From 6066400ed6b0fe288ebbea82389f59838a534706 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 28 Jun 2015 18:47:58 +0100 Subject: [PATCH] JAL-1705 example GFF3 with network of ensembl relationships for locus intersecting with a specific ENSG --- test/jalview/ext/ensembl/ENSG00000157764.gff | 56 ++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 test/jalview/ext/ensembl/ENSG00000157764.gff diff --git a/test/jalview/ext/ensembl/ENSG00000157764.gff b/test/jalview/ext/ensembl/ENSG00000157764.gff new file mode 100644 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 -- 1.7.10.2