
15689 name: coding_variant_quality
15690 synonym: "coding variant quality" EXACT []
15691 is_a: SO:0001761 ! variant_quality
15692 created_by: kareneilbeck
15693 creation_date: 2011-06-24T03:32:25Z
15698 is_a: SO:0001814 ! coding_variant_quality
15699 created_by: kareneilbeck
15700 creation_date: 2011-06-24T03:33:16Z
15704 name: non_synonymous
15705 synonym: "non synonymous" RELATED []
15706 is_a: SO:0001814 ! coding_variant_quality
15707 created_by: kareneilbeck
15708 creation_date: 2011-06-24T03:33:36Z
15713 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]
15714 is_a: SO:0000863 ! mRNA_attribute
15715 created_by: kareneilbeck
15716 creation_date: 2011-06-24T03:34:03Z
15720 name: protein_altering_variant
15721 def: "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]
15722 synonym: "protein altering variant" EXACT []
15723 is_a: SO:0001580 ! coding_sequence_variant
15724 created_by: kareneilbeck
15725 creation_date: 2011-06-24T03:38:02Z
15729 name: synonymous_variant
15731 def: "A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]
15732 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.
15733 synonym: "ANNOVAR:synonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
15734 synonym: "coding-synon" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
15735 synonym: "silent mutation" RELATED []
15736 synonym: "silent substitution" RELATED []
15737 synonym: "silent_mutation" RELATED []
15738 synonym: "snpEff:SYNONYMOUS_CODING" EXACT VAR []
15739 synonym: "synonymous codon" EXACT []
15740 synonym: "synonymous_coding" EXACT []
15741 synonym: "synonymous_codon" EXACT []
15742 synonym: "VAAST:synonymous_codon" EXACT VAR []
15743 xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
15744 xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
15745 xref: http://en.wikipedia.org/wiki/Synonymous_mutation
15746 is_a: SO:0001580 ! coding_sequence_variant
15747 created_by: kareneilbeck
15748 creation_date: 2011-06-24T03:38:30Z
15752 name: inframe_indel
15753 def: "A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]
15754 synonym: "inframe change in CDS length" EXACT []
15755 synonym: "inframe indel" EXACT []
15756 is_a: SO:0001650 ! inframe_variant
15757 created_by: kareneilbeck
15758 creation_date: 2011-06-27T11:25:33Z
15762 name: inframe_insertion
15764 def: "An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]
15765 synonym: "ANNOVAR:nonframeshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
15766 synonym: "inframe codon gain" RELATED []
15767 synonym: "inframe increase in CDS length" EXACT []
15768 synonym: "inframe insertion" EXACT []
15769 synonym: "inframe_codon_gain" EXACT []
15770 synonym: "snpEFF:CODON_INSERTION" EXACT VAR []
15771 is_a: SO:0001820 ! inframe_indel
15772 is_a: SO:0001908 ! internal_feature_elongation
15773 created_by: kareneilbeck
15774 creation_date: 2011-06-27T11:26:22Z
15778 name: inframe_deletion
15780 def: "An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]
15781 synonym: "ANNOVAR:nonframeshift deletion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
15782 synonym: "inframe codon loss" RELATED []
15783 synonym: "inframe decrease in CDS length" EXACT []
15784 synonym: "inframe deletion" RELATED []
15785 synonym: "inframe_codon_loss" EXACT []
15786 synonym: "snpEff:CODON_DELETION" RELATED VAR []
15787 is_a: SO:0001820 ! inframe_indel
15788 is_a: SO:0001906 ! feature_truncation
15789 created_by: kareneilbeck
15790 creation_date: 2011-06-27T11:27:10Z
15794 name: conservative_inframe_insertion
15795 def: "An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]
15796 synonym: "conservative increase in CDS length" EXACT []
15797 synonym: "conservative inframe insertion" EXACT []
15798 is_a: SO:0001821 ! inframe_insertion
15799 created_by: kareneilbeck
15800 creation_date: 2011-06-27T11:28:02Z
15804 name: disruptive_inframe_insertion
15805 def: "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]
15806 synonym: "disruptive increase in CDS length" EXACT []
15807 synonym: "disruptive inframe insertion" EXACT []
15808 synonym: "snpEff:CODON_CHANGE_PLUS_CODON_INSERTION" EXACT VAR []
15809 is_a: SO:0001821 ! inframe_insertion
15810 created_by: kareneilbeck
15811 creation_date: 2011-06-27T11:28:37Z
15815 name: conservative_inframe_deletion
15816 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]
15817 synonym: "conservative decrease in CDS length" RELATED []
15818 synonym: "conservative inframe deletion" EXACT []
15819 is_a: SO:0001822 ! inframe_deletion
15820 created_by: kareneilbeck
15821 creation_date: 2011-06-27T11:30:43Z
15825 name: disruptive_inframe_deletion
15826 def: "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]
15827 synonym: "disruptive decrease in CDS length" EXACT []
15828 synonym: "disruptive inframe deletion" EXACT []
15829 synonym: "snpEff:CODON_CHANGE_PLUS_CODON_DELETION" EXACT VAR []
15830 is_a: SO:0001822 ! inframe_deletion
15831 created_by: kareneilbeck
15832 creation_date: 2011-06-27T11:31:31Z
15837 def: "A sequencer read of an mRNA substrate." [SO:ke]
15838 comment: Requested by Bayer Cropscience June, 2011.
15839 synonym: "mRNA read" EXACT []
15840 is_a: SO:0000150 ! read
15841 created_by: kareneilbeck
15842 creation_date: 2011-06-28T04:04:32Z
15846 name: genomic_DNA_read
15847 def: "A sequencer read of a genomic DNA substrate." [SO:ke]
15848 synonym: "genomic DNA read" EXACT []
15849 is_a: SO:0000150 ! read
15850 created_by: kareneilbeck
15851 creation_date: 2011-06-28T04:06:10Z
15856 def: "A contig composed of mRNA_reads." [SO:ke]
15857 comment: Requested by Bayer Cropscience June, 2011.
15858 synonym: "mRNA contig" RELATED []
15859 is_a: SO:0000149 ! contig
15860 created_by: kareneilbeck
15861 creation_date: 2011-06-28T04:07:09Z
15865 name: AFLP_fragment
15866 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]
15867 comment: Requested by Bayer Cropscience June, 2011.
15868 synonym: "AFLP" EXACT []
15869 synonym: "AFLP fragment" EXACT []
15870 synonym: "AFLP-PCR" EXACT []
15871 synonym: "amplified fragment length polymorphism" EXACT []
15872 synonym: "amplified fragment length polymorphism PCR" EXACT []
15873 xref: http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism "wiki"
15874 is_a: SO:0000006 ! PCR_product
15875 created_by: kareneilbeck
15876 creation_date: 2011-07-14T12:12:35Z
15880 name: protein_hmm_match
15881 def: "A match to a protein HMM such as pfam." [SO:ke]
15882 synonym: "protein hmm match" EXACT []
15883 is_a: SO:0000349 ! protein_match
15884 created_by: kareneilbeck
15885 creation_date: 2011-08-11T03:20:27Z
15889 name: immunoglobulin_region
15890 def: "A region of immunoglobulin sequence, either constant or variable." [SO:ke]
15891 synonym: "immunoglobulin region" EXACT []
15892 is_a: SO:0000839 ! polypeptide_region
15893 created_by: kareneilbeck
15894 creation_date: 2011-09-01T03:27:20Z
15899 def: "The variable region of an immunoglobulin polypeptide sequence." [SO:ke]
15900 synonym: "V region" EXACT []
15901 is_a: SO:0001832 ! immunoglobulin_region
15902 created_by: kareneilbeck
15903 creation_date: 2011-09-01T03:28:40Z
15908 def: "The constant region of an immunoglobulin polypeptide sequence." [SO:ke]
15909 synonym: "C region" EXACT []
15910 is_a: SO:0001832 ! immunoglobulin_region
15911 created_by: kareneilbeck
15912 creation_date: 2011-09-01T03:29:41Z
15917 def: "Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]
15918 synonym: "N-region" EXACT []
15919 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
15920 created_by: kareneilbeck
15921 creation_date: 2011-09-01T03:50:16Z
15926 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]
15927 synonym: "S region" EXACT []
15928 is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
15929 created_by: kareneilbeck
15930 creation_date: 2011-09-01T03:52:05Z
15934 name: mobile_element_insertion
15935 def: "A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]
15936 comment: Requested by the EBI.
15937 synonym: "mobile element insertion" EXACT []
15938 is_a: SO:0000667 ! insertion
15939 relationship: contains SO:0001037 ! mobile_genetic_element
15940 created_by: kareneilbeck
15941 creation_date: 2011-10-04T12:36:52Z
15945 name: novel_sequence_insertion
15946 def: "An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]
15947 comment: Requested by the NCBI.
15948 synonym: "novel sequence insertion" EXACT []
15949 is_a: SO:0000667 ! insertion
15950 created_by: kareneilbeck
15951 creation_date: 2011-10-04T01:14:50Z
15955 name: CSL_response_element
15956 def: "A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]
15957 synonym: "CSL response element" EXACT []
15958 is_a: SO:0001659 ! promoter_element
15959 created_by: kareneilbeck
15960 creation_date: 2011-10-07T03:37:43Z
15965 def: "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]
15966 synonym: "GATA box" EXACT []
15967 synonym: "GATA element" RELATED []
15968 is_a: SO:0001660 ! core_promoter_element
15969 created_by: kareneilbeck
15970 creation_date: 2011-10-07T03:42:05Z
15974 name: polymorphic_pseudogene
15975 def: "Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]
15976 comment: This terms is used by Ensembl and Vega.
15977 synonym: "polymorphic psuedogene" EXACT []
15978 is_a: SO:0000336 ! pseudogene
15979 created_by: kareneilbeck
15980 creation_date: 2011-10-07T03:46:57Z
15984 name: AP_1_binding_site
15985 def: "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]
15986 synonym: "AP-1 binding site" EXACT []
15987 is_a: SO:0001659 ! promoter_element
15988 created_by: kareneilbeck
15989 creation_date: 2011-10-07T03:54:52Z
15994 def: "A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]
15995 synonym: "ATF/CRE site" EXACT [PMID:11483993]
15996 synonym: "cyclic AMP response element" EXACT []
15997 is_a: SO:0001659 ! promoter_element
15998 created_by: kareneilbeck
15999 creation_date: 2011-10-07T03:58:48Z
16004 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]
16005 synonym: "copper-response element" EXACT []
16006 is_a: SO:0001659 ! promoter_element
16007 created_by: kareneilbeck
16008 creation_date: 2011-10-07T04:02:51Z
16013 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]
16014 synonym: "DNA damage response element" EXACT []
16015 is_a: SO:0001659 ! promoter_element
16016 created_by: kareneilbeck
16017 creation_date: 2011-10-07T04:17:25Z
16022 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]
16023 synonym: "FLEX element" RELATED []
16024 is_a: SO:0001659 ! promoter_element
16025 created_by: kareneilbeck
16026 creation_date: 2011-10-07T04:20:01Z
16030 name: forkhead_motif
16031 def: "A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]
16032 synonym: "forkhead motif" EXACT []
16033 is_a: SO:0001659 ! promoter_element
16034 created_by: kareneilbeck
16035 creation_date: 2011-10-07T04:22:06Z
16040 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]
16041 synonym: "homol D box" EXACT []
16042 is_a: SO:0001660 ! core_promoter_element
16043 created_by: kareneilbeck
16044 creation_date: 2011-10-07T04:24:14Z
16049 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]
16050 synonym: "homol E box" EXACT []
16051 is_a: SO:0001659 ! promoter_element
16052 created_by: kareneilbeck
16053 creation_date: 2011-10-07T04:26:09Z
16058 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]
16059 synonym: "heat shock element" EXACT []
16060 is_a: SO:0001659 ! promoter_element
16061 created_by: kareneilbeck
16062 creation_date: 2011-10-07T04:29:10Z
16066 name: iron_repressed_GATA_element
16067 def: "A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]
16068 comment: The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes.
16069 synonym: "IDP (GATA)" EXACT []
16070 synonym: "iron repressed GATA element" EXACT []
16071 is_a: SO:0001840 ! GATA_box
16072 created_by: kareneilbeck
16073 creation_date: 2011-10-07T04:32:42Z
16077 name: mating_type_M_box
16078 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]
16079 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.
16080 synonym: "mating type M-box" EXACT []
16081 is_a: SO:0001659 ! promoter_element
16082 created_by: kareneilbeck
16083 creation_date: 2011-10-07T04:39:43Z
16087 name: androgen_response_element
16088 def: "A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]
16089 synonym: "androgen response element" EXACT []
16090 synonym: "ARE" EXACT []
16091 is_a: SO:0000713 ! DNA_motif
16092 created_by: kareneilbeck
16093 creation_date: 2011-10-10T04:52:44Z
16098 def: "A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]
16099 synonym: "single molecule fish probe" EXACT []
16100 synonym: "smFISH probe" RELATED []
16101 is_a: SO:0000051 ! probe
16102 created_by: kareneilbeck
16103 creation_date: 2011-10-10T05:00:30Z
16108 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]
16109 synonym: "MluI cell cycle box" EXACT []
16110 is_a: SO:0001659 ! promoter_element
16111 created_by: kareneilbeck
16112 creation_date: 2011-10-10T05:09:45Z
16117 def: "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]
16118 synonym: "CCAAT motif" EXACT []
16119 is_a: SO:0001659 ! promoter_element
16120 created_by: kareneilbeck
16121 creation_date: 2011-10-10T05:13:54Z
16126 def: "A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]
16127 synonym: "Ace2 upstream activating sequence" EXACT []
16128 is_a: SO:0001659 ! promoter_element
16129 created_by: kareneilbeck
16130 creation_date: 2011-10-10T05:19:10Z
16135 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]
16136 synonym: "TR box" EXACT []
16137 is_a: SO:0001659 ! promoter_element
16138 created_by: kareneilbeck
16139 creation_date: 2011-10-10T05:22:13Z
16144 def: "A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]
16145 synonym: "STREP motif" RELATED []
16146 synonym: "stress-starvation response element of Schizosaccharomyces pombe" EXACT []
16147 is_a: SO:0001659 ! promoter_element
16148 created_by: kareneilbeck
16149 creation_date: 2011-10-14T10:25:02Z
16153 name: rDNA_intergenic_spacer_element
16154 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]
16155 synonym: "rDIS" EXACT []
16156 is_a: SO:0000713 ! DNA_motif
16157 created_by: kareneilbeck
16158 creation_date: 2011-10-19T11:23:09Z
16162 name: sterol_regulatory_element
16163 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]
16164 synonym: "SRE" BROAD [GO:mah]
16165 is_a: SO:0001659 ! promoter_element
16166 created_by: kareneilbeck
16167 creation_date: 2011-10-19T03:02:05Z
16171 name: GT_dinucleotide_repeat
16172 def: "A dinucleotide repeat region composed of GT repeating elements." [SO:ke]
16173 comment: paper:PMID:16043634.
16174 synonym: "d(GT)n" EXACT []
16175 is_a: SO:0000290 ! dinucleotide_repeat_microsatellite_feature
16176 created_by: kareneilbeck
16177 creation_date: 2011-10-19T03:54:37Z
16181 name: GTT_trinucleotide_repeat
16182 def: "A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]
16183 synonym: "d(GTT)" EXACT []
16184 is_a: SO:0000291 ! trinucleotide_repeat_microsatellite_feature
16185 created_by: kareneilbeck
16186 creation_date: 2011-10-19T03:56:54Z
16190 name: Sap1_recognition_motif
16191 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]
16192 synonym: "Sap1 recognitions site" EXACT []
16193 is_a: SO:0000713 ! DNA_motif
16194 created_by: kareneilbeck
16195 creation_date: 2011-10-19T04:24:16Z
16200 def: "An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]
16201 synonym: "calcineurin-dependent response element" EXACT [PMID:16928959]
16202 synonym: "CDRE motif" EXACT []
16203 is_a: SO:0001659 ! promoter_element
16204 created_by: kareneilbeck
16205 creation_date: 2011-10-20T10:12:19Z
16209 name: BAC_read_contig
16210 def: "A contig of BAC reads." [GMOD:ea]
16211 comment: Requested by Bayer Cropscience December, 2011.
16212 synonym: "BAC read contig" EXACT []
16213 is_a: SO:0000149 ! contig
16214 relationship: has_origin SO:0000153 ! BAC
16215 relationship: part_of SO:0000153 ! BAC
16216 created_by: kareneilbeck
16217 creation_date: 2012-01-17T02:45:04Z
16221 name: candidate_gene
16222 def: "A gene suspected of being involved in the expression of a trait." [GMOD:ea]
16223 comment: Requested by Bayer Cropscience December, 2011.
16224 synonym: "candidate gene" EXACT []
16225 synonym: "target gene" EXACT []
16226 is_a: SO:0000704 ! gene
16227 created_by: kareneilbeck
16228 creation_date: 2012-01-17T02:53:03Z
16232 name: positional_candidate_gene
16233 def: "A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]
16234 comment: Requested by Bayer Cropscience December, 2011.
16235 synonym: "positional candidate gene" EXACT []
16236 synonym: "positional target gene" RELATED []
16237 is_a: SO:0001867 ! candidate_gene
16238 created_by: kareneilbeck
16239 creation_date: 2012-01-17T02:54:42Z
16243 name: functional_candidate_gene
16244 def: "A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]
16245 comment: Requested by Bayer Cropscience December, 2011.
16246 synonym: "functional candidate gene" EXACT []
16247 synonym: "functional target gene" EXACT []
16248 is_a: SO:0001867 ! candidate_gene
16249 created_by: kareneilbeck
16250 creation_date: 2012-01-17T02:57:30Z
16255 def: "A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]
16256 synonym: "eRNA" EXACT []
16257 is_a: SO:0000655 ! ncRNA
16258 relationship: transcribed_from SO:0000165 ! enhancer
16259 created_by: kareneilbeck
16260 creation_date: 2012-01-17T03:09:35Z
16265 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]
16266 is_a: SO:0001659 ! promoter_element
16267 created_by: kareneilbeck
16268 creation_date: 2012-01-17T03:14:02Z
16272 name: rearrangement_region
16273 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]
16274 comment: NCBI definition: An orphan rearrangement between chromosomal location observed in isolation.
