Mercurial > repos > devteam > gffread
diff test-data/Homo_sapiens.GRCh37_19.71.gff3 @ 6:6ea09f60dee9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 956566e1f7b4390719db56b7488a720ccad181a4"
| author | iuc |
|---|---|
| date | Fri, 01 Nov 2019 12:54:52 -0400 |
| parents | 5f6e6582c01d |
| children | 4dea02886337 |
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--- a/test-data/Homo_sapiens.GRCh37_19.71.gff3 Tue Oct 01 12:20:13 2019 -0400 +++ b/test-data/Homo_sapiens.GRCh37_19.71.gff3 Fri Nov 01 12:54:52 2019 -0400 @@ -1,4 +1,5 @@ -# gffread test-data/Homo_sapiens.GRCh37_19.71.gtf -o test-data/Homo_sapiens.GRCh37_19.71.gff3 +# gffread /tmp/tmpq6d_yfqc/files/9/2/2/dataset_922cd54b-d77c-48fb-abf7-6fc8d8fdb97c.dat -o output.gff3 +# gffread v0.11.4 ##gff-version 3 19 snRNA transcript 223158 223261 . - . ID=ENST00000410397;geneID=ENSG00000222329;gene_name=U6 19 snRNA exon 223158 223261 . - . Parent=ENST00000410397 @@ -9,55 +10,55 @@ 19 processed_pseudogene exon 239145 239247 . - . Parent=ENST00000588755 19 processed_pseudogene transcript 279495 280170 . + . ID=ENST00000589981;geneID=ENSG00000267447;gene_name=VN2R11P 19 processed_pseudogene exon 279495 280170 . + . Parent=ENST00000589981 -19 protein_coding mRNA 281043 291386 . - . ID=ENST00000269812;geneID=ENSG00000141934;gene_name=PPAP2C +19 protein_coding transcript 281043 291386 . - . ID=ENST00000269812;geneID=ENSG00000141934;gene_name=PPAP2C 19 protein_coding exon 281043 281537 . - . