git://source.jalview.org / jalview.git / commitdiff
? search:
summary | shortlog | log | commit | commitdiff | tree
raw | patch | inline | side by side (parent: a23cc41)
JAL-1705 example GFF3 with network of ensembl relationships for locus intersecting...
authorJim Procter <jprocter@issues.jalview.org>
Sun, 28 Jun 2015 17:47:58 +0000 (18:47 +0100)
committerJim Procter <jprocter@issues.jalview.org>
Sun, 28 Jun 2015 17:47:58 +0000 (18:47 +0100)
test/jalview/ext/ensembl/ENSG00000157764.gff [new file with mode: 0644] patch | blob

diff --git a/test/jalview/ext/ensembl/ENSG00000157764.gff b/test/jalview/ext/ensembl/ENSG00000157764.gff
new file mode 100644 (file)
index 0000000..21cef29
--- /dev/null
+++ b/test/jalview/ext/ensembl/ENSG00000157764.gff
@@ -0,0 +1,56 @@
+##gff-version 3
+# retrieved via http://rest.ensembl.org/overlap/id/ENSG00000157764?feature=gene&feature=transcript&feature=cds&content-type=text/x-gff3
+##sequence-region   7 140719327 140924764
+7      ensembl_havana  gene    140719327       140722790       .       +       .       ID=gene:ENSG00000090266;assembly_name=GRCh38;biotype=protein_coding;description=NADH dehydrogenase (ubiquinone) 1 beta subcomplex%2C 2%2C 8kDa [Source:HGNC Symbol%3BAcc:HGNC:7697];external_name=NDUFB2;logic_name=ensembl_havana_gene;version=11
+7      ensembl_havana  gene    140719327       140924764       .       -       .       ID=gene:ENSG00000157764;assembly_name=GRCh38;biotype=protein_coding;description=B-Raf proto-oncogene%2C serine/threonine kinase [Source:HGNC Symbol%3BAcc:HGNC:1097];external_name=BRAF;logic_name=ensembl_havana_gene;version=11
+7      ensembl snRNA_gene      140884072       140884178       .       +       .       ID=gene:ENSG00000271932;assembly_name=GRCh38;biotype=snRNA;description=RNA%2C U6 small nuclear 85%2C pseudogene [Source:HGNC Symbol%3BAcc:HGNC:47048];external_name=RNU6-85P;logic_name=ncrna;version=1
+7      ensembl_havana  transcript      140719327       140722790       .       +       .       ID=transcript:ENST00000476279;Parent=gene:ENSG00000090266;assembly_name=GRCh38;biotype=protein_coding;external_name=NDUFB2-003;logic_name=havana;version=4
+7      ensembl_havana  transcript      140719327       140721955       .       +       .       ID=transcript:ENST00000461457;Parent=gene:ENSG00000090266;assembly_name=GRCh38;biotype=protein_coding;external_name=NDUFB2-004;logic_name=havana;version=1
+7      ensembl_havana  transcript      140719327       140783157       .       -       .       ID=transcript:ENST00000496384;Parent=gene:ENSG00000157764;assembly_name=GRCh38;biotype=protein_coding;external_name=BRAF-003;logic_name=havana;version=5
+7      ensembl_havana  transcript      140734479       140924764       .       -       .       ID=transcript:ENST00000288602;Parent=gene:ENSG00000157764;assembly_name=GRCh38;biotype=protein_coding;external_name=BRAF-001;logic_name=ensembl_havana_transcript;version=9
+7      ensembl_havana  NMD_transcript_variant  140734521       140754211       .       -       .       ID=transcript:ENST00000479537;Parent=gene:ENSG00000157764;assembly_name=GRCh38;biotype=nonsense_mediated_decay;external_name=BRAF-005;logic_name=havana;version=4
+7      ensembl_havana  NMD_transcript_variant  140734597       140924658       .       -       .       ID=transcript:ENST00000497784;Parent=gene:ENSG00000157764;assembly_name=GRCh38;biotype=nonsense_mediated_decay;external_name=BRAF-002;logic_name=havana;version=1
+7      ensembl_havana  aberrant_processed_transcript   140834061       140924709       .       -       .       ID=transcript:ENST00000469930;Parent=gene:ENSG00000157764;assembly_name=GRCh38;biotype=retained_intron;external_name=BRAF-004;logic_name=havana;version=1
+7      ensembl snRNA   140884072       140884178       .       +       .       ID=transcript:ENST00000605989;Parent=gene:ENSG00000271932;assembly_name=GRCh38;biotype=snRNA;external_name=RNU6-85P-201;logic_name=ncrna;version=1
+7      havana  CDS     140696745       140696842       .       +       0       ID=CDS:ENSP00000419087;Parent=transcript:ENST00000476279;assembly_name=GRCh38
+7      havana  CDS     140702866       140703010       .       +       1       ID=CDS:ENSP00000419087;Parent=transcript:ENST00000476279;assembly_name=GRCh38
+7      havana  CDS     140704860       140704934       .       +       0       ID=CDS:ENSP00000419087;Parent=transcript:ENST00000476279;assembly_name=GRCh38
+7      havana  CDS     140696745       140696842       .       +       0       ID=CDS:ENSP00000420062;Parent=transcript:ENST00000461457;assembly_name=GRCh38
+7      havana  CDS     140721552       140721744       .       +       1       ID=CDS:ENSP00000420062;Parent=transcript:ENST00000461457;assembly_name=GRCh38
+7      havana  CDS     140783021       140783157       .       -       2       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140781576       140781693       .       -       0       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140777991       140778075       .       -       2       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140776912       140777088       .       -       1       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140754187       140754233       .       -       1       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140753275       140753393       .       -       2       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140749287       140749418       .       -       0       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140739812       140739946       .       -       0       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140734617       140734770       .       -       0       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      havana  CDS     140726494       140726516       .       -       2       ID=CDS:ENSP00000419060;Parent=transcript:ENST00000496384;assembly_name=GRCh38
+7      ensembl_havana  CDS     140924566       140924703       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140850111       140850212       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140834609       140834872       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140808892       140808995       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140807960       140808062       .       -       1       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140801412       140801560       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140800362       140800481       .       -       1       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140794308       140794467       .       -       1       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140787548       140787584       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140783021       140783157       .       -       2       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140781576       140781693       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140777991       140778075       .       -       2       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140776912       140777088       .       -       1       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140754187       140754233       .       -       1       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140753275       140753393       .       -       2       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140749287       140749418       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140739812       140739946       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      ensembl_havana  CDS     140734597       140734770       .       -       0       ID=CDS:ENSP00000288602;Parent=transcript:ENST00000288602;assembly_name=GRCh38
+7      havana  CDS     140754187       140754211       .       -       0       ID=CDS:ENSP00000418033;Parent=transcript:ENST00000479537;assembly_name=GRCh38
+7      havana  CDS     140753275       140753393       .       -       2       ID=CDS:ENSP00000418033;Parent=transcript:ENST00000479537;assembly_name=GRCh38
+7      havana  CDS     140749287       140749418       .       -       0       ID=CDS:ENSP00000418033;Parent=transcript:ENST00000479537;assembly_name=GRCh38
+7      havana  CDS     140747415       140747447       .       -       0       ID=CDS:ENSP00000418033;Parent=transcript:ENST00000479537;assembly_name=GRCh38
+7      havana  CDS     140924566       140924658       .       -       0       ID=CDS:ENSP00000420119;Parent=transcript:ENST00000497784;assembly_name=GRCh38
+7      havana  CDS     140850111       140850212       .       -       0       ID=CDS:ENSP00000420119;Parent=transcript:ENST00000497784;assembly_name=GRCh38
+7      havana  CDS     140834609       140834872       .       -       0       ID=CDS:ENSP00000420119;Parent=transcript:ENST00000497784;assembly_name=GRCh38
+7      havana  CDS     140808892       140808995       .       -       0       ID=CDS:ENSP00000420119;Parent=transcript:ENST00000497784;assembly_name=GRCh38
+7      havana  CDS     140808295       140808316       .       -       1       ID=CDS:ENSP00000420119;Parent=transcript:ENST00000497784;assembly_name=GRCh38