16275 synonym: "rearrangement region" EXACT []
16276 is_a: SO:0001411 ! biological_region
16277 is_a: SO:0001785 ! structural_alteration
16278 created_by: kareneilbeck
16279 creation_date: 2012-02-03T04:38:35Z
16283 name: interchromosomal_breakpoint
16284 def: "A rearrangement breakpoint between two different chromosomes." [NCBI:th]
16285 synonym: "interchromosomal breakpoint" EXACT []
16286 is_a: SO:0001021 ! chromosome_breakpoint
16287 created_by: kareneilbeck
16288 creation_date: 2012-02-03T04:43:45Z
16292 name: intrachromosomal_breakpoint
16293 def: "A rearrangement breakpoint within the same chromosome." [NCBI:th]
16294 synonym: "intrachromosomal breakpoint" EXACT []
16295 is_a: SO:0001021 ! chromosome_breakpoint
16296 created_by: kareneilbeck
16297 creation_date: 2012-02-03T04:44:53Z
16301 name: unassigned_supercontig
16302 def: "A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]
16303 comment: Requested by Bayer Cropscience January, 2012.
16304 synonym: "unassigned scaffold" RELATED []
16305 synonym: "unassigned supercontig" EXACT []
16306 is_a: SO:0000148 ! supercontig
16307 created_by: kareneilbeck
16308 creation_date: 2012-02-14T05:02:20Z
16312 name: partial_genomic_sequence_assembly
16313 def: "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]
16314 comment: Requested by Bayer Cropscience January, 2012.
16315 synonym: "partial genomic sequence assembly" EXACT []
16316 synonym: "pseudomolecule" BROAD []
16317 synonym: "sequence assembly with N-gaps" EXACT []
16318 is_a: SO:0000353 ! sequence_assembly
16319 created_by: kareneilbeck
16320 creation_date: 2012-02-14T05:05:32Z
16325 def: "A non-coding RNA over 200nucleotides in length." [HGNC:mw]
16326 synonym: "long non-coding RNA" EXACT []
16327 is_a: SO:0000655 ! ncRNA
16328 created_by: kareneilbeck
16329 creation_date: 2012-02-14T05:18:01Z
16333 name: feature_variant
16334 def: "A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]
16335 comment: Created in conjunction with the EBI.
16336 synonym: "feature alteration" EXACT []
16337 is_a: SO:0001537 ! structural_variant
16338 created_by: kareneilbeck
16339 creation_date: 2012-04-03T11:27:27Z
16343 name: feature_ablation
16344 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]
16345 comment: Created in conjunction with the EBI.
16346 synonym: "feature ablation" EXACT []
16347 is_a: SO:0001537 ! structural_variant
16348 created_by: kareneilbeck
16349 creation_date: 2012-04-03T11:36:48Z
16353 name: feature_amplification
16354 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]
16355 comment: Created in conjunction with the EBI.
16356 synonym: "feature amplification" EXACT []
16357 is_a: SO:0001537 ! structural_variant
16358 created_by: kareneilbeck
16359 creation_date: 2012-04-03T11:37:48Z
16363 name: feature_translocation
16364 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]
16365 comment: Created in conjunction with the EBI.
16366 synonym: "feature translocation" EXACT []
16367 is_a: SO:0001537 ! structural_variant
16368 created_by: kareneilbeck
16369 creation_date: 2012-04-03T11:38:52Z
16373 name: feature_fusion
16374 def: "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]
16375 comment: Created in conjunction with the EBI.
16376 synonym: "feature fusion" EXACT []
16377 is_a: SO:0001537 ! structural_variant
16378 created_by: kareneilbeck
16379 creation_date: 2012-04-03T11:39:20Z
16383 name: transcript_translocation
16384 def: "A feature translocation where the region contains a transcript." [SO:ke]
16385 comment: Created in conjunction with the EBI.
16386 synonym: "transcript translocation" EXACT []
16387 is_a: SO:0001881 ! feature_translocation
16388 created_by: kareneilbeck
16389 creation_date: 2012-04-03T12:29:52Z
16393 name: regulatory_region_translocation
16394 def: "A feature translocation where the region contains a regulatory region." [SO:ke]
16395 comment: Created in conjunction with the EBI.
16396 synonym: "regulatory region translocation" EXACT []
16397 is_a: SO:0001881 ! feature_translocation
16398 created_by: kareneilbeck
16399 creation_date: 2012-04-03T12:31:04Z
16403 name: TFBS_translocation
16404 def: "A feature translocation where the region contains a transcription factor binding site." [SO:ke]
16405 comment: Created in conjunction with the EBI.
16406 synonym: "TFBS binding site translocation" EXACT []
16407 synonym: "transcription factor binding site translocation" EXACT []
16408 is_a: SO:0001884 ! regulatory_region_translocation
16409 created_by: kareneilbeck
16410 creation_date: 2012-04-03T12:31:15Z
16414 name: transcript_fusion
16415 def: "A feature fusion where the deletion brings together transcript regions." [SO:ke]
16416 comment: Created in conjunction with the EBI.
16417 synonym: "transcript fusion" EXACT []
16418 is_a: SO:0001882 ! feature_fusion
16419 created_by: kareneilbeck
16420 creation_date: 2012-04-03T12:34:56Z
16424 name: regulatory_region_fusion
16425 def: "A feature fusion where the deletion brings together regulatory regions." [SO:ke]
16426 comment: Created in conjunction with the EBI.
16427 synonym: "regulatory region fusion" EXACT []
16428 is_a: SO:0001882 ! feature_fusion
16429 created_by: kareneilbeck
16430 creation_date: 2012-04-03T12:35:58Z
16435 def: "A fusion where the deletion brings together transcription factor binding sites." [SO:ke]
16436 comment: Created in conjunction with the EBI.
16437 synonym: "TFBS fusion " EXACT []
16438 synonym: "transcription factor binding site fusion" EXACT []
16439 is_a: SO:0001887 ! regulatory_region_fusion
16440 created_by: kareneilbeck
16441 creation_date: 2012-04-03T12:36:42Z
16445 name: transcript_amplification
16446 def: "A feature amplification of a region containing a transcript." [SO:ke]
16447 comment: Created in conjunction with the EBI.
16448 synonym: "transcript amplification" EXACT []
16449 is_a: SO:0001880 ! feature_amplification
16450 created_by: kareneilbeck
16451 creation_date: 2012-04-03T12:39:23Z
16455 name: transcript_regulatory_region_fusion
16456 def: "A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]
16457 comment: Created in conjunction with the EBI.
16458 synonym: "transcript regulatory region fusion" EXACT []
16459 is_a: SO:0001882 ! feature_fusion
16460 created_by: kareneilbeck
16461 creation_date: 2012-04-03T12:40:17Z
16465 name: regulatory_region_amplification
16466 def: "A feature amplification of a region containing a regulatory region." [SO:ke]
16467 comment: Created in conjunction with the EBI.
16468 synonym: "regulatory region amplification" EXACT []
16469 is_a: SO:0001880 ! feature_amplification
16470 created_by: kareneilbeck
16471 creation_date: 2012-04-03T12:41:28Z
16475 name: TFBS_amplification
16476 def: "A feature amplification of a region containing a transcription factor binding site." [SO:ke]
16477 comment: Created in conjunction with the EBI.
16478 synonym: "TFBS amplification " EXACT []
16479 synonym: "transcription factor binding site amplification" EXACT []
16480 is_a: SO:0001891 ! regulatory_region_amplification
16481 created_by: kareneilbeck
16482 creation_date: 2012-04-03T12:42:48Z
16486 name: transcript_ablation
16487 def: "A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]
16488 comment: Created in conjunction with the EBI.
16489 synonym: "transcript ablation" EXACT []
16490 is_a: SO:0001879 ! feature_ablation
16491 created_by: kareneilbeck
16492 creation_date: 2012-04-03T12:44:19Z
16496 name: regulatory_region_ablation
16497 def: "A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]
16498 comment: Created in conjunction with the EBI.
16499 synonym: "regulatory region ablation" EXACT []
16500 is_a: SO:0001879 ! feature_ablation
16501 created_by: kareneilbeck
16502 creation_date: 2012-04-03T12:45:13Z
16506 name: TFBS_ablation
16507 def: "A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]
16508 comment: Created in conjunction with the EBI.
16509 synonym: "TFBS ablation" EXACT []
16510 synonym: "transcription factor binding site ablation" EXACT []
16511 is_a: SO:0001894 ! regulatory_region_ablation
16512 created_by: kareneilbeck
16513 creation_date: 2012-04-03T12:45:56Z
16517 name: transposable_element_CDS
16518 def: "A CDS that is part of a transposable element." [SO:ke]
16519 synonym: "transposable element CDS" EXACT []
16520 is_a: SO:0000316 ! CDS
16521 relationship: part_of SO:0000101 ! transposable_element
16522 created_by: kareneilbeck
16523 creation_date: 2012-04-05T01:57:04Z
16527 name: transposable_element_pseudogene
16528 def: "A pseudogene contained within a transposable element." [SO:ke]
16529 synonym: "transposable element pseudogene" EXACT []
16530 is_a: SO:0000336 ! pseudogene
16531 relationship: part_of SO:0000101 ! transposable_element
16532 created_by: kareneilbeck
16533 creation_date: 2012-04-05T04:09:45Z
16538 def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]
16539 comment: For the S. pombe project - requested by Val Wood.
16540 synonym: "dg repeat" EXACT []
16541 is_a: SO:0001797 ! centromeric_repeat
16542 relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region
16543 created_by: kareneilbeck
16544 creation_date: 2012-04-06T11:48:48Z
16549 def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]
16550 comment: For the S. pombe project - requested by Val Wood.
16551 synonym: "dh repeat" EXACT []
16552 is_a: SO:0001797 ! centromeric_repeat
16553 relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region
16554 created_by: kareneilbeck
16555 creation_date: 2012-04-06T11:50:07Z
16559 name: M26_binding_site
16560 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]
16561 synonym: "m26 site" EXACT []
16562 is_a: SO:0000713 ! DNA_motif
16563 created_by: kareneilbeck
16564 creation_date: 2012-04-06T12:02:10Z
16569 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]
16570 synonym: "AACCCT box" EXACT []
16571 is_a: SO:0001660 ! core_promoter_element
16572 created_by: kareneilbeck
16573 creation_date: 2012-04-06T12:05:24Z
16577 name: splice_region
16578 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]
16579 synonym: "splice region" RELATED []
16580 is_a: SO:0000835 ! primary_transcript_region
16581 relationship: part_of SO:0000185 ! primary_transcript
16582 created_by: kareneilbeck
16583 creation_date: 2012-04-06T12:23:32Z
16587 name: intronic_lncRNA
16588 def: "A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]
16589 synonym: "intronic lncRNA" EXACT []
16590 is_a: SO:0001877 ! lnc_RNA
16591 created_by: kareneilbeck
16592 creation_date: 2012-04-06T04:34:17Z
16596 name: antisense_lncRNA
16597 def: "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]
16598 synonym: "antisense lncRNA" RELATED []
16599 synonym: "natural antisense transcript" EXACT []
16600 is_a: SO:0001877 ! lnc_RNA
16601 created_by: kareneilbeck
16602 creation_date: 2012-04-06T04:36:44Z
16606 name: regional_centromere_outer_repeat_transcript
16607 def: "A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]
16608 synonym: "centromere outer repeat transcript" EXACT []
16609 synonym: "regional centromere outer repeat region transcript" EXACT []
16610 synonym: "regional_centromere_outer_repeat_region_transcript" EXACT []
16611 is_a: SO:0000185 ! primary_transcript
16612 relationship: derives_from SO:0001799 ! regional_centromere_outer_repeat_region
16613 created_by: kareneilbeck
16614 creation_date: 2012-04-11T04:54:22Z
16618 name: feature_truncation
16619 def: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]
16620 synonym: "feature truncation" EXACT []
16621 is_a: SO:0001878 ! feature_variant
16622 created_by: kareneilbeck
16623 creation_date: 2012-04-12T05:05:28Z
16627 name: feature_elongation
16628 def: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]
16629 synonym: "feature elongation" EXACT []
16630 is_a: SO:0001878 ! feature_variant
16631 created_by: kareneilbeck
16632 creation_date: 2012-04-12T05:05:56Z
16636 name: internal_feature_elongation
16637 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]
16638 synonym: "internal feature elongation" EXACT []
16639 is_a: SO:0001907 ! feature_elongation
16640 created_by: kareneilbeck
16641 creation_date: 2012-04-12T05:06:20Z
16645 name: frameshift_elongation
16646 def: "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]
16647 synonym: "ANNOVAR:frameshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
16648 synonym: "frameshift elongation" EXACT []
16649 is_a: SO:0001589 ! frameshift_variant
16650 is_a: SO:0001908 ! internal_feature_elongation
16651 created_by: kareneilbeck
16652 creation_date: 2012-04-12T05:10:05Z
16656 name: frameshift_truncation
16657 def: "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]
16658 synonym: "ANNOVAR:frameshit deletion" EXACT ebi_variants [http://www.openbioinformatics.org/annovar/annovar_download.html]
16659 synonym: "frameshft truncation" EXACT []
16660 is_a: SO:0001589 ! frameshift_variant
16661 is_a: SO:0001906 ! feature_truncation
16662 created_by: kareneilbeck
16663 creation_date: 2012-04-12T05:10:45Z
16667 name: copy_number_increase
16668 def: "A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]
16669 synonym: "copy number increase" EXACT []
16670 is_a: SO:0001563 ! copy_number_change
16671 created_by: kareneilbeck
16672 creation_date: 2012-04-13T11:26:32Z
16676 name: copy_number_decrease
16677 def: "A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]
16678 is_a: SO:0001563 ! copy_number_change
16679 created_by: kareneilbeck
16680 creation_date: 2012-04-13T11:27:52Z
16684 name: bacterial_RNApol_promoter_sigma_ecf
16685 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]
16686 comment: Requested by Kevin Clancy - invitrogen -May 2012.
16687 synonym: "bacterial RNApol promoter sigma ecf " EXACT []
16688 is_a: SO:0000613 ! bacterial_RNApol_promoter
16689 created_by: kareneilbeck
16690 creation_date: 2012-06-11T02:41:33Z
16694 name: rDNA_replication_fork_barrier
16695 def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]
16696 comment: Requested by Midori - June 2012.
16697 synonym: "DNA spacer replication fork barrier" EXACT []
16698 synonym: "rDNA replication fork barrier" EXACT []
16699 synonym: "RFB" EXACT []
16700 synonym: "RTS1 barrier" EXACT []
16701 synonym: "RTS1 element" EXACT []
16702 is_a: SO:0000713 ! DNA_motif
16703 created_by: kareneilbeck
16704 creation_date: 2012-06-11T02:55:02Z
16708 name: transcription_start_cluster
16709 def: "A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]
16710 synonym: "transcriptional initiation cluster" EXACT []
16711 synonym: "transcriptional start site cluster" EXACT []
16712 synonym: "TSC" EXACT []
16713 synonym: "TSS cluster" EXACT []
16714 is_a: SO:0001410 ! experimental_feature
16715 created_by: kareneilbeck
16716 creation_date: 2012-10-17T12:09:50Z
16721 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]
16722 synonym: "CAGE tag" EXACT []
16723 is_a: SO:0000324 ! tag
16724 created_by: kareneilbeck
16725 creation_date: 2012-10-17T12:36:58Z
16730 def: "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]
16731 synonym: "CAGE cluster" EXACT []
16732 synonym: "CAGE peak" EXACT []
16733 synonym: "CAGE_peak" EXACT []
16734 is_a: SO:0001915 ! transcription_start_cluster
16735 created_by: kareneilbeck
16736 creation_date: 2012-10-17T12:42:03Z
16740 name: 5_methylcytosine
16741 def: "A cytosine methylated at the 5 carbon." [SO:rtapella]
16742 synonym: "5 methylcytosine" EXACT []
16743 synonym: "5-mC" EXACT []
16744 synonym: "m-5C" EXACT []
16745 synonym: "m5c" EXACT []
16746 xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
16747 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
16748 is_a: SO:0000114 ! methylated_cytosine
16749 created_by: kareneilbeck
16750 creation_date: 2012-10-17T12:46:10Z
16754 name: 4_methylcytosine
16755 def: "A cytosine methylated at the 4 nitrogen." [SO:rtapella]
16756 synonym: "4-mC" EXACT []
16757 synonym: "4-methylcytosine" EXACT []
16758 synonym: "m-4C" EXACT []
16759 synonym: "m4c" EXACT []
16760 synonym: "N4 methylcytosine" EXACT []
16761 synonym: "N4-methylcytosine" EXACT []
16762 synonym: "N4_methylcytosine" EXACT []
16763 xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
16764 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
16765 is_a: SO:0000114 ! methylated_cytosine
16766 created_by: kareneilbeck
16767 creation_date: 2012-10-17T12:50:40Z
16771 name: N6_methyladenine
16772 def: "An adenine methylated at the 6 nitrogen." [SO:rtapella]
16773 synonym: "6-mA" EXACT []
16774 synonym: "6-methyladenine" EXACT []
16775 synonym: "6mA" EXACT []
16776 synonym: "m-6A" EXACT []
16777 synonym: "m6a" EXACT []
16778 synonym: "N6-methyladenine" EXACT []
16779 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
16780 is_a: SO:0000161 ! methylated_adenine
16781 created_by: kareneilbeck
16782 creation_date: 2012-10-17T12:54:23Z
16786 name: mitochondrial_contig
16787 def: "A contig of mitochondria derived sequences." [GMOD:ea]
16788 comment: Requested by Bayer Cropscience, October, 2012.
16789 synonym: "mitochondrial contig" EXACT []
16790 is_a: SO:0000149 ! contig
16791 relationship: has_origin SO:0000737 ! mitochondrial_sequence
16792 created_by: kareneilbeck
16793 creation_date: 2012-10-31T12:34:38Z
16797 name: mitochondrial_supercontig
16798 def: "A scaffold composed of mitochondrial contigs." [GMOD:ea]
16799 synonym: "mitochondrial scaffold" EXACT []
16800 synonym: "mitochondrial supercontig" EXACT []
16801 synonym: "mitochondrial_scaffold" EXACT []
16802 is_a: SO:0000148 ! supercontig
16803 created_by: kareneilbeck
16804 creation_date: 2012-10-31T12:42:45Z
16809 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]
16810 comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
16811 synonym: "telomeric repeat containing RNA" RELATED []
16812 is_a: SO:0001927 ! telomeric_transcript
16813 created_by: kareneilbeck
16814 creation_date: 2012-10-31T01:06:40Z
16819 def: "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]
16820 comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
16821 is_a: SO:0001927 ! telomeric_transcript
16822 created_by: kareneilbeck
16823 creation_date: 2012-10-31T01:11:49Z
16828 def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats." [PMID:22139915]
16829 comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
16830 is_a: SO:0001927 ! telomeric_transcript
16831 created_by: kareneilbeck
16832 creation_date: 2012-10-31T01:24:37Z
16837 def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts." [PMID:22139915]
16838 comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
16839 synonym: "anti-ARRET" EXACT []
16840 is_a: SO:0001927 ! telomeric_transcript
16841 created_by: kareneilbeck
16842 creation_date: 2012-10-31T01:40:22Z
16846 name: telomeric_transcript
16847 def: "A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]
16848 synonym: "telomeric transcript" EXACT []
16849 is_a: SO:0000655 ! ncRNA
16850 created_by: kareneilbeck
16851 creation_date: 2012-10-31T01:42:15Z
16855 name: distal_duplication
16856 def: "A duplication of the distal region of a chromosome." [SO:bm]
16857 comment: This term is used by Complete Genomics in the structural variant analysis files.
16858 synonym: "distal duplication" EXACT []
16859 is_a: SO:1000035 ! duplication
16860 created_by: kareneilbeck
16861 creation_date: 2012-10-31T01:56:44Z
16865 name: mitochondrial_DNA_read
16866 def: "A sequencer read of a mitochondrial DNA sample." [GMOD:ea]
16867 comment: Requested by Bayer Cropscience, October, 2012.
16868 synonym: "mitochondrial DNA read" EXACT []
16869 is_a: SO:0000150 ! read
16870 relationship: has_origin SO:0001032 ! mitochondrial_DNA
16871 created_by: kareneilbeck
16872 creation_date: 2012-11-14T04:39:56Z
16876 name: chloroplast_DNA_read
16877 def: "A sequencer read of a chloroplast DNA sample." [GMOD:ea]
16878 comment: Requested by Bayer Cropscience, October, 2012.
16879 synonym: "chloroplast DNA read" EXACT []
16880 is_a: SO:0000150 ! read
16881 relationship: has_origin SO:0001033 ! chloroplast_DNA
16882 created_by: kareneilbeck
16883 creation_date: 2012-11-14T04:43:45Z
16887 name: consensus_gDNA
16888 def: "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]
16889 comment: Requested by Bayer Cropscience November, 2012.
16890 synonym: "consensus gDNA" EXACT []
16891 synonym: "consensus genomic DNA" EXACT []
16892 is_a: SO:0000994 ! consensus_region
16893 created_by: kareneilbeck
16894 creation_date: 2012-11-28T12:53:14Z
16898 name: restriction_enzyme_five_prime_single_strand_overhang
16899 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]
16900 synonym: "restriction enzyme five prime single strand overhang" EXACT []
16901 is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang
16902 created_by: kareneilbeck
16903 creation_date: 2013-03-06T09:50:44Z
16907 name: restriction_enzyme_three_prime_single_strand_overhang
16908 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]
16909 synonym: "restriction enzyme three prime single strand overhang" EXACT []
16910 is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang
16911 created_by: kareneilbeck
16912 creation_date: 2013-03-06T09:52:14Z
16916 name: monomeric_repeat
16917 def: "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]
16918 synonym: "monomeric repeat" EXACT []
16919 is_a: SO:0000705 ! tandem_repeat
16920 created_by: kareneilbeck
16921 creation_date: 2013-03-06T09:59:15Z
16925 name: H3K20_trimethylation_site
16926 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]
16927 synonym: "H3K20 trimethylation site" EXACT []
16928 is_a: SO:0001701 ! histone_methylation_site
16929 created_by: kareneilbeck
16930 creation_date: 2013-03-06T10:13:48Z
16934 name: H3K36_acetylation_site
16935 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]
16936 synonym: "H3K36 acetylation site" EXACT []
16937 synonym: "H3K36ac" EXACT []
16938 is_a: SO:0001973 ! histone_3_acetylation_site
16939 created_by: kareneilbeck
16940 creation_date: 2013-03-06T10:16:55Z
16944 name: H2BK12_acetylation_site
16945 def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]
16946 synonym: "H2BK12 acetylation site" EXACT []
16947 synonym: "H2BK12ac" RELATED []
16948 is_a: SO:0001702 ! histone_acetylation_site
16949 created_by: kareneilbeck
16950 creation_date: 2013-03-06T10:19:13Z
16954 name: H2AK5_acetylation_site
16955 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]
16956 synonym: "H2AK5 acetylation site" EXACT []
16957 synonym: "H2AK5ac" EXACT []
16958 is_a: SO:0001702 ! histone_acetylation_site
16959 created_by: kareneilbeck
16960 creation_date: 2013-03-06T10:20:57Z
16964 name: H4K12_acetylation_site
16965 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]
16966 synonym: "H4K12 acetylation site" EXACT []
16967 synonym: "H4K12ac" EXACT []
16968 is_a: SO:0001972 ! histone_4_acylation_site
16969 created_by: kareneilbeck
16970 creation_date: 2013-03-06T10:26:15Z
16974 name: H2BK120_acetylation_site
16975 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]
16976 synonym: "H2BK120 acetylation site" EXACT []
16977 synonym: "H2BK120ac" EXACT []
16978 is_a: SO:0001702 ! histone_acetylation_site
16979 created_by: kareneilbeck
16980 creation_date: 2013-03-06T10:28:38Z
16984 name: H4K91_acetylation_site
16985 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]
16986 synonym: "H4K91 acetylation site" EXACT []
16987 is_a: SO:0001972 ! histone_4_acylation_site
16988 created_by: kareneilbeck
16989 creation_date: 2013-03-06T10:41:04Z
16993 name: H2BK20_acetylation_site
16994 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]
16995 synonym: "H2BK20 acetylation site" RELATED []
16996 synonym: "H2BK20ac" EXACT []
16997 is_a: SO:0001702 ! histone_acetylation_site
16998 created_by: kareneilbeck
16999 creation_date: 2013-03-06T10:44:31Z
17003 name: H3K4ac_acetylation_site
17004 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]
17005 synonym: "H3K4ac" EXACT []
17006 synonym: "H3K4ac acetylation site" EXACT []
17007 is_a: SO:0001973 ! histone_3_acetylation_site
17008 created_by: kareneilbeck
17009 creation_date: 2013-03-06T10:46:32Z
17013 name: H2AK9_acetylation_site
17014 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]
17015 synonym: "H2AK9 acetylation site" EXACT []
17016 synonym: "H2AK9ac" EXACT []
17017 is_a: SO:0001702 ! histone_acetylation_site
17018 created_by: kareneilbeck
17019 creation_date: 2013-03-06T10:48:11Z
17023 name: H3K56_acetylation_site
17024 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]
17025 synonym: "H3K56 acetylation site" EXACT []
17026 synonym: "H3K56ac" EXACT []
17027 is_a: SO:0001973 ! histone_3_acetylation_site
17028 created_by: kareneilbeck
17029 creation_date: 2013-03-06T10:51:14Z
17033 name: H2BK15_acetylation_site
17034 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]
17035 synonym: "H2BK15 acetylation site" EXACT []
17036 synonym: "H2BK15ac" EXACT []
17037 is_a: SO:0001702 ! histone_acetylation_site
17038 created_by: kareneilbeck
17039 creation_date: 2013-03-06T10:53:23Z
17043 name: H3R2_monomethylation_site
17044 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]
17045 synonym: " H3R2me1" EXACT []
17046 synonym: "H3R2 monomethylation site" EXACT []
17047 is_a: SO:0001701 ! histone_methylation_site
17048 created_by: kareneilbeck
17049 creation_date: 2013-03-06T10:57:13Z
17053 name: H3R2_dimethylation_site
17054 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]
17055 synonym: "H3R2 dimethylation site" EXACT []
17056 synonym: "H3R2me2" EXACT []
17057 is_a: SO:0001701 ! histone_methylation_site
17058 created_by: kareneilbeck
17059 creation_date: 2013-03-06T10:59:17Z
17063 name: H4R3_dimethylation_site
17064 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]
17065 synonym: "H4R3 dimethylation site" EXACT []
17066 synonym: "H4R3me2" EXACT []
17067 is_a: SO:0001701 ! histone_methylation_site
17068 created_by: kareneilbeck
17069 creation_date: 2013-03-06T11:01:27Z
17073 name: H4K4_trimethylation_site
17074 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]
17075 synonym: " H4K4me3" EXACT []
17076 synonym: "H4K4 trimethylation site" EXACT []
17077 is_a: SO:0001701 ! histone_methylation_site
17078 created_by: kareneilbeck
17079 creation_date: 2013-03-06T11:03:29Z
17083 name: H3K23_dimethylation_site
17084 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]
17085 synonym: "H3K23 dimethylation site" EXACT []
17086 synonym: "H3K23me2" EXACT []
17087 is_a: SO:0001701 ! histone_methylation_site
17088 created_by: kareneilbeck
17089 creation_date: 2013-03-06T11:05:33Z
17093 name: promoter_flanking_region
17094 def: "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]
17095 synonym: "promoter flanking region" EXACT []
17096 is_a: SO:0001055 ! transcriptional_cis_regulatory_region
17097 created_by: kareneilbeck
17098 creation_date: 2013-03-06T11:36:25Z
17102 name: restriction_enzyme_assembly_scar
17103 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]
17104 is_a: SO:0001954 ! restriction_enzyme_region
17105 created_by: kareneilbeck
17106 creation_date: 2013-03-06T03:18:11Z
17110 name: restriction_enzyme_region
17111 def: "A region related to restriction enzyme function." [SO:ke]
17112 comment: Not a great term for annotation, but used to classify the various regions related to restriction enzymes.
17113 synonym: "restriction enzyme region" RELATED []
17114 is_a: SO:0001411 ! biological_region
17115 created_by: kareneilbeck
17116 creation_date: 2013-03-06T03:23:34Z
17120 name: protein_stability_element
17121 def: "A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]
17122 synonym: "protein stability element" RELATED []
17123 is_a: SO:0000839 ! polypeptide_region
17124 created_by: kareneilbeck
17125 creation_date: 2013-03-06T03:32:47Z
17129 name: protease_site
17130 def: "A polypeptide_region that codes for a protease cleavage site." [SO:ke]
17131 synonym: "protease site" EXACT []
17132 is_a: SO:0000839 ! polypeptide_region
17133 created_by: kareneilbeck
17134 creation_date: 2013-03-06T03:36:28Z
17138 name: RNA_stability_element
17139 def: "RNA secondary structure that affects the stability of an RNA molecule." [SO:ke]
17140 synonym: "rna stability element" RELATED []
17141 created_by: kareneilbeck
17142 creation_date: 2013-03-06T03:38:35Z
17147 name: lariat_intron
17148 def: "A kind of intron whereby the excision is driven by lariat formation." [SO:ke]
17149 comment: Requested by PomBase 3604508.
17150 synonym: "lariat intron" EXACT []
17151 is_a: SO:0000188 ! intron
17152 created_by: kareneilbeck
17153 creation_date: 2013-03-07T10:58:40Z
17158 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]
17159 synonym: "polypyrimidine initiator" EXACT []
17160 synonym: "TCT element" EXACT []
17161 is_a: SO:0001660 ! core_promoter_element
17162 created_by: kareneilbeck
17163 creation_date: 2013-05-17T04:38:48Z
17167 name: 5_hydroxymethylcytosine
17168 def: "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]
17169 synonym: "5-hmC" EXACT []
17170 synonym: "5-hydroxymethylcytosine" EXACT []
17171 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17172 is_a: SO:0000114 ! methylated_cytosine
17173 created_by: kareneilbeck
17174 creation_date: 2013-05-17T05:05:31Z
17178 name: 5_formylcytosine
17179 def: "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]
17180 synonym: "5-fC" EXACT []
17181 synonym: "5-formylcytosine" EXACT []
17182 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17183 is_a: SO:0001963 ! modified_cytosine
17184 created_by: kareneilbeck
17185 creation_date: 2013-05-17T05:06:13Z
17189 name: modified_adenine
17190 def: "A modified adenine DNA base feature." [SO:ke]
17191 is_a: SO:0000305 ! modified_DNA_base
17192 created_by: kareneilbeck
17193 creation_date: 2013-05-20T01:22:30Z
17197 name: modified_cytosine
17198 def: "A modified cytosine DNA base feature." [SO:ke]
17199 is_a: SO:0000305 ! modified_DNA_base
17200 created_by: kareneilbeck
17201 creation_date: 2013-05-20T01:23:47Z
17205 name: modified_guanine
17206 def: "A modified guanine DNA base feature." [SO:ke]
17207 is_a: SO:0000305 ! modified_DNA_base
17208 created_by: kareneilbeck
17209 creation_date: 2013-05-20T01:25:31Z
17214 def: "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
17215 synonym: "8-oxoG" EXACT []
17216 synonym: "8-oxoguanine" EXACT []
17217 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17218 is_a: SO:0001964 ! modified_guanine
17219 created_by: kareneilbeck
17220 creation_date: 2013-05-20T01:27:51Z
17224 name: 5_carboxylcytosine
17225 def: "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]
17226 synonym: "5-caC" EXACT []
17227 synonym: "5-carboxycytosine" EXACT []
17228 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17229 is_a: SO:0001963 ! modified_cytosine
17230 created_by: kareneilbeck
17231 creation_date: 2013-05-20T01:30:01Z
17236 def: "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
17237 synonym: "8-oxoA" EXACT []
17238 synonym: "8-oxoadenine" EXACT []
17239 xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
17240 is_a: SO:0001962 ! modified_adenine
17241 created_by: kareneilbeck
17242 creation_date: 2013-05-20T01:31:05Z
17246 name: coding_transcript_variant
17247 def: "A transcript variant of a protein coding gene." [SO:ke]
17248 synonym: "coding transcript variant" EXACT []
17249 is_a: SO:0001576 ! transcript_variant
17250 created_by: kareneilbeck
17251 creation_date: 2013-05-22T04:34:49Z
17255 name: coding_transcript_intron_variant
17256 def: "A transcript variant occurring within an intron of a coding transcript." [SO:ke]
17257 synonym: "coding sequence intron variant" EXACT []
17258 is_a: SO:0001627 ! intron_variant
17259 is_a: SO:0001968 ! coding_transcript_variant
17260 created_by: kareneilbeck
17261 creation_date: 2013-05-23T10:54:17Z
17265 name: non_coding_transcript_intron_variant
17266 def: "A transcript variant occurring within an intron of a non coding transcript." [SO:ke]
17267 synonym: "non coding transcript intron variant" EXACT []
17268 is_a: SO:0001619 ! non_coding_transcript_variant
17269 is_a: SO:0001627 ! intron_variant
17270 created_by: kareneilbeck
17271 creation_date: 2013-05-23T10:55:03Z
17275 name: zinc_finger_binding_site
17276 synonym: "zinc finger binding site" EXACT []
17277 synonym: "zinc_fing" EXACT BS [unirot:features]
17278 is_a: SO:0001429 ! DNA_binding_site
17279 created_by: kareneilbeck
17280 creation_date: 2013-07-29T04:41:53Z
17284 name: histone_4_acylation_site
17285 def: "A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
17286 synonym: "H4ac" EXACT []
17287 is_a: SO:0001702 ! histone_acetylation_site
17288 created_by: kareneilbeck
17289 creation_date: 2013-07-30T10:43:04Z
17293 name: histone_3_acetylation_site
17294 def: "A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
17295 synonym: "H3ac" EXACT []
17296 is_a: SO:0001702 ! histone_acetylation_site
17297 created_by: kareneilbeck
17298 creation_date: 2013-07-30T10:46:42Z
17302 name: CTCF_binding_site
17303 def: "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]
17304 synonym: "CCCTF binding site" EXACT []
17305 synonym: "CTCF binding site" EXACT []
17306 is_a: SO:0001659 ! promoter_element
17307 created_by: kareneilbeck
17308 creation_date: 2013-07-30T10:59:11Z
17312 name: five_prime_sticky_end_restriction_enzyme_cleavage_site
17313 def: "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]
17314 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.
17315 synonym: "five prime sticky end restriction enzyme cleavage site" EXACT []
17316 is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
17317 created_by: kareneilbeck
17318 creation_date: 2013-07-30T11:32:16Z
17322 name: three_prime_sticky_end_restriction_enzyme_cleavage_site
17323 def: "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]
17324 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.
17325 synonym: "three prime sticky end restriction enzyme cleavage site" EXACT []
17326 is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
17327 created_by: kareneilbeck
17328 creation_date: 2013-07-30T11:37:19Z
17332 name: ribonuclease_site
17333 def: "A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]
17334 synonym: "ribonuclease site" EXACT []
17335 is_a: SO:0000833 ! transcript_region
17336 created_by: kareneilbeck
17337 creation_date: 2013-07-30T11:41:06Z
17342 def: "A region of sequence where developer information is encoded." [SO:ke]
17343 comment: Requested by Jackie Quinn for use in synthetic biology.
17344 synonym: "DNA signature" EXACT []
17345 is_a: SO:0000804 ! engineered_region
17346 created_by: kareneilbeck
17347 creation_date: 2013-07-30T11:49:22Z
17351 name: RNA_stability_element
17352 def: "A motif that affects the stability of RNA." [PMID:22495308, SO:ke]
17353 synonym: "RNA stability element" EXACT []
17354 is_a: SO:0000715 ! RNA_motif
17355 created_by: kareneilbeck
17356 creation_date: 2013-07-30T03:33:53Z
17361 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]
17362 comment: A plant specific region.
17363 synonym: "G-box" EXACT []
17364 synonym: "GBF binding sequence" EXACT []
17365 is_a: SO:0001678 ! regulatory_promoter_element
17366 created_by: kareneilbeck
17367 creation_date: 2013-07-30T04:00:50Z
17372 def: "An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]
17373 synonym: "L-box" EXACT []
17374 synonym: "L-box promoter element" EXACT []
17375 is_a: SO:0001678 ! regulatory_promoter_element
17376 created_by: kareneilbeck
17377 creation_date: 2013-07-30T04:12:19Z
17382 def: "A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]
17383 synonym: "I-box promoter motif" EXACT []
17384 is_a: SO:0001678 ! regulatory_promoter_element
17385 created_by: kareneilbeck
17386 creation_date: 2013-07-30T04:17:55Z
17390 name: 5_prime_UTR_premature_start_codon_variant
17391 def: "A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]
17392 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.
17393 synonym: "5' UTR premature start codon variant" EXACT []
17394 synonym: "snpEff:START_GAINED" EXACT VAR []
17395 is_a: SO:0001623 ! 5_prime_UTR_variant
17396 created_by: kareneilbeck
17397 creation_date: 2013-07-30T04:36:25Z
17401 name: silent_mating_type_cassette_array
17402 def: "A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]
17403 synonym: "silent mating-type cassette" RELATED []
17404 is_a: SO:0005854 ! gene_cassette_array
17405 created_by: kareneilbeck
17406 creation_date: 2013-07-31T02:40:38Z
17410 name: Okazaki_fragment
17411 def: "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]
17412 comment: Requested by Midori Harris, 2013.
17413 synonym: "Okazaki fragment" EXACT []
17414 is_a: SO:0001411 ! biological_region
17415 created_by: kareneilbeck
17416 creation_date: 2013-07-31T02:57:55Z
17420 name: upstream_transcript_variant
17421 def: "A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]
17422 comment: Requested by Graham Ritchie, EBI/Sanger.
17423 synonym: "upstream transcript variant" EXACT []
17424 is_a: SO:0001628 ! intergenic_variant
17425 created_by: kareneilbeck
17426 creation_date: 2013-07-31T03:46:14Z
17430 name: downstream_transcript_variant
17431 comment: Requested by Graham Ritchie, EBI/Sanger.
17432 synonym: "downstream transcript variant" EXACT []
17433 is_a: SO:0001628 ! intergenic_variant
17434 created_by: kareneilbeck
17435 creation_date: 2013-07-31T03:47:51Z
17439 name: 5_prime_UTR_premature_start_codon_gain_variant
17440 def: "A 5' UTR variant where a premature start codon is gained." [Sanger:am]
17441 synonym: "5 prime UTR premature start codon gain variant" EXACT []
17442 is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
17443 created_by: kareneilbeck
17444 creation_date: 2013-07-31T03:53:06Z
17448 name: 5_prime_UTR_premature_start_codon_loss_variant
17449 def: "A 5' UTR variant where a premature start codon is lost." [SANGER:am]
17450 is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
17451 created_by: kareneilbeck
17452 creation_date: 2013-07-31T03:56:48Z
17456 name: five_prime_UTR_premature_start_codon_location_variant
17457 def: "A 5' UTR variant where a premature start codon is moved." [SANGER:am]
17458 is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
17459 created_by: kareneilbeck
17460 creation_date: 2013-07-31T03:57:47Z
17464 name: consensus_AFLP_fragment
17465 def: "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]
17466 comment: Requested by Bayer Cropscience September, 2013.
17467 synonym: "consensus AFLP fragment" EXACT []
17468 synonym: "consensus amplified fragment length polymorphism fragment" EXACT []
17469 is_a: SO:0000994 ! consensus_region
17470 created_by: kareneilbeck
17471 creation_date: 2013-09-24T10:43:41Z
17475 name: nonsynonymous_variant
17476 def: "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]
17477 synonym: "non_synonymous_coding" EXACT [http://ensembl.org/info/docs/variation/index.html]
17478 synonym: "nonsynonymous variant" EXACT []
17479 is_a: SO:0001650 ! inframe_variant
17480 created_by: kareneilbeck
17481 creation_date: 2013-10-16T11:47:51Z
17485 name: extended_cis_splice_site
17486 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]
17487 comment: Added by Andy Menzies (Sanger).
17488 synonym: "extended cis splice site" EXACT []
17489 is_a: SO:0001419 ! cis_splice_site
17490 created_by: kareneilbeck
17491 creation_date: 2014-01-04T06:20:00Z
17495 name: intron_base_5
17496 def: "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]
17497 synonym: "intron base 5" EXACT []
17498 is_a: SO:0001014 ! intron_domain
17499 relationship: part_of SO:0001993 ! extended_cis_splice_site
17500 created_by: kareneilbeck
17501 creation_date: 2014-01-04T06:26:02Z
17505 name: extended_intronic_splice_region_variant
17506 def: "A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]
17507 comment: Added by Andy Menzies (Sanger).
17508 synonym: "extended intronic splice region variant" EXACT []
17509 is_a: SO:0001568 ! splicing_variant
17510 created_by: kareneilbeck
17511 creation_date: 2014-01-04T06:37:27Z
17515 name: extended_intronic_splice_region
17516 def: "Region of intronic sequence within 10 bases of an exon." [SANGER:am]
17517 synonym: "extended intronic splice region " EXACT []
17518 is_a: SO:0001014 ! intron_domain
17519 created_by: kareneilbeck
17520 creation_date: 2014-01-04T06:41:23Z
17525 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]
17526 is_a: SO:0000628 ! chromosomal_structural_element
17527 created_by: kareneilbeck
17528 creation_date: 2014-01-05T07:02:01Z
17533 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]
17534 synonym: "gRNA" RELATED []
17535 synonym: "guide RNA" RELATED []
17536 synonym: "small guide RNA" EXACT []
17537 is_a: SO:0000696 ! oligo
17538 created_by: kareneilbeck
17539 creation_date: 2014-01-05T07:25:08Z
17543 name: mating_type_region_motif
17544 def: "DNA motif that is a component of a mating type region." [SO:ke]
17545 synonym: "mating type region motif" EXACT []
17546 is_a: SO:0000713 ! DNA_motif
17547 relationship: part_of SO:0001789 ! mating_type_region
17548 created_by: kareneilbeck
17549 creation_date: 2014-01-05T07:30:17Z
17554 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]
17555 comment: Requested by Janos Demeter, SGD.
17556 synonym: "Y-region" EXACT []
17557 is_a: SO:0001999 ! mating_type_region_motif
17558 created_by: kareneilbeck
17559 creation_date: 2014-01-05T07:33:30Z
17564 def: "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]
17565 comment: Requested by Janos Demeter, SGD.
17566 synonym: "Z1-region" EXACT []
17567 is_a: SO:0001999 ! mating_type_region_motif
17568 created_by: kareneilbeck
17569 creation_date: 2014-01-05T07:34:59Z
17574 def: "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]
17575 comment: Requested by Janos Demeter, SGD.
17576 synonym: "Z2-segment" EXACT []
17577 is_a: SO:0001999 ! mating_type_region_motif
17578 created_by: kareneilbeck
17579 creation_date: 2014-01-05T07:36:45Z
17583 name: ARS_consensus_sequence
17584 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]
17585 synonym: "ACS" EXACT []
17586 synonym: "ARS consensus sequence" EXACT []
17587 is_a: SO:0000713 ! DNA_motif
17588 relationship: part_of SO:0000436 ! ARS
17589 created_by: kareneilbeck
17590 creation_date: 2014-01-05T07:47:48Z
17595 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]
17596 comment: Requested by Antonia Locke, (Pombe).
17597 synonym: "DSR motif" EXACT []
17598 is_a: SO:0000713 ! DNA_motif
17599 created_by: kareneilbeck
17600 creation_date: 2014-01-05T07:51:27Z
17604 name: zinc_repressed_element
17605 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]
17606 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.
17607 synonym: "zinc repressed element" EXACT []
17608 is_a: SO:0001659 ! promoter_element
17609 created_by: kareneilbeck
17610 creation_date: 2014-01-05T09:23:27Z
17615 def: "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]
17616 synonym: "multiple nucleotide substitution" EXACT []
17617 synonym: "multiple nucleotide variant" EXACT []
17618 is_a: SO:1000002 ! substitution
17619 created_by: kareneilbeck
17620 creation_date: 2014-01-13T03:48:40Z
17624 name: rare_amino_acid_variant
17625 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]
17626 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.
17627 synonym: "rare amino acid variant" EXACT []
17628 is_a: SO:0001586 ! non_conservative_missense_variant
17629 created_by: kareneilbeck
17630 creation_date: 2014-03-24T02:24:01Z
17634 name: selenocysteine_loss
17635 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]
17636 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.
17637 synonym: "selenocysteine loss" EXACT []
17638 is_a: SO:0002008 ! rare_amino_acid_variant
17639 created_by: kareneilbeck
17640 creation_date: 2014-03-24T02:29:44Z
17644 name: pyrrolysine_loss
17645 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]
17646 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.
17647 synonym: "pyrrolysine loss" EXACT []
17648 is_a: SO:0002008 ! rare_amino_acid_variant
17649 created_by: kareneilbeck
17650 creation_date: 2014-03-24T02:30:16Z
17654 name: intragenic_variant
17655 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]
17656 comment: Requested by Pablo Cingolani, for use in SnpEff.
17657 synonym: "intragenic variant" EXACT []
17658 synonym: "snpEff:INTRAGENIC" EXACT VAR []
17659 is_a: SO:0001576 ! transcript_variant
17660 created_by: kareneilbeck
17661 creation_date: 2014-03-24T02:33:13Z
17666 def: "A codon variant that changes at least one base of the canonical start codon." [SO:ke]
17667 comment: Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
17668 synonym: "snpEff:START_LOST" EXACT VAR []
17669 is_a: SO:0001582 ! initiator_codon_variant
17670 is_a: SO:0001992 ! nonsynonymous_variant
17671 created_by: kareneilbeck
17672 creation_date: 2014-03-24T02:41:28Z
17676 name: 5_prime_UTR_truncation
17677 def: "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence." [SO:ke]
17678 synonym: "5 prime UTR truncation" EXACT []
17679 synonym: "snpEff:UTR_5_DELETED" EXACT VAR []
17680 is_a: SO:0001623 ! 5_prime_UTR_variant
17681 created_by: kareneilbeck
17682 creation_date: 2014-03-25T10:46:42Z
17686 name: 5_prime_UTR_elongation
17687 def: "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]
17688 synonym: "5 prime UTR elongation" EXACT []
17689 is_a: SO:0001623 ! 5_prime_UTR_variant
17690 created_by: kareneilbeck
17691 creation_date: 2014-03-25T10:48:26Z
17695 name: 3_prime_UTR_truncation
17696 def: "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence." [SO:ke]
17697 synonym: "3 prime UTR truncation" EXACT []
17698 synonym: "snpEff:UTR_3_DELETED" EXACT VAR []
17699 is_a: SO:0001624 ! 3_prime_UTR_variant
17700 created_by: kareneilbeck
17701 creation_date: 2014-03-25T10:54:50Z
17705 name: 3_prime_UTR_elongation
17706 def: "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]
17707 synonym: "3 prime UTR elongation" EXACT []
17708 is_a: SO:0001624 ! 3_prime_UTR_variant
17709 created_by: kareneilbeck
17710 creation_date: 2014-03-25T10:55:33Z
17714 name: conserved_intergenic_variant
17715 def: "A sequence variant located in a conserved intergenic region, between genes." [SO:ke]
17716 comment: Requested by Uma Paila (UVA) for snpEff.
17717 synonym: "conserved intergenic variant" EXACT []
17718 synonym: "snpEff:INTERGENIC_CONSERVED" EXACT VAR []
17719 is_a: SO:0001628 ! intergenic_variant
17720 created_by: kareneilbeck
17721 creation_date: 2014-03-25T02:54:39Z
17725 name: conserved_intron_variant
17726 def: "A transcript variant occurring within a conserved region of an intron." [SO:ke]
17727 comment: Requested by Uma Paila (UVA) for snpEff.
17728 synonym: "conserved intron variant" EXACT []
17729 synonym: "snpEff:INTRON_CONSERVED" EXACT VAR []
17730 is_a: SO:0001627 ! intron_variant
17731 created_by: kareneilbeck
17732 creation_date: 2014-03-25T02:58:41Z
17736 name: start_retained_variant
17737 def: "A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]
17738 comment: Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
17739 is_a: SO:0001582 ! initiator_codon_variant
17740 is_a: SO:0001819 ! synonymous_variant
17741 created_by: kareneilbeck
17742 creation_date: 2014-03-28T10:08:41Z
17746 name: boundary_element
17747 def: "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]
17748 comment: Requested by Antonia Lock.
17749 synonym: "boundary element" EXACT []
17750 is_a: SO:0000713 ! DNA_motif
17751 created_by: kareneilbeck
17752 creation_date: 2014-05-30T14:45:37Z
17756 name: mating_type_region_replication_fork_barrier
17757 def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]
17758 comment: Requested by Midori Harris.
17759 synonym: "mating type region replication fork barrier" EXACT []
17760 is_a: SO:0000713 ! DNA_motif
17761 created_by: kareneilbeck
17762 creation_date: 2014-05-30T14:57:26Z
17767 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]
17768 synonym: "primal small RNA" EXACT []
17769 is_a: SO:0000655 ! ncRNA
17770 created_by: kareneilbeck
17771 creation_date: 2014-05-30T15:01:24Z
17775 name: multiplexing_sequence_identifier
17776 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]
17777 synonym: "multiplexing sequence identifier" EXACT []
17778 is_a: SO:0000324 ! tag
17779 created_by: kareneilbeck
17780 creation_date: 2014-05-30T15:13:16Z
17786 def: "The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR." [SGD:jd]
17787 comment: MERGED COMMENT:\nTARGET COMMENT: Requested by Janos Demeter, SGD.\n--------------------\nSOURCE COMMENT: Requested by Janos Demeter, SGD.
17788 synonym: "W-region" EXACT []
17789 is_a: SO:0001999 ! mating_type_region_motif
17790 created_by: kareneilbeck
17791 creation_date: 2014-07-11T13:20:08Z
17795 name: cis_acting_homologous_chromosome_pairing_region
17796 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]
17797 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.
17798 synonym: "cis-acting homologous chromosome pairing region" EXACT []
17799 is_a: SO:0000713 ! DNA_motif
17800 created_by: kareneilbeck
17801 creation_date: 2014-07-14T11:40:34Z
17805 name: intein_encoding_region
17806 def: "The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]
17807 comment: Requested by Janos Demeter 2014.
17808 is_a: SO:0000842 ! gene_component_region
17809 created_by: kareneilbeck
17810 creation_date: 2014-07-14T11:53:21Z
17815 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]
17816 synonym: "upstream ORF" EXACT []
17817 is_a: SO:0000236 ! ORF
17818 created_by: kareneilbeck
17819 creation_date: 2014-07-14T11:59:23Z
17824 def: "An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]
17825 synonym: "small ORF" EXACT []
17826 synonym: "smORF" EXACT []
17827 is_a: SO:0000236 ! ORF
17828 created_by: kareneilbeck
17829 creation_date: 2014-07-14T12:02:33Z
17834 def: "A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]
17835 synonym: "translated nested antisense gene" EXACT []
17836 is_a: SO:0000236 ! ORF
17837 created_by: kareneilbeck
17838 creation_date: 2014-07-14T12:04:32Z
17843 def: "One of two segments of homology found at all three mating loci (HML, MAT and HMR)." [SGD:jd]
17844 synonym: "x-region" EXACT []
17845 is_a: SO:0001999 ! mating_type_region_motif
17846 created_by: kareneilbeck
17847 creation_date: 2014-07-14T18:43:21Z
17852 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]
17853 synonym: "short hairpin RNA" EXACT []
17854 synonym: "small hairpin RNA" EXACT []
17855 xref: http:http:en.wikipedia.org/wiki/Small_hairpin_RNA "wikipedia"
17856 is_a: SO:0000655 ! ncRNA
17857 created_by: kareneilbeck
17858 creation_date: 2014-10-23T09:16:29Z
17863 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]
17864 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.
17865 synonym: "microRNA-offset RNA" EXACT []
17866 is_a: SO:0000370 ! small_regulatory_ncRNA
17867 relationship: part_of SO:0001244 ! pre_miRNA
17868 created_by: kareneilbeck
17869 creation_date: 2015-01-09T13:57:43Z
17874 def: "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA." [SO:ke]
17875 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.
17876 synonym: "loop-origin miRs" EXACT []
17877 is_a: SO:0000370 ! small_regulatory_ncRNA
17878 relationship: part_of SO:0001244 ! pre_miRNA
17879 created_by: kareneilbeck
17880 creation_date: 2015-01-09T14:02:02Z
17884 name: miR_encoding_snoRNA_primary_transcript
17885 def: "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
17886 synonym: "miR encoding snoRNA primary transcript" EXACT []
17887 is_a: SO:0000232 ! snoRNA_primary_transcript
17888 relationship: has_part SO:0001244 ! pre_miRNA
17889 created_by: kareneilbeck
17890 creation_date: 2015-01-09T15:02:13Z
17894 name: lncRNA_primary_transcript
17895 def: "A primary transcript encoding a lncRNA." [SO:ke]
17896 synonym: "lncRNA primary transcript" EXACT []
17897 is_a: SO:0000483 ! nc_primary_transcript
17898 created_by: kareneilbeck
17899 creation_date: 2015-01-09T15:23:03Z
17903 name: miR_encoding_lncRNA_primary_transcript
17904 def: "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
17905 synonym: "miR encoding lncRNA primary transcript" EXACT []
17906 is_a: SO:0002035 ! lncRNA_primary_transcript
17907 relationship: has_part SO:0001244 ! pre_miRNA
17908 created_by: kareneilbeck
17909 creation_date: 2015-01-09T15:23:48Z
17913 name: miR_encoding_tRNA_primary_transcript
17914 def: "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
17915 synonym: "miR encoding tRNA primary transcript" EXACT []
17916 is_a: SO:0000210 ! tRNA_primary_transcript
17917 relationship: has_part SO:0001244 ! pre_miRNA
17918 created_by: kareneilbeck
17919 creation_date: 2015-01-09T15:28:23Z
17923 name: shRNA_primary_transcript
17924 def: "A primary transcript encoding an shRNA." [SO:ke]
17925 synonym: "shRNA primary transcript" EXACT []
17926 is_a: SO:0000483 ! nc_primary_transcript
17927 created_by: kareneilbeck
17928 creation_date: 2015-01-09T15:30:43Z
17932 name: miR_encoding_shRNA_primary_transcript
17933 def: "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
17934 synonym: "miR encoding shRNA primary transcript" EXACT []
17935 is_a: SO:0002038 ! shRNA_primary_transcript
17936 relationship: has_part SO:0001244 ! pre_miRNA
17937 created_by: kareneilbeck
17938 creation_date: 2015-01-09T15:32:00Z
17942 name: vaultRNA_primary_transcript
17943 def: "A primary transcript encoding a vaultRNA." [SO:ke]
17944 synonym: "vaultRNA primary transcript" EXACT []
17945 is_a: SO:0000483 ! nc_primary_transcript
17946 created_by: kareneilbeck
17947 creation_date: 2015-01-09T15:33:33Z
17951 name: miR_encoding_vaultRNA_primary_transcript
17952 def: "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
17953 synonym: "miR encoding vaultRNA primary transcript" EXACT []
17954 is_a: SO:0002040 ! vaultRNA_primary_transcript
17955 relationship: has_part SO:0001244 ! pre_miRNA
17956 created_by: kareneilbeck
17957 creation_date: 2015-01-09T15:34:32Z
17961 name: Y_RNA_primary_transcript
17962 def: "A primary transcript encoding a Y-RNA." [SO:ke]
17963 synonym: "Y-RNA primary transcript" EXACT []
17964 is_a: SO:0000483 ! nc_primary_transcript
17965 created_by: kareneilbeck
17966 creation_date: 2015-01-09T15:36:51Z
17970 name: miR_encoding_Y_RNA_primary_transcript
17971 def: "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
17972 synonym: "miR encoding Y-RNA primary transcript" EXACT []
17973 is_a: SO:0002042 ! Y_RNA_primary_transcript
17974 relationship: has_part SO:0001244 ! pre_miRNA
17975 created_by: kareneilbeck
17976 creation_date: 2015-01-09T15:37:46Z
17981 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]
17982 comment: Requested by Rama - SGD.
17983 synonym: "TCS element" EXACT []
17984 synonym: "TEA Consensus Sequence " EXACT []
17985 is_a: SO:0001659 ! promoter_element
17986 created_by: kareneilbeck
17987 creation_date: 2015-02-09T15:02:53Z
17991 name: pheromone_response_element
17992 def: "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]." [PMID:1489142, SO:ke]
17993 comment: Requested by Rama, SGD.
17994 synonym: "pheromone response element" EXACT []
17995 synonym: "PRE" EXACT []
17996 is_a: SO:0000235 ! TF_binding_site
17997 is_a: SO:0001659 ! promoter_element
17998 created_by: kareneilbeck
17999 creation_date: 2015-02-09T15:05:43Z
18004 def: "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae." [PMID:1489142, SO:ke]
18005 comment: Requested by Rama, SGD.
18006 synonym: "filamentation and invasion response element" EXACT []
18007 is_a: SO:0001461 ! enhancer_binding_site
18008 created_by: kareneilbeck
18009 creation_date: 2015-02-09T15:09:47Z
18013 name: transcription_pause_site
18014 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]
18015 synonym: "transcription pause site" EXACT []
18016 is_a: SO:0001679 ! transcription_regulatory_region
18017 created_by: kareneilbeck
18018 creation_date: 2015-02-09T15:32:52Z
18022 name: disabled_reading_frame
18023 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]
18024 synonym: "disabled ORF" EXACT []
18025 synonym: "disabled_reading frame" RELATED []
18026 synonym: "dORF" EXACT []
18027 is_a: SO:0000717 ! reading_frame
18028 created_by: kareneilbeck
18029 creation_date: 2015-02-09T16:15:46Z
18033 name: H3K27_acetylation_site
18034 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]
18035 comment: Requested by: Sagar Jain, Richard Scheuermann.
18036 synonym: "H3K27 acetylation site" EXACT []
18037 is_a: SO:0001973 ! histone_3_acetylation_site
18038 created_by: kareneilbeck
18039 creation_date: 2015-05-14T10:17:11Z
18043 name: constitutive_promoter
18044 def: "A promoter that allows for continual transcription of gene." [SO:ke]
18045 synonym: "constitutive promoter" EXACT []
18046 is_a: SO:0000167 ! promoter
18047 created_by: kareneilbeck
18048 creation_date: 2015-05-14T10:39:09Z
18052 name: inducible_promoter
18053 def: "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors." [SO:ke]
18054 synonym: "inducible promoter" EXACT []
18055 is_a: SO:0000167 ! promoter
18056 created_by: kareneilbeck
18057 creation_date: 2015-05-14T10:39:56Z
18061 name: dominant_negative_variant
18062 def: "A variant where the mutated gene product adversely affects the other (wild type) gene product." [SO:ke]
18063 comment: Requested by Deanna Church.
18064 synonym: "dominant negative" EXACT []
18065 synonym: "dominant negative variant" EXACT []
18066 is_a: SO:0001536 ! functional_variant
18067 created_by: kareneilbeck
18068 creation_date: 2015-05-14T11:16:28Z
18072 name: gain_of_function_variant
18073 def: "A sequence variant whereby new or enhanced function is conferred on the gene product." [SO:ke]
18074 synonym: "gain of function variant" EXACT []
18075 is_a: SO:0001536 ! functional_variant
18076 created_by: kareneilbeck
18077 creation_date: 2015-05-14T11:20:47Z
18081 name: loss_of_function_variant
18082 def: "A sequence variant whereby the gene product has diminished or abolished function." [SO:ke]
18083 synonym: "loss of function variant" EXACT []
18084 is_a: SO:0001536 ! functional_variant
18085 created_by: kareneilbeck
18086 creation_date: 2015-05-14T11:21:29Z
18090 name: null_mutation
18091 def: "A variant whereby the gene product is not functional or the gene product is not produced." [SO:ke]
18092 synonym: "null mutation" EXACT []
18093 is_a: SO:0001536 ! functional_variant
18094 created_by: kareneilbeck
18095 creation_date: 2015-05-14T11:21:57Z
18099 name: intronic_splicing_silencer
18100 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]
18101 comment: Requested by Javier Diez Perez.
18102 synonym: "intronic splicing silencer" EXACT []
18103 synonym: "ISS" EXACT []
18104 is_a: SO:0000625 ! silencer
18105 relationship: part_of SO:0000188 ! intron
18106 created_by: kareneilbeck
18107 creation_date: 2015-05-14T12:24:10Z
18111 name: intronic_splicing_enhancer
18112 synonym: "ISE" EXACT []
18113 created_by: kareneilbeck
18114 creation_date: 2015-05-14T12:28:31Z
18119 name: exonic_splicing_silencer
18120 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]
18121 comment: Requested by Javier Diez Perez.
18122 synonym: "ESS" EXACT []
18123 synonym: "exonic splicing silencer" EXACT []
18124 is_a: SO:0000625 ! silencer
18125 is_a: SO:0000852 ! exon_region
18126 created_by: kareneilbeck
18127 creation_date: 2015-05-14T12:42:12Z
18131 name: recombination_enhancer
18132 def: "A regulatory_region that promotes or induces the process of recombination." [PMID:8861911, SGD:se]
18133 synonym: "recombination enhancer" EXACT []
18134 is_a: SO:0001681 ! recombination_regulatory_region
18135 created_by: kareneilbeck
18136 creation_date: 2015-05-14T13:08:58Z
18140 name: interchomosomal_translocation
18141 def: "A translocation where the regions involved are from different chromosomes." [NCBI:th]
18142 is_a: SO:1000044 ! chromosomal_translocation
18143 created_by: kareneilbeck
18144 creation_date: 2015-06-18T11:10:30Z
18148 name: intrachomosomal_translocation
18149 def: "A translocation where the regions involved are from the same chromosome." [NCBI:th]
18150 is_a: SO:1000044 ! chromosomal_translocation
18151 created_by: kareneilbeck
18152 creation_date: 2015-06-18T11:10:51Z
18156 name: complex_chromosomal_rearrangement
18157 def: "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis." [NCBI:th]
18158 synonym: "complex chromosomal rearrangement" EXACT []
18159 is_a: SO:0001784 ! complex_structural_alteration
18160 created_by: kareneilbeck
18161 creation_date: 2015-06-18T11:24:55Z
18165 name: alu_insertion
18166 def: "An insertion of sequence from the Alu family of mobile elements." [NCBI:th]
18167 synonym: "alu insertion" EXACT []
18168 is_a: SO:0001837 ! mobile_element_insertion
18169 created_by: kareneilbeck
18170 creation_date: 2015-06-18T11:30:36Z
18174 name: LINE1_insertion
18175 def: "An insertion from the Line1 family of mobile elements." [NCBI:th]
18176 synonym: "line1 insertion" RELATED []
18177 is_a: SO:0001837 ! mobile_element_insertion
18178 created_by: kareneilbeck
18179 creation_date: 2015-06-18T11:34:44Z
18183 name: SVA_insertion
18184 def: "An insertion of sequence from the SVA family of mobile elements." [NCBI:th]
18185 is_a: SO:0001837 ! mobile_element_insertion
18186 created_by: kareneilbeck
18187 creation_date: 2015-06-18T11:36:12Z
18191 name: regulatory_region
18192 def: "A region of sequence that is involved in the control of a biological process." [SO:ke]
18194 synonym: "regulatory region" EXACT []
18195 xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki"
18196 is_a: SO:0000831 ! gene_member_region
18200 name: U14_snoRNA_primary_transcript
18201 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]
18202 synonym: "4.5S snRNA primary transcript" EXACT []
18203 synonym: "U14 snoRNA primary transcript" EXACT []
18204 is_a: SO:0000232 ! snoRNA_primary_transcript
18208 name: methylation_guide_snoRNA
18209 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]
18210 comment: Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
18211 synonym: "methylation guide snoRNA" EXACT []
18212 is_a: SO:0000593 ! C_D_box_snoRNA
18213 relationship: derives_from SO:0000580 ! methylation_guide_snoRNA_primary_transcript
18217 name: rRNA_cleavage_RNA
18218 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]
18219 synonym: "rRNA cleavage RNA" EXACT []
18220 is_a: SO:0000655 ! ncRNA
18221 relationship: derives_from SO:0000582 ! rRNA_cleavage_snoRNA_primary_transcript
18225 name: exon_of_single_exon_gene
18226 def: "An exon that is the only exon in a gene." [RSC:cb]
18227 synonym: "exon of single exon gene" EXACT []
18228 synonym: "single_exon" RELATED []
18229 synonym: "singleton exon" EXACT []
18230 is_a: SO:0000147 ! exon
18234 name: cassette_array_member
18235 synonym: "cassette array member" EXACT []
18236 is_a: SO:0005848 ! gene_cassette_member
18240 name: gene_cassette_member
18241 synonym: "gene cassette member" EXACT []
18242 is_a: SO:0000081 ! gene_array_member
18246 name: gene_subarray_member
18247 synonym: "gene subarray member" EXACT []
18248 is_a: SO:0000081 ! gene_array_member
18252 name: primer_binding_site
18253 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]
18254 synonym: "primer binding site" EXACT []
18255 xref: http://en.wikipedia.org/wiki/Primer_binding_site "wiki"
18256 is_a: SO:0001655 ! nucleotide_binding_site
18257 relationship: part_of SO:0000186 ! LTR_retrotransposon
18262 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]
18263 comment: This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
18264 synonym: "gene array" EXACT []
18265 is_a: SO:0005855 ! gene_group
18269 name: gene_subarray
18270 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]
18271 comment: This would include, for example, a cluster of genes encoding different histones.
18272 synonym: "gene subarray" EXACT []
18273 is_a: SO:0005855 ! gene_group
18277 name: gene_cassette
18278 def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]
18279 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.
18280 synonym: "gene cassette" EXACT []
18281 xref: http://en.wikipedia.org/wiki/Gene_cassette "wiki"
18282 is_a: SO:0000704 ! gene
18286 name: gene_cassette_array
18287 def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]
18288 comment: This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
18289 synonym: "gene cassette array" EXACT []
18290 is_a: SO:0005855 ! gene_group
18291 relationship: has_part SO:0005853 ! gene_cassette
18296 def: "A collection of related genes." [SO:ma]
18298 synonym: "gene group" EXACT []
18299 is_a: SO:0001411 ! biological_region
18303 name: selenocysteine_tRNA_primary_transcript
18304 def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
18305 synonym: "selenocysteine tRNA primary transcript" EXACT []
18306 is_a: SO:0000210 ! tRNA_primary_transcript
18310 name: selenocysteinyl_tRNA
18311 def: "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]
18312 synonym: "selenocysteinyl tRNA" EXACT []
18313 synonym: "selenocysteinyl-transfer ribonucleic acid" EXACT []
18314 synonym: "selenocysteinyl-transfer RNA" EXACT []
18315 is_a: SO:0000253 ! tRNA
18316 relationship: derives_from SO:0005856 ! selenocysteine_tRNA_primary_transcript
18320 name: syntenic_region
18321 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]
18322 synonym: "syntenic region" EXACT []
18323 is_a: SO:0000330 ! conserved_region
18324 relationship: has_quality SO:0000860 ! syntenic
18328 name: biochemical_region_of_peptide
18329 def: "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]
18332 synonym: "biochemical motif" EXACT []
18333 synonym: "biochemical region of peptide" EXACT []
18334 synonym: "biochemical_region" RELATED []
18335 is_a: SO:0001067 ! polypeptide_motif
18339 name: molecular_contact_region
18340 def: "A region that is involved a contact with another molecule." [EBIBS:GAR]
18343 synonym: "molecular contact region" RELATED []
18344 is_a: SO:0100001 ! biochemical_region_of_peptide
18348 name: intrinsically_unstructured_polypeptide_region
18349 def: "A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]
18351 synonym: "disordered region" RELATED BS []
18352 synonym: "intrinsically unstructured polypeptide region" EXACT []
18353 is_a: SO:0001070 ! polypeptide_structural_region
18357 name: catmat_left_handed_three
18358 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/]
18360 synonym: "catmat-3l" EXACT []
18361 is_a: SO:0001078 ! polypeptide_secondary_structure
18365 name: catmat_left_handed_four
18366 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/]
18368 synonym: "catmat-4l" EXACT []
18369 is_a: SO:0001078 ! polypeptide_secondary_structure
18373 name: catmat_right_handed_three
18374 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/]
18376 synonym: "catmat-3r" EXACT []
18377 is_a: SO:0001078 ! polypeptide_secondary_structure
18381 name: catmat_right_handed_four
18382 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/]
18384 synonym: "catmat-4r" EXACT []
18385 is_a: SO:0001078 ! polypeptide_secondary_structure
18389 name: alpha_beta_motif
18390 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/]
18392 synonym: "alpha beta motif" EXACT []
18393 is_a: SO:0001078 ! polypeptide_secondary_structure
18397 name: lipoprotein_signal_peptide
18398 def: "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]
18400 synonym: "lipoprotein signal peptide" EXACT []
18401 synonym: "prokaryotic membrane lipoprotein lipid attachment site" EXACT []
18402 is_a: SO:0100011 ! cleaved_peptide_region
18407 def: "An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]
18409 synonym: "no output" EXACT BS []
18410 is_a: SO:0000703 ! experimental_result_region
18414 name: cleaved_peptide_region
18415 def: "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]
18419 synonym: "cleaved peptide region" EXACT []
18420 is_a: SO:0000839 ! polypeptide_region
18421 relationship: part_of SO:0001063 ! immature_peptide_region
18426 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]
18428 synonym: "coil" RELATED BS []
18429 synonym: "peptide coil" EXACT []
18430 synonym: "random coil" RELATED BS []
18431 is_a: SO:0001078 ! polypeptide_secondary_structure
18435 name: hydrophobic_region_of_peptide
18436 def: "Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]
18439 synonym: "hydropathic" RELATED []
18440 synonym: "hydrophobic region of peptide" RELATED []
18441 synonym: "hydrophobic_region" EXACT []
18442 synonym: "hydrophobicity" RELATED []
18443 is_a: SO:0000839 ! polypeptide_region
18447 name: n_terminal_region
18448 def: "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]
18450 synonym: "N-region" RELATED []
18451 is_a: SO:0100011 ! cleaved_peptide_region
18452 relationship: part_of SO:0000418 ! signal_peptide
18456 name: c_terminal_region
18457 def: "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]
18459 synonym: "C-region" RELATED []
18460 is_a: SO:0100011 ! cleaved_peptide_region
18461 relationship: part_of SO:0000418 ! signal_peptide
18465 name: central_hydrophobic_region_of_signal_peptide
18466 def: "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]
18468 synonym: "central hydrophobic region of signal peptide" EXACT []
18469 synonym: "central_hydrophobic_region" RELATED []
18470 synonym: "H-region" RELATED []
18471 is_a: SO:0100011 ! cleaved_peptide_region
18472 relationship: part_of SO:0000418 ! signal_peptide
18476 name: polypeptide_conserved_motif
18477 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]
18479 synonym: "motif" RELATED []
18480 is_a: SO:0001067 ! polypeptide_motif
18484 name: polypeptide_binding_motif
18485 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]
18487 synonym: "binding" RELATED [uniprot:feature_type]
18488 synonym: "polypeptide binding motif" EXACT []
18489 is_a: SO:0100001 ! biochemical_region_of_peptide
18493 name: polypeptide_catalytic_motif
18494 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]
18496 synonym: "catalytic_motif" RELATED []
18497 synonym: "polypeptide catalytic motif" EXACT []
18498 is_a: SO:0100001 ! biochemical_region_of_peptide
18502 name: polypeptide_DNA_contact
18503 def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]
18505 synonym: "DNA_bind" EXACT BS [uniprot:feature]
18506 synonym: "polypeptide DNA contact" EXACT []
18507 is_a: SO:0001429 ! DNA_binding_site
18508 is_a: SO:0100002 ! molecular_contact_region
18512 name: polypeptide_conserved_region
18513 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]
18515 synonym: "polypeptide conserved region" EXACT []
18516 is_a: SO:0000839 ! polypeptide_region
18521 def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]
18523 xref: loinc:LA6690-7 "Substitution"
18524 is_a: SO:0001059 ! sequence_alteration
18525 is_a: SO:0001411 ! biological_region
18529 name: complex_substitution
18530 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]
18532 synonym: "complex substitution" EXACT []
18533 is_a: SO:1000002 ! substitution
18537 name: point_mutation
18538 def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]
18540 synonym: "point mutation" EXACT []
18541 xref: http://en.wikipedia.org/wiki/Point_mutation "wiki"
18542 is_a: SO:0001483 ! SNV
18547 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]
18548 is_a: SO:0001483 ! SNV
18552 name: pyrimidine_transition
18553 def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]
18554 synonym: "pyrimidine transition" EXACT []
18555 is_a: SO:1000009 ! transition
18559 name: C_to_T_transition
18560 def: "A transition of a cytidine to a thymine." [SO:ke]
18561 synonym: "C to T transition" EXACT []
18562 is_a: SO:1000010 ! pyrimidine_transition
18566 name: C_to_T_transition_at_pCpG_site
18567 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]
18568 synonym: "C to T transition at pCpG site" EXACT []
18569 is_a: SO:1000011 ! C_to_T_transition
18573 name: T_to_C_transition
18574 synonym: "T to C transition" EXACT []
18575 is_a: SO:1000010 ! pyrimidine_transition
18579 name: purine_transition
18580 def: "A substitution of a purine, A or G, for another purine." [SO:ke]
18581 synonym: "purine transition" EXACT []
18582 is_a: SO:1000009 ! transition
18586 name: A_to_G_transition
18587 def: "A transition of an adenine to a guanine." [SO:ke]
18588 synonym: "A to G transition" EXACT []
18589 is_a: SO:1000014 ! purine_transition
18593 name: G_to_A_transition
18594 def: "A transition of a guanine to an adenine." [SO:ke]
18595 synonym: "G to A transition" EXACT []
18596 is_a: SO:1000014 ! purine_transition
18601 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]
18602 xref: http://en.wikipedia.org/wiki/Transversion "wiki"
18603 is_a: SO:0001483 ! SNV
18607 name: pyrimidine_to_purine_transversion
18608 def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]
18609 synonym: "pyrimidine to purine transversion" EXACT []
18610 is_a: SO:1000017 ! transversion
18614 name: C_to_A_transversion
18615 def: "A transversion from cytidine to adenine." [SO:ke]
18616 synonym: "C to A transversion" EXACT []
18617 is_a: SO:1000018 ! pyrimidine_to_purine_transversion
18621 name: C_to_G_transversion
18622 synonym: "C to G transversion" EXACT []
18623 is_a: SO:1000018 ! pyrimidine_to_purine_transversion
18627 name: T_to_A_transversion
18628 def: "A transversion from T to A." [SO:ke]
18629 synonym: "T to A transversion" EXACT []
18630 is_a: SO:1000018 ! pyrimidine_to_purine_transversion
18634 name: T_to_G_transversion
18635 def: "A transversion from T to G." [SO:ke]
18636 synonym: "T to G transversion" EXACT []
18637 is_a: SO:1000018 ! pyrimidine_to_purine_transversion
18641 name: purine_to_pyrimidine_transversion
18642 def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]
18643 synonym: "purine to pyrimidine transversion" EXACT []
18644 is_a: SO:1000017 ! transversion
18648 name: A_to_C_transversion
18649 def: "A transversion from adenine to cytidine." [SO:ke]
18650 synonym: "A to C transversion" EXACT []
18651 is_a: SO:1000023 ! purine_to_pyrimidine_transversion
18655 name: A_to_T_transversion
18656 def: "A transversion from adenine to thymine." [SO:ke]
18657 synonym: "A to T transversion" EXACT []
18658 is_a: SO:1000023 ! purine_to_pyrimidine_transversion
18662 name: G_to_C_transversion
18663 def: "A transversion from guanine to cytidine." [SO:ke]
18664 synonym: "G to C transversion" EXACT []
18665 is_a: SO:1000023 ! purine_to_pyrimidine_transversion
18669 name: G_to_T_transversion
18670 def: "A transversion from guanine to thymine." [SO:ke]
18671 synonym: "G to T transversion" EXACT []
18672 is_a: SO:1000023 ! purine_to_pyrimidine_transversion
18676 name: intrachromosomal_mutation
18677 def: "A chromosomal structure variation within a single chromosome." [SO:ke]
18678 synonym: "intrachromosomal mutation" EXACT []
18679 is_a: SO:1000183 ! chromosome_structure_variation
18680 relationship: has_quality SO:0001510 ! intrachromosomal
18684 name: chromosomal_deletion
18685 def: "An incomplete chromosome." [SO:ke]
18686 synonym: "(bacteria)&Dgr;" RELATED []
18687 synonym: "(Drosophila)Df" RELATED []
18688 synonym: "(fungi)D" RELATED []
18689 synonym: "chromosomal deletion" EXACT []
18690 synonym: "deficiency" EXACT []
18691 xref: http://en.wikipedia.org/wiki/Chromosomal_deletion "wiki"
18692 is_a: SO:1000028 ! intrachromosomal_mutation
18693 relationship: has_part SO:0000159 ! deletion
18697 name: chromosomal_inversion
18698 def: "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]
18699 synonym: "(bacteria)IN" RELATED []
18700 synonym: "(Drosophila)In" RELATED []
18701 synonym: "(fungi)In" RELATED []
18702 synonym: "chromosomal inversion" EXACT []
18703 xref: http://en.wikipedia.org/wiki/Chromosomal_inversion "wiki"
18704 is_a: SO:1000028 ! intrachromosomal_mutation
18705 relationship: has_part SO:1000036 ! inversion
18709 name: interchromosomal_mutation
18710 def: "A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]
18711 synonym: "interchromosomal mutation" EXACT []
18712 is_a: SO:1000183 ! chromosome_structure_variation
18713 relationship: has_quality SO:0001511 ! interchromosomal
18718 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]
18719 comment: Indels can have a different number of bases than the corresponding reference sequence.
18720 xref: http://en.wikipedia.org/wiki/Indel "wiki"
18721 xref: loinc:LA9659-9 "Insertion and Deletion"
18722 is_a: SO:0001059 ! sequence_alteration
18727 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]
18728 synonym: "nucleotide duplication" EXACT []
18729 synonym: "nucleotide_duplication" RELATED []
18730 xref: loinc:LA6686-5 "Duplication"
18731 is_a: SO:0000667 ! insertion
18736 def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
18739 synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
18740 xref: loinc:LA6689-9 "Inversion"
18741 is_a: SO:0001059 ! sequence_alteration
18742 is_a: SO:0001411 ! biological_region
18746 name: chromosomal_duplication
18747 def: "An extra chromosome." [SO:ke]
18748 synonym: "(Drosophila)Dp" RELATED []
18749 synonym: "(fungi)Dp" RELATED []
18750 synonym: "chromosomal duplication" EXACT []
18751 xref: http://en.wikipedia.org/wiki/Chromosomal_duplication "wiki"
18752 is_a: SO:1000183 ! chromosome_structure_variation
18756 name: intrachromosomal_duplication
18757 def: "A duplication that occurred within a chromosome." [SO:ke]
18758 synonym: "intrachromosomal duplication" EXACT []
18759 is_a: SO:1000028 ! intrachromosomal_mutation
18760 is_a: SO:1000037 ! chromosomal_duplication
18761 relationship: has_part SO:1000035 ! duplication
18765 name: direct_tandem_duplication
18766 def: "A tandem duplication where the individual regions are in the same orientation." [SO:ke]
18767 synonym: "direct tandem duplication" EXACT []
18768 is_a: SO:1000173 ! tandem_duplication
18772 name: inverted_tandem_duplication
18773 def: "A tandem duplication where the individual regions are not in the same orientation." [SO:ke]
18774 synonym: "inverted tandem duplication" EXACT []
18775 synonym: "mirror duplication" RELATED []
18776 is_a: SO:1000173 ! tandem_duplication
18780 name: intrachromosomal_transposition
18781 def: "A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]
18782 synonym: "(Drosophila)Tp" RELATED []
18783 synonym: "intrachromosomal transposition" EXACT []
18784 is_a: SO:0000453 ! chromosomal_transposition
18785 is_a: SO:1000038 ! intrachromosomal_duplication
18786 relationship: has_part SO:0000199 ! translocation
18787 relationship: has_part SO:1000035 ! duplication
18791 name: compound_chromosome
18792 def: "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]
18793 synonym: "compound chromosome" EXACT []
18794 is_a: SO:1000183 ! chromosome_structure_variation
18798 name: Robertsonian_fusion
18799 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]
18800 synonym: "centric-fusion translocations" EXACT []
18801 synonym: "Robertsonian fusion" EXACT []
18802 synonym: "whole-arm translocations" EXACT []
18803 xref: http://en.wikipedia.org/wiki/Robertsonian_fusion "wiki"
18804 is_a: SO:1000044 ! chromosomal_translocation
18808 name: chromosomal_translocation
18809 def: "An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]
18810 synonym: "(Drosophila)T" RELATED []
18811 synonym: "(fungi)T" RELATED []
18812 synonym: "chromosomal translocation" EXACT []
18813 xref: http://en.wikipedia.org/wiki/Chromosomal_translocation "wiki"
18814 is_a: SO:0000199 ! translocation
18815 is_a: SO:1000031 ! interchromosomal_mutation
18819 name: ring_chromosome
18820 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]
18821 synonym: "(Drosophila)R" RELATED []
18822 synonym: "(fungi)C" RELATED []
18823 synonym: "ring chromosome" EXACT []
18824 xref: http://en.wikipedia.org/wiki/Ring_chromosome "wiki"
18825 is_a: SO:1000028 ! intrachromosomal_mutation
18826 relationship: has_quality SO:0000988 ! circular
18830 name: pericentric_inversion
18831 def: "A chromosomal inversion that includes the centromere." [FB:reference_manual]
18832 synonym: "pericentric inversion" EXACT []
18833 is_a: SO:1000030 ! chromosomal_inversion
18834 relationship: has_quality SO:0001518 ! pericentric
18838 name: paracentric_inversion
18839 def: "A chromosomal inversion that does not include the centromere." [FB:reference_manual]
18840 synonym: "paracentric inversion" EXACT []
18841 is_a: SO:1000030 ! chromosomal_inversion
18842 relationship: has_quality SO:0001519 ! paracentric
18846 name: reciprocal_chromosomal_translocation
18847 def: "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]
18848 synonym: "reciprocal chromosomal translocation" EXACT []
18849 is_a: SO:1000044 ! chromosomal_translocation
18853 name: sequence_variation_affecting_transcript
18856 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]
18857 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18858 synonym: "mutation affecting transcript" EXACT []
18859 synonym: "mutation causing partially characterised change in transcript" RELATED []
18860 synonym: "mutation causing uncharacterised change in transcript" RELATED []
18861 synonym: "sequence variant causing partially characterised change in transcript" EXACT []
18862 synonym: "sequence variant causing uncharacterised change in transcript" EXACT []
18863 synonym: "sequence variation affecting transcript" EXACT []
18864 synonym: "sequence_variant_causing_partially_characterised_change_in_transcript" EXACT []
18865 synonym: "sequence_variant_causing_uncharacterised_change_in_transcript" EXACT []
18867 replaced_by: SO:0001576
18871 name: sequence_variant_causing_no_change_in_transcript
18872 def: "No effect on the state of the RNA." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
18873 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.
18874 synonym: "mutation causing no change in transcript" RELATED []
18875 synonym: "sequence variant causing no change in transcript" EXACT []
18880 name: sequence_variation_affecting_coding_sequence
18881 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]
18882 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18883 synonym: "mutation affecting coding sequence" EXACT []
18884 synonym: "sequence variation affecting coding sequence" RELATED []
18886 replaced_by: SO:0001580
18890 name: sequence_variant_causing_initiator_codon_change_in_transcript
18891 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]
18892 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18893 synonym: "mutation causing initiator codon change in transcript" RELATED []
18894 synonym: "sequence variant causing initiator codon change in transcript" EXACT []
18896 replaced_by: SO:0001582
18900 name: sequence_variant_causing_amino_acid_coding_codon_change_in_transcript
18901 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]
18902 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18903 synonym: "mutaton causing amino acid coding codon change in transcript" RELATED []
18904 synonym: "sequence variant causing amino acid coding codon change in transcript" EXACT []
18906 consider: SO:0001606
18910 name: sequence_variant_causing_synonymous_codon_change_in_transcript
18911 def: "The changed codon has the same translation product as the original codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
18912 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18913 synonym: "mutation causing synonymous codon change in transcript" RELATED []
18914 synonym: "sequence variant causing synonymous codon change in transcript" EXACT []
18916 replaced_by: SO:0001819
18920 name: sequence_variant_causing_non_synonymous_codon_change_in_transcript
18921 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]
18922 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18923 synonym: "mutation causing non synonymous codon change in transcript" RELATED []
18924 synonym: "non-synonymous codon change in transcript" EXACT []
18925 synonym: "sequence variant causing non synonymous codon change in transcript" EXACT []
18927 consider: SO:0001583
18931 name: sequence_variant_causing_missense_codon_change_in_transcript
18932 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]
18933 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18934 synonym: "mutation causing missense codon change in transcript" RELATED []
18935 synonym: "sequence variant causing missense codon change in transcript" EXACT []
18937 consider: SO:0001583
18941 name: sequence_variant_causing_conservative_missense_codon_change_in_transcript
18942 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]
18943 comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
18944 synonym: "mutation causing conservative missense codon change in transcript" RELATED []
18945 synonym: "sequence variant causing conservative missense codon change in transcript" EXACT []
18947 replaced_by: SO:0001585
18951 name: sequence_variant_causing_nonconservative_missense_codon_change_in_transcript
18952 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]
18953 comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
18954 synonym: "mutation causing nonconservative missense codon change in transcript" RELATED []
18955 synonym: "sequence variant causing nonconservative missense codon change in transcript" EXACT []
18957 consider: SO:0001586
18961 name: sequence_variant_causing_nonsense_codon_change_in_transcript
18962 def: "The nucleotide change in the codon triplet creates a terminator codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
18963 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18964 synonym: "mutation causing nonsense codon change in transcript" RELATED []
18965 synonym: "sequence variant causing nonsense codon change in transcript" EXACT []
18967 consider: SO:0001587
18971 name: sequence_variant_causing_terminator_codon_change_in_transcript
18972 def: "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke]
18973 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18974 synonym: "mutation causing terminator codon change in transcript" RELATED []
18975 synonym: "sequence variant causing terminator codon change in transcript" EXACT []
18977 consider: SO:0001590
18981 name: sequence_variation_affecting_reading_frame
18982 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]
18983 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
18984 synonym: "mutation affecting reading frame" EXACT []
18985 synonym: "sequence variation affecting reading frame" RELATED []
18990 name: frameshift_sequence_variation
18991 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]
18992 synonym: "frameshift mutation" EXACT []
18993 synonym: "frameshift sequence variation" RELATED []
18994 synonym: "out of frame mutation" RELATED []
18995 xref: http://en.wikipedia.org/wiki/Frameshift_mutation "wiki"
19000 name: sequence_variant_causing_plus_1_frameshift_mutation
19001 def: "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke]
19002 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19003 synonym: "plus 1 frameshift mutation" EXACT []
19004 synonym: "sequence variant causing plus 1 frameshift mutation" EXACT []
19006 replaced_by: SO:0001594
19010 name: sequence_variant_causing_minus_1_frameshift
19011 def: "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke]
19012 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19013 synonym: "minus 1 frameshift mutation" EXACT []
19014 synonym: "sequence variant causing minus 1 frameshift" EXACT []
19016 replaced_by: SO:0001592
19020 name: sequence_variant_causing_plus_2_frameshift
19021 def: "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke]
19022 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19023 synonym: "plus 2 frameshift mutation" EXACT []
19024 synonym: "sequence variant causing plus 2 frameshift" EXACT []
19026 replaced_by: SO:0001595
19030 name: sequence_variant_causing_minus_2_frameshift
19031 def: "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke]
19032 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19033 synonym: "minus 2 frameshift mutation" EXACT []
19034 synonym: "sequence variant causing minus 2 frameshift" EXACT []
19036 replaced_by: SO:0001593
19040 name: sequence_variant_affecting_transcript_processing
19041 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]
19042 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19043 synonym: "mutation affecting transcript processing" RELATED []
19044 synonym: "sequence variant affecting transcript processing" EXACT []
19046 replaced_by: SO:0001543
19050 name: sequence_variant_affecting_splicing
19051 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]
19052 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19053 synonym: "mutation affecting splicing" RELATED []
19054 synonym: "sequence variant affecting splicing" EXACT []
19056 replaced_by: SO:0001568
19060 name: sequence_variant_affecting_splice_donor
19061 def: "A sequence_variant_effect that changes the splice donor sequence." [SO:ke]
19062 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19063 synonym: "mutation affecting splice donor" RELATED []
19064 synonym: "sequence variant affecting splice donor" RELATED []
19065 synonym: "splice donor mutation" EXACT []
19067 replaced_by: SO:0001575
19071 name: sequence_variant_affecting_splice_acceptor
19072 def: "A sequence_variant_effect that changes the splice acceptor sequence." [SO:ke]
19073 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19074 synonym: "mutation affecting splicing" RELATED []
19075 synonym: "sequence variant affecting splice acceptor" RELATED []
19076 synonym: "splice acceptor mutation" EXACT []
19078 replaced_by: SO:0001574
19082 name: sequence_variant_causing_cryptic_splice_activation
19083 def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19084 comment: A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.
19085 synonym: "cryptic splice activator sequence variant" EXACT []
19086 synonym: "mutation causing cryptic splice activator" RELATED []
19087 synonym: "sequence variant causing cryptic splice activator" EXACT []
19089 replaced_by: SO:0001569
19093 name: sequence_variant_affecting_editing
19094 def: "Sequence variant affects the editing of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19095 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19096 synonym: "mutation affecting editing" RELATED []
19097 synonym: "sequence variant affecting editing" EXACT []
19099 replaced_by: SO:0001544
19103 name: sequence_variant_affecting_transcription
19104 def: "Mutation affects the process of transcription, its initiation, progression or termination." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19105 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19106 synonym: "mutation affecting transcription" RELATED []
19107 synonym: "sequence variant affecting transcription" EXACT []
19109 replaced_by: SO:0001549
19113 name: sequence_variant_decreasing_rate_of_transcription
19114 def: "A sequence variation that decreases the rate a which transcription of the sequence occurs." [SO:ke]
19115 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19116 synonym: "mutation decreasing rate of transcription" RELATED []
19117 synonym: "sequence variation decreasing rate of transcription" EXACT []
19122 name: sequence_variation_affecting_transcript_sequence
19123 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19124 synonym: "mutation affecting transcript sequence" EXACT []
19125 synonym: "sequence variation affecting transcript sequence" EXACT []
19130 name: sequence_variant_increasing_rate_of_transcription
19131 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19132 synonym: "mutation increasing rate of transcription" RELATED []
19133 synonym: "sequence variation increasing rate of transcription" EXACT []
19138 name: sequence_variant_affecting_rate_of_transcription
19139 def: "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke]
19140 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19141 synonym: "mutation affecting rate of transcription" RELATED []
19142 synonym: "sequence variant affecting rate of transcription" EXACT []
19144 replaced_by: SO:0001550
19148 name: sequence variant_affecting_transcript_stability
19149 def: "Sequence variant affects the stability of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19150 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19151 synonym: "mutation affecting transcript stability" RELATED []
19152 synonym: "sequence variant affecting transcript stability" EXACT []
19154 replaced_by: SO:0001546
19158 name: sequence_variant_increasing_transcript_stability
19159 def: "Sequence variant increases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19160 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19161 synonym: "mutation increasing transcript stability" RELATED []
19162 synonym: "sequence variant increasing transcript stability" EXACT []
19167 name: sequence_variant_decreasing_transcript_stability
19168 def: "Sequence variant decreases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19169 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19170 synonym: "mutation decreasing transcript stability" RELATED []
19171 synonym: "sequence variant decreasing transcript stability" EXACT []
19176 name: sequence_variation_affecting_level_of_transcript
19177 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]
19178 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19179 synonym: "mutation affecting level of transcript" RELATED []
19180 synonym: "sequence variation affecting level of transcript" EXACT []
19182 replaced_by: SO:0001540
19186 name: sequence_variation_decreasing_level_of_transcript
19187 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]
19188 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19189 synonym: "mutation decreasing level of transcript" EXACT []
19190 synonym: "sequence variation decreasing level of transcript" RELATED []
19195 name: sequence_variation_increasing_level_of_transcript
19196 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]
19197 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19198 synonym: "mutation increasing level of transcript" EXACT []
19199 synonym: "sequence variation increasing level of transcript" EXACT []
19204 name: sequence_variant_affecting_translational_product
19207 def: "A sequence variant causing a change in primary translation product of a transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19208 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19209 synonym: "mutation affecting translational product" RELATED []
19210 synonym: "mutation causing partially characterised change of translational product" RELATED []
19211 synonym: "mutation causing uncharacterised change of translational product" RELATED []
19212 synonym: "sequence variant affecting translational product" EXACT []
19213 synonym: "sequence variant causing partially characterised change of translational product" EXACT []
19214 synonym: "sequence variant causing uncharacterised change of translational product" EXACT []
19215 synonym: "sequence_variant_causing_partially_characterised_change_of_translational_product" EXACT []
19216 synonym: "sequence_variant_causing_uncharacterised_change_of_translational_product" EXACT []
19218 replaced_by: SO:0001553
19222 name: sequence_variant_causing_no_change_of_translational_product
19223 def: "The sequence variant at RNA level does not lead to any change in polypeptide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19224 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.
19225 synonym: "mutation causing no change of translational product" RELATED []
19226 synonym: "sequence variant causing no change of translational product" EXACT []
19231 name: sequence_variant_causing_complex_change_of_translational_product
19232 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]
19233 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19234 synonym: "mutation causing complex change of translational product" RELATED []
19235 synonym: "sequence variant causing complex change of translational product" EXACT []
19237 consider: SO:0001539
19241 name: sequence_variant_causing_amino_acid_substitution
19242 def: "The replacement of a single amino acid by another." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19243 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19244 synonym: "mutation causing amino acid substitution" RELATED []
19245 synonym: "sequence variant causing amino acid substitution" EXACT []
19247 replaced_by: SO:0001606
19251 name: sequence_variant_causing_conservative_amino_acid_substitution
19252 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19253 synonym: "mutation causing conservative amino acid substitution" RELATED []
19254 synonym: "sequence variant causing conservative amino acid substitution" EXACT []
19256 replaced_by: SO:0001607
19260 name: sequence_variant_causing_nonconservative_amino_acid_substitution
19261 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19262 synonym: "mutation causing nonconservative amino acid substitution" RELATED []
19263 synonym: "sequence variant causing nonconservative amino acid substitution" EXACT []
19265 replaced_by: SO:0001607
19269 name: sequence_variant_causing_amino_acid_insertion
19270 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]
19271 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19272 synonym: "mutation causing amino acid insertion" RELATED []
19273 synonym: "sequence variant causing amino acid insertion" EXACT []
19275 replaced_by: SO:0001605
19279 name: sequence_variant_causing_amino_acid_deletion
19280 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]
19281 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19282 synonym: "mutation causing amino acid deletion" RELATED []
19283 synonym: "sequence variant causing amino acid deletion" EXACT []
19285 consider: SO:0001825
19289 name: sequence_variant_causing_polypeptide_truncation
19290 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]
19291 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19292 synonym: "mutation causing polypeptide truncation" RELATED []
19293 synonym: "sequence variant causing polypeptide truncation" EXACT []
19295 replaced_by: SO:0001587
19299 name: sequence_variant_causing_polypeptide_elongation
19300 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]
19301 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19302 synonym: "mutation causing polypeptide elongation" RELATED []
19303 synonym: "sequence variant causing polypeptide elongation" EXACT []
19305 replaced_by: SO:0001609
19309 name: mutation_causing_polypeptide_N_terminal_elongation
19310 def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19311 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19312 synonym: "mutation causing polypeptide N terminal elongation" EXACT []
19313 synonym: "polypeptide N-terminal elongation" EXACT []
19315 replaced_by: SO:0001611
19319 name: mutation_causing_polypeptide_C_terminal_elongation
19320 def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
19321 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19322 synonym: "mutation causing polypeptide C terminal elongation" EXACT []
19323 synonym: "polypeptide C-terminal elongation" EXACT []
19325 replaced_by: SO:0001610
19329 name: sequence_variant_affecting_level_of_translational_product
19330 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19331 synonym: "mutation affecting level of translational product" RELATED []
19332 synonym: "sequence variant affecting level of translational product" EXACT []
19334 replaced_by: SO:0001553
19338 name: sequence_variant_decreasing_level_of_translation_product
19339 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19340 synonym: "mutationdecreasing level of translation product" RELATED []
19341 synonym: "sequence variant decreasing level of translation product" EXACT []
19343 replaced_by: SO:0001555
19347 name: sequence_variant_increasing_level_of_translation_product
19348 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19349 synonym: "mutationt increasing level of translation product" RELATED []
19350 synonym: "sequence variant increasing level of translation product" EXACT []
19355 name: sequence_variant_affecting_polypeptide_amino_acid_sequence
19356 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19357 synonym: "mutation affecting polypeptide amino acid sequence" RELATED []
19358 synonym: "sequence variant affecting polypeptide amino acid sequence" EXACT []
19360 replaced_by: SO:0001603
19364 name: mutation_causing_inframe_polypeptide_N_terminal_elongation
19365 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19366 synonym: "inframe polypeptide N-terminal elongation" EXACT []
19367 synonym: "mutation causing inframe polypeptide N terminal elongation" EXACT []
19369 replaced_by: SO:0001614
19373 name: mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
19374 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19375 synonym: "mutation causing out of frame polypeptide N terminal elongation" EXACT []
19376 synonym: "out of frame polypeptide N-terminal elongation" EXACT []
19378 replaced_by: SO:0001615
19382 name: mutaton_causing_inframe_polypeptide_C_terminal_elongation
19383 synonym: "inframe_polypeptide C-terminal elongation" EXACT []
19384 synonym: "mutaton causing inframe polypeptide C terminal elongation" EXACT []
19386 replaced_by: SO:0001612
19390 name: mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
19391 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19392 synonym: "mutation causing out of frame polypeptide C terminal elongation" EXACT []
19393 synonym: "out of frame polypeptide C-terminal elongation" EXACT []
19395 replaced_by: SO:0001613
19399 name: frame_restoring_sequence_variant
19400 def: "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
19401 synonym: "frame restoring mutation" EXACT []
19402 synonym: "frame restoring sequence variant" EXACT []
19407 name: sequence_variant_affecting_3D_structure_of_polypeptide
19410 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]
19411 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19412 synonym: "mutation affecting 3D structure of polypeptide" RELATED []
19413 synonym: "mutation causing partially characterised 3D structural change" RELATED []
19414 synonym: "mutation causing uncharacterised 3D structural change" RELATED []
19415 synonym: "sequence variant affecting 3D structure of polypeptide" EXACT []
19416 synonym: "sequence variant affecting 3D-structure of polypeptide" EXACT []
19417 synonym: "sequence variant causing partially characterised 3D structural change" EXACT []
19418 synonym: "sequence variant causing uncharacterised 3D structural change" EXACT []
19419 synonym: "sequence_variant_causing_partially_characterised_3D_structural_change" EXACT []
19420 synonym: "sequence_variant_causing_uncharacterised_3D_structural_change" EXACT []
19422 replaced_by: SO:0001599
19426 name: sequence_variant_causing_no_3D_structural_change
19427 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.
19428 synonym: "mutation causing no 3D structural change" RELATED []
19429 synonym: "sequence variant causing no 3D structural change" EXACT []
19434 name: sequence_variant_causing_complex_3D_structural_change
19435 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19436 synonym: "mutation causing complex 3D structural change" RELATED []
19437 synonym: "sequence variant causing complex 3D structural change" EXACT []
19439 replaced_by: SO:0001600
19443 name: sequence_variant_causing_conformational_change
19444 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19445 synonym: "mutation causing conformational change" RELATED []
19446 synonym: "sequence variant causing conformational change" EXACT []
19448 replaced_by: SO:0001601
19452 name: sequence_variant_affecting_polypeptide_function
19453 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19454 synonym: "mutation affecting polypeptide function" RELATED []
19455 synonym: "sequence variant affecting polypeptide function" EXACT []
19457 replaced_by: SO:0001554
19461 name: sequence_variant_causing_loss_of_function_of_polypeptide
19462 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19463 synonym: "loss of function of polypeptide" RELATED []
19464 synonym: "mutation causing loss of function of polypeptide" RELATED []
19465 synonym: "sequence variant causing loss of function of polypeptide" EXACT []
19467 replaced_by: SO:0001559
19471 name: sequence_variant_causing_inactive_ligand_binding_site
19472 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19473 synonym: "mutation causing inactive ligand binding site" RELATED []
19474 synonym: "sequence variant causing inactive ligand binding site" EXACT []
19476 replaced_by: SO:0001560
19480 name: sequence_variant_causing_inactive_catalytic_site
19481 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19482 synonym: "mutation causing inactive catalytic site" RELATED []
19483 synonym: "sequence variant causing inactive catalytic site" EXACT []
19485 replaced_by: SO:0001618
19489 name: sequence_variant_causing_polypeptide_localization_change
19490 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19491 synonym: "mutation causing polypeptide localization change" RELATED []
19492 synonym: "sequence variant causing polypeptide localization change" EXACT []
19494 replaced_by: SO:0001558
19498 name: sequence_variant_causing_polypeptide_post_translational_processing_change
19499 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19500 synonym: "mutation causing polypeptide post translational processing change" RELATED []
19501 synonym: "polypeptide post-translational processing affected" EXACT []
19502 synonym: "sequence variant causing polypeptide post translational processing change" EXACT []
19504 replaced_by: SO:0001562
19508 name: polypeptide_post_translational_processing_affected
19509 synonym: "polypeptide_post-translational_processing_affected" RELATED []
19514 name: sequence_variant_causing_partial_loss_of_function_of_polypeptide
19515 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19516 synonym: "mutation causing partial loss of function of polypeptide" RELATED []
19517 synonym: "partial loss of function of polypeptide" EXACT []
19518 synonym: "sequence variant causing partial loss of function of polypeptide" EXACT []
19520 replaced_by: SO:0001561
19524 name: sequence_variant_causing_gain_of_function_of_polypeptide
19525 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19526 synonym: "gain of function of polypeptide" EXACT []
19527 synonym: "mutation causing gain of function of polypeptide" RELATED []
19528 synonym: "sequence variant causing gain of function of polypeptide" EXACT []
19530 replaced_by: SO:0001557
19534 name: sequence_variant_affecting_transcript_secondary_structure
19535 def: "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke]
19536 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19537 synonym: "mutation affecting transcript secondary structure" RELATED []
19538 synonym: "sequence variant affecting transcript secondary structure" EXACT []
19540 replaced_by: SO:0001596
19544 name: sequence_variant_causing_compensatory_transcript_secondary_structure_mutation
19545 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19546 synonym: "mutation causing compensatory transcript secondary structure mutation" RELATED []
19547 synonym: "sequence variant causing compensatory transcript secondary structure mutation" EXACT []
19549 replaced_by: SO:0001597
19553 name: sequence_variant_effect
19554 def: "The effect of a change in nucleotide sequence." [SO:ke]
19555 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.
19556 synonym: "sequence variant effect" RELATED []
19561 name: sequence_variant_causing_polypeptide_fusion
19562 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19563 synonym: "mutation causing polypeptide fusion" RELATED []
19564 synonym: "sequence variant causing polypeptide fusion" EXACT []
19566 replaced_by: SO:0001616
19570 name: autosynaptic_chromosome
19571 def: "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]
19572 synonym: "(Drosophila)A" RELATED []
19573 synonym: "autosynaptic chromosome" EXACT []
19574 is_a: SO:1000183 ! chromosome_structure_variation
19578 name: homo_compound_chromosome
19579 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]
19580 synonym: "homo compound chromosome" EXACT []
19581 synonym: "homo-compound chromosome" EXACT []
19582 is_a: SO:1000042 ! compound_chromosome
19586 name: hetero_compound_chromosome
19587 def: "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]
19588 synonym: "hetero compound chromosome" EXACT []
19589 synonym: "hetero-compound chromosome" EXACT []
19590 is_a: SO:1000042 ! compound_chromosome
19594 name: chromosome_fission
19595 def: "A chromosome that occurred by the division of a larger chromosome." [SO:ke]
19596 synonym: "chromosome fission" EXACT []
19597 is_a: SO:1000028 ! intrachromosomal_mutation
19601 name: dexstrosynaptic_chromosome
19602 def: "An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]
19603 synonym: "dexstrosynaptic chromosome" EXACT []
19604 is_a: SO:1000136 ! autosynaptic_chromosome
19608 name: laevosynaptic_chromosome
19609 def: "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]
19610 synonym: "laevosynaptic chromosome" EXACT []
19611 is_a: SO:1000136 ! autosynaptic_chromosome
19615 name: free_duplication
19616 def: "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]
19617 synonym: "free duplication" EXACT []
19618 is_a: SO:1000037 ! chromosomal_duplication
19622 name: free_ring_duplication
19623 def: "A ring chromosome which is a copy of another chromosome." [SO:ke]
19624 synonym: "(Drosophila)R" RELATED []
19625 synonym: "free ring duplication" EXACT []
19626 is_a: SO:1000045 ! ring_chromosome
19627 is_a: SO:1000144 ! free_duplication
19628 relationship: has_quality SO:0001516 ! free
19632 name: deficient_translocation
19633 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]
19634 synonym: "(Drosophila)Df" RELATED []
19635 synonym: "(Drosophila)DfT" RELATED []
19636 synonym: "deficient translocation" EXACT []
19637 is_a: SO:1000029 ! chromosomal_deletion
19638 is_a: SO:1000044 ! chromosomal_translocation
19639 relationship: has_part SO:0000159 ! deletion
19643 name: inversion_cum_translocation
19644 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]
19645 synonym: "(Drosophila)InT" RELATED []
19646 synonym: "(Drosophila)T" RELATED []
19647 synonym: "inversion cum translocation" EXACT []
19648 is_a: SO:1000030 ! chromosomal_inversion
19649 is_a: SO:1000044 ! chromosomal_translocation
19650 relationship: has_part SO:1000036 ! inversion
19654 name: bipartite_duplication
19655 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]
19656 synonym: "(Drosophila)bDp" RELATED []
19657 synonym: "bipartite duplication" EXACT []
19658 is_a: SO:1000031 ! interchromosomal_mutation
19659 is_a: SO:1000038 ! intrachromosomal_duplication
19663 name: cyclic_translocation
19664 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]
19665 synonym: "cyclic translocation" EXACT []
19666 is_a: SO:0002060 ! interchomosomal_translocation
19670 name: bipartite_inversion
19671 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]
19672 synonym: "(Drosophila)bIn" RELATED []
19673 synonym: "bipartite inversion" EXACT []
19674 is_a: SO:1000030 ! chromosomal_inversion
19678 name: uninverted_insertional_duplication
19679 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]
19680 synonym: "(Drosophila)eDp" RELATED []
19681 synonym: "uninverted insertional duplication" EXACT []
19682 is_a: SO:1000154 ! insertional_duplication
19686 name: inverted_insertional_duplication
19687 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]
19688 synonym: "(Drosophila)iDp" RELATED []
19689 synonym: "inverted insertional duplication" EXACT []
19690 is_a: SO:1000154 ! insertional_duplication
19694 name: insertional_duplication
19695 def: "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]
19696 synonym: "(Drosophila)Dpp" RELATED []
19697 synonym: "insertional duplication" EXACT []
19698 is_a: SO:1000037 ! chromosomal_duplication
19702 name: interchromosomal_transposition
19703 def: "A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]
19704 synonym: "(Drosophila)Tp" RELATED []
19705 synonym: "interchromosomal transposition" EXACT []
19706 is_a: SO:0000453 ! chromosomal_transposition
19707 is_a: SO:1000031 ! interchromosomal_mutation
19711 name: inverted_interchromosomal_transposition
19712 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]
19713 synonym: "(Drosophila)iTp" RELATED []
19714 synonym: "inverted interchromosomal transposition" EXACT []
19715 is_a: SO:1000155 ! interchromosomal_transposition
19719 name: uninverted_interchromosomal_transposition
19720 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]
19721 synonym: "(Drosophila)eTp" RELATED []
19722 synonym: "uninverted interchromosomal transposition" EXACT []
19723 is_a: SO:1000155 ! interchromosomal_transposition
19727 name: inverted_intrachromosomal_transposition
19728 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]
19729 synonym: "(Drosophila)iTp" RELATED []
19730 synonym: "inverted intrachromosomal transposition" EXACT []
19731 is_a: SO:1000148 ! inversion_cum_translocation
19732 relationship: has_part SO:1000036 ! inversion
19736 name: uninverted_intrachromosomal_transposition
19737 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]
19738 synonym: "(Drosophila)eTp" RELATED []
19739 synonym: "uninverted intrachromosomal transposition" EXACT []
19740 is_a: SO:1000041 ! intrachromosomal_transposition
19741 relationship: has_part SO:0001514 ! direct
19745 name: unoriented_insertional_duplication
19746 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]
19747 comment: Flag - unknown in the definition.
19748 synonym: "(Drosophila)uDp" RELATED []
19749 synonym: "unoriented insertional duplication" EXACT []
19750 is_a: SO:1000154 ! insertional_duplication
19754 name: unoriented_interchromosomal_transposition
19755 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]
19756 comment: FLAG - term describes an unknown.
19757 synonym: "(Drosophila)uTp" RELATED []
19758 synonym: "unorientated interchromosomal transposition" EXACT []
19759 is_a: SO:1000155 ! interchromosomal_transposition
19763 name: unoriented_intrachromosomal_transposition
19764 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]
19765 comment: FLAG - definition describes an unknown.
19766 synonym: "(Drosophila)uTp" RELATED []
19767 synonym: "unorientated intrachromosomal transposition" EXACT []
19768 is_a: SO:1000041 ! intrachromosomal_transposition
19772 name: uncharacterized_chromosomal_mutation
19773 synonym: "uncharacterized chromosomal mutation" EXACT []
19774 is_a: SO:1000183 ! chromosome_structure_variation
19778 name: deficient_inversion
19779 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]
19780 synonym: "(Drosophila)Df" RELATED []
19781 synonym: "(Drosophila)DfIn" RELATED []
19782 synonym: "deficient inversion" EXACT []
19783 is_a: SO:1000029 ! chromosomal_deletion
19784 is_a: SO:1000030 ! chromosomal_inversion
19785 relationship: has_part SO:0000159 ! deletion
19786 relationship: has_part SO:1000036 ! inversion
19790 name: tandem_duplication
19791 def: "A duplication consisting of 2 identical adjacent regions." [SO:ke]
19793 synonym: "erverted" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
19794 synonym: "tandem duplication" EXACT []
19795 is_a: SO:1000035 ! duplication
19799 name: partially_characterized_chromosomal_mutation
19800 synonym: "partially characterized chromosomal mutation" EXACT []
19801 is_a: SO:1000170 ! uncharacterized_chromosomal_mutation
19805 name: sequence_variant_affecting_gene_structure
19806 def: "A sequence_variant_effect that changes the gene structure." [SO:ke]
19807 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19808 synonym: "mutation affecting gene structure" RELATED []
19809 synonym: "sequence variant affecting gene structure" EXACT []
19811 replaced_by: SO:0001564
19815 name: sequence_variant_causing_gene_fusion
19816 def: "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene." [SO:ke]
19817 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19818 synonym: "mutation causing gene fusion" RELATED []
19819 synonym: "sequence variant causing gene fusion" EXACT []
19821 replaced_by: SO:0001565
19825 name: chromosome_number_variation
19826 def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
19827 synonym: "chromosome number variation" EXACT []
19828 is_a: SO:0000240 ! chromosome_variation
19832 name: chromosome_structure_variation
19833 synonym: "chromosome structure variation" EXACT []
19834 is_a: SO:0000240 ! chromosome_variation
19838 name: sequence_variant_causes_exon_loss
19839 def: "A sequence variant affecting splicing and causes an exon loss." [SO:ke]
19840 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19841 synonym: "mutation causes exon loss" RELATED []
19842 synonym: "sequence variant causes exon loss" EXACT []
19847 name: sequence_variant_causes_intron_gain
19848 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]
19849 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19850 synonym: "mutation causes intron gain" RELATED []
19851 synonym: "sequence variant causes intron gain" EXACT []
19856 name: sequence_variant_causing_cryptic_splice_donor_activation
19857 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19858 synonym: "sequence variant causing cryptic splice donor activation" EXACT []
19860 replaced_by: SO:0001571
19864 name: sequence_variant_causing_cryptic_splice_acceptor_activation
19865 comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
19866 synonym: "sequence variant causing cryptic splice acceptor activation" EXACT []
19868 replaced_by: SO:0001570
19872 name: alternatively_spliced_transcript
19873 def: "A transcript that is alternatively spliced." [SO:xp]
19874 synonym: "alternatively spliced transcript" EXACT []
19875 is_a: SO:0000673 ! transcript
19876 relationship: has_quality SO:0000877 ! alternatively_spliced
19880 name: encodes_1_polypeptide
19881 def: "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]
19882 synonym: "encodes 1 polypeptide" EXACT []
19883 is_a: SO:0000463 ! encodes_alternately_spliced_transcripts
19887 name: encodes_greater_than_1_polypeptide
19888 def: "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]
19889 synonym: "encodes greater than 1 polypeptide" EXACT []
19890 is_a: SO:0000463 ! encodes_alternately_spliced_transcripts
19894 name: encodes_different_polypeptides_different_stop
19895 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]
19896 synonym: "encodes different polypeptides different stop" EXACT []
19897 is_a: SO:1001195 ! encodes_overlapping_peptides
19901 name: encodes_overlapping_peptides_different_start
19902 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]
19903 synonym: "encodes overlapping peptides different start" EXACT []
19904 is_a: SO:1001195 ! encodes_overlapping_peptides
19908 name: encodes_disjoint_polypeptides
19909 def: "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]
19910 synonym: "encodes disjoint polypeptides" EXACT []
19911 is_a: SO:1001189 ! encodes_greater_than_1_polypeptide
19915 name: encodes_overlapping_polypeptides_different_start_and_stop
19916 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]
19917 synonym: "encodes overlapping polypeptides different start and stop" EXACT []
19918 is_a: SO:1001195 ! encodes_overlapping_peptides
19922 name: alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
19927 name: encodes_overlapping_peptides
19928 def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]
19929 synonym: "encodes overlapping peptides" EXACT []
19930 is_a: SO:1001189 ! encodes_greater_than_1_polypeptide
19935 def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]
19936 is_a: SO:0000654 ! maxicircle_gene
19937 is_a: SO:0001431 ! cryptic_gene
19938 relationship: has_quality SO:0000976 ! cryptic
19942 name: dicistronic_primary_transcript
19943 def: "A primary transcript that has the quality dicistronic." [SO:xp]
19944 synonym: "dicistronic primary transcript" EXACT []
19945 is_a: SO:0000079 ! dicistronic_transcript
19946 is_a: SO:0000631 ! polycistronic_primary_transcript
19947 relationship: has_quality SO:0000879 ! dicistronic
19951 name: member_of_regulon
19952 synonym: "member of regulon" EXACT []
19953 is_a: SO:0000081 ! gene_array_member
19957 name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
19958 synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED []
19963 name: CDS_independently_known
19964 def: "A CDS with the evidence status of being independently known." [SO:xp]
19965 synonym: "CDS independently known" EXACT []
19966 is_a: SO:0000316 ! CDS
19967 relationship: has_quality SO:0000906 ! independently_known
19972 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]
19973 synonym: "orphan CDS" EXACT []
19974 is_a: SO:1001254 ! CDS_predicted
19975 relationship: has_origin SO:0000910 ! orphan
19979 name: CDS_supported_by_domain_match_data
19980 def: "A CDS that is supported by domain similarity." [SO:xp]
19981 synonym: "CDS supported by domain match data" EXACT []
19982 is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
19983 relationship: has_quality SO:0000908 ! supported_by_domain_match
19987 name: CDS_supported_by_sequence_similarity_data
19988 def: "A CDS that is supported by sequence similarity data." [SO:xp]
19989 synonym: "CDS supported by sequence similarity data" EXACT []
19990 is_a: SO:1001254 ! CDS_predicted
19991 relationship: has_quality SO:0000907 ! supported_by_sequence_similarity
19995 name: CDS_predicted
19996 def: "A CDS that is predicted." [SO:ke]
19997 synonym: "CDS predicted" EXACT []
19998 is_a: SO:0000316 ! CDS
19999 relationship: has_quality SO:0000732 ! predicted
20003 name: status_of_coding_sequence
20008 name: CDS_supported_by_EST_or_cDNA_data
20009 def: "A CDS that is supported by similarity to EST or cDNA data." [SO:xp]
20010 synonym: "CDS supported by EST or cDNA data" EXACT []
20011 is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
20012 relationship: has_quality SO:0000909 ! supported_by_EST_or_cDNA
20016 name: internal_Shine_Dalgarno_sequence
20017 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]
20018 synonym: "internal Shine Dalgarno sequence" EXACT []
20019 synonym: "internal Shine-Dalgarno sequence" EXACT []
20020 is_a: SO:0000243 ! internal_ribosome_entry_site
20021 is_a: SO:1001268 ! recoding_stimulatory_region
20026 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]
20027 synonym: "recoded mRNA" EXACT []
20028 is_a: SO:0000234 ! mRNA
20029 relationship: has_quality SO:0000881 ! recoded
20033 name: minus_1_translationally_frameshifted
20034 def: "An attribute describing a translational frameshift of -1." [SO:ke]
20035 synonym: "minus 1 translationally frameshifted" EXACT []
20036 is_a: SO:0000887 ! translationally_frameshifted
20040 name: plus_1_translationally_frameshifted
20041 def: "An attribute describing a translational frameshift of +1." [SO:ke]
20042 synonym: "plus 1 translationally frameshifted" EXACT []
20043 is_a: SO:0000887 ! translationally_frameshifted
20047 name: mRNA_recoded_by_translational_bypass
20048 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]
20049 synonym: "mRNA recoded by translational bypass" EXACT []
20050 is_a: SO:1001261 ! recoded_mRNA
20051 relationship: has_quality SO:0000886 ! recoded_by_translational_bypass
20055 name: mRNA_recoded_by_codon_redefinition
20056 def: "A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]
20057 synonym: "mRNA recoded by codon redefinition" EXACT []
20058 is_a: SO:1001261 ! recoded_mRNA
20059 relationship: has_quality SO:0000882 ! codon_redefined
20063 name: stop_codon_redefinition_as_selenocysteine
20068 name: stop_codon_readthrough
20073 name: recoding_stimulatory_region
20074 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]
20075 synonym: "recoding stimulatory region" EXACT []
20076 synonym: "recoding stimulatory signal" EXACT []
20077 is_a: SO:0000836 ! mRNA_region
20081 name: four_bp_start_codon
20082 def: "A non-canonical start codon with 4 base pairs." [SO:ke]
20083 synonym: "4bp start codon" EXACT []
20084 synonym: "four bp start codon" EXACT []
20085 is_a: SO:0000680 ! non_canonical_start_codon
20089 name: stop_codon_redefinition_as_pyrrolysine
20094 name: archaeal_intron
20095 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]
20096 comment: Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
20097 synonym: "archaeal intron" EXACT []
20098 is_a: SO:0001216 ! endonuclease_spliced_intron
20103 def: "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]
20104 comment: Could be a cross product with Gene ontology, GO:0006388.
20105 synonym: "pre-tRNA intron" EXACT []
20106 synonym: "tRNA intron" EXACT []
20107 is_a: SO:0001216 ! endonuclease_spliced_intron
20111 name: CTG_start_codon
20112 def: "A non-canonical start codon of sequence CTG." [SO:ke]
20113 synonym: "CTG start codon" EXACT []
20114 is_a: SO:0000680 ! non_canonical_start_codon
20118 name: SECIS_element
20119 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]
20120 synonym: "SECIS element" EXACT []
20121 xref: http://en.wikipedia.org/wiki/SECIS_element "wiki"
20122 is_a: SO:1001268 ! recoding_stimulatory_region
20127 def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]
20128 is_a: SO:0001411 ! biological_region
20132 name: three_prime_recoding_site
20133 def: "The recoding stimulatory signal located downstream of the recoding site." [SO:ke]
20134 synonym: "three prime recoding site" EXACT []
20135 is_a: SO:1001268 ! recoding_stimulatory_region
20139 name: three_prime_stem_loop_structure
20140 def: "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]
20141 synonym: "three prime stem loop structure" EXACT []
20142 is_a: SO:1001277 ! three_prime_recoding_site
20146 name: five_prime_recoding_site
20147 def: "The recoding stimulatory signal located upstream of the recoding site." [SO:ke]
20148 synonym: "five prime recoding site" EXACT []
20149 is_a: SO:1001268 ! recoding_stimulatory_region
20153 name: flanking_three_prime_quadruplet_recoding_signal
20154 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]
20155 synonym: "flanking three prime quadruplet recoding signal" EXACT []
20156 is_a: SO:1001277 ! three_prime_recoding_site
20160 name: UAG_stop_codon_signal
20161 def: "A stop codon signal for a UAG stop codon redefinition." [SO:ke]
20162 synonym: "UAG stop codon signal" EXACT []
20163 is_a: SO:1001288 ! stop_codon_signal
20167 name: UAA_stop_codon_signal
20168 def: "A stop codon signal for a UAA stop codon redefinition." [SO:ke]
20169 synonym: "UAA stop codon signal" EXACT []
20170 is_a: SO:1001288 ! stop_codon_signal
20175 def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]
20177 xref: http://en.wikipedia.org/wiki/Regulon "wiki"
20178 is_a: SO:0005855 ! gene_group
20182 name: UGA_stop_codon_signal
20183 def: "A stop codon signal for a UGA stop codon redefinition." [SO:ke]
20184 synonym: "UGA stop codon signal" EXACT []
20185 is_a: SO:1001288 ! stop_codon_signal
20189 name: three_prime_repeat_recoding_signal
20190 def: "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]
20191 synonym: "three prime repeat recoding signal" EXACT []
20192 is_a: SO:1001277 ! three_prime_recoding_site
20196 name: distant_three_prime_recoding_signal
20197 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]
20198 synonym: "distant three prime recoding signal" EXACT []
20199 is_a: SO:1001277 ! three_prime_recoding_site
20203 name: stop_codon_signal
20204 def: "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]
20205 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.
20206 synonym: "stop codon signal" EXACT []
20207 is_a: SO:1001268 ! recoding_stimulatory_region
20211 name: databank_entry
20212 def: "The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]
20214 synonym: "accession" RELATED []
20215 synonym: "databank entry" EXACT []
20216 is_a: SO:0000695 ! reagent
20221 def: "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]
20222 comment: Requested by tracker 2021594, July 2008, by Alex.
20223 synonym: "gene segment" EXACT []
20224 is_a: SO:0000842 ! gene_component_region
20229 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]
20233 id: associated_with
20234 name: associated_with
20235 comment: This relationship is vague and up for discussion.
20238 id: complete_evidence_for_feature
20239 name: complete_evidence_for_feature
20240 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]
20241 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.
20242 is_transitive: true
20243 is_a: evidence_for_feature ! evidence_for_feature
20248 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]
20249 comment: Example: A splice_junction connects_on exon, exon, mature_transcript.
20250 created_by: kareneilbeck
20251 creation_date: 2010-10-14T01:38:51Z
20256 def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267]
20257 comment: The inverse is contains. Example: intein contained_by immature_peptide_region.
20258 is_transitive: true
20259 created_by: kareneilbeck
20260 creation_date: 2010-10-14T01:26:16Z
20265 def: "The inverse of contained_by." [PMID:20226267]
20266 comment: Example: pre_miRNA contains miRNA_loop.
20267 is_transitive: true
20268 created_by: kareneilbeck
20269 creation_date: 2010-10-14T01:32:15Z
20275 is_transitive: true
20278 id: disconnected_from
20279 name: disconnected_from
20280 def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267]
20281 created_by: kareneilbeck
20282 creation_date: 2010-10-14T01:42:10Z
20287 created_by: kareneilbeck
20288 creation_date: 2009-08-19T02:19:45Z
20293 created_by: kareneilbeck
20294 creation_date: 2009-08-19T02:19:11Z
20297 id: evidence_for_feature
20298 name: evidence_for_feature
20299 def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke]
20300 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.
20301 is_transitive: true
20306 def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke]
20307 comment: Tracker id: 2594157.
20312 def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267]
20313 comment: Example CDS finished_by stop_codon.
20314 created_by: kareneilbeck
20315 creation_date: 2010-10-14T01:45:45Z
20320 def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267]
20321 comment: Example: stop_codon finishes CDS.
20322 created_by: kareneilbeck
20323 creation_date: 2010-10-14T02:17:53Z
20328 def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke]
20329 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.
20330 created_by: kareneilbeck
20331 creation_date: 2011-06-28T12:51:10Z
20340 created_by: kareneilbeck
20341 creation_date: 2009-08-19T02:27:04Z
20346 created_by: kareneilbeck
20347 creation_date: 2009-08-19T02:27:24Z
20350 id: has_integral_part
20351 name: has_integral_part
20352 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]
20353 comment: Example: mRNA has_integral_part CDS.
20354 is_a: has_part ! has_part
20355 created_by: kareneilbeck
20356 creation_date: 2009-08-19T12:01:46Z
20365 def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1]
20366 comment: Example: operon has_part gene.
20371 comment: The relationship between a feature and an attribute.
20375 name: homologous_to
20378 is_a: similar_to ! similar_to
20381 id: integral_part_of
20382 name: integral_part_of
20383 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]
20384 comment: Example: exon integral_part_of transcript.
20385 is_a: part_of ! part_of
20386 created_by: kareneilbeck
20387 creation_date: 2009-08-19T12:03:28Z
20390 id: is_consecutive_sequence_of
20391 name: is_consecutive_sequence_of
20392 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]
20393 comment: Example: region is consecutive_sequence of base.
20394 created_by: kareneilbeck
20395 creation_date: 2010-10-14T02:19:48Z
20400 def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke]
20401 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.
20402 created_by: kareneilbeck
20403 creation_date: 2011-06-28T12:53:16Z
20406 id: maximally_overlaps
20407 name: maximally_overlaps
20408 def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267]
20409 comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
20410 created_by: kareneilbeck
20411 creation_date: 2010-10-14T01:34:48Z
20416 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.
20418 is_transitive: true
20419 is_a: part_of ! part_of
20422 id: non_functional_homolog_of
20423 name: non_functional_homolog_of
20424 def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
20426 is_a: homologous_to ! homologous_to
20430 name: orthologous_to
20433 is_a: homologous_to ! homologous_to
20438 def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267]
20439 comment: Example: coding_exon overlaps CDS.
20440 created_by: kareneilbeck
20441 creation_date: 2010-10-14T01:33:15Z
20445 name: paralogous_to
20448 is_a: homologous_to ! homologous_to
20453 def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1]
20454 comment: Example: amino_acid part_of polypeptide.
20456 is_transitive: true
20459 id: partial_evidence_for_feature
20460 name: partial_evidence_for_feature
20461 def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke]
20462 is_a: evidence_for_feature ! evidence_for_feature
20470 name: processed_from
20471 def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1]
20472 comment: Example: miRNA processed_from miRNA_primary_transcript.
20473 created_by: kareneilbeck
20474 creation_date: 2009-08-19T12:14:00Z
20478 name: processed_into
20479 def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1]
20480 comment: Example: miRNA_primary_transcript processed into miRNA.
20481 created_by: kareneilbeck
20482 creation_date: 2009-08-19T12:15:02Z
20485 id: recombined_from
20486 name: recombined_from
20487 created_by: kareneilbeck
20488 creation_date: 2009-08-19T02:21:03Z
20492 name: recombined_to
20493 created_by: kareneilbeck
20494 creation_date: 2009-08-19T02:20:07Z
20509 def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267]
20510 comment: Example: CDS started_by start_codon.
20511 created_by: kareneilbeck
20512 creation_date: 2010-10-14T01:43:55Z
20517 def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267]
20518 comment: Example: start_codon starts CDS.
20519 created_by: kareneilbeck
20520 creation_date: 2010-10-14T01:47:53Z
20523 id: trans_spliced_from
20524 name: trans_spliced_from
20525 created_by: kareneilbeck
20526 creation_date: 2009-08-19T02:22:14Z
20529 id: trans_spliced_to
20530 name: trans_spliced_to
20531 created_by: kareneilbeck
20532 creation_date: 2009-08-19T02:22:00Z
20535 id: transcribed_from
20536 name: transcribed_from
20537 def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1]
20538 comment: Example: primary_transcript transcribed_from gene.
20539 created_by: kareneilbeck
20540 creation_date: 2009-08-19T12:05:39Z
20544 name: transcribed_to
20545 def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1]
20546 comment: Example: gene transcribed_to primary_transcript.
20547 created_by: kareneilbeck
20548 creation_date: 2009-08-19T12:08:24Z
20552 name: translates_to
20553 def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1]
20554 comment: Example: codon translates_to amino_acid.
20555 created_by: kareneilbeck
20556 creation_date: 2009-08-19T12:11:53Z
20560 name: translation_of
20561 def: "X is translation of Y if Y is translated by ribosome to create X." [http://precedings.nature.com/documents/3495/version/1]
20562 comment: Example: Polypeptide translation_of CDS.
20563 created_by: kareneilbeck
20564 creation_date: 2009-08-19T12:09:59Z
20569 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]
20570 comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.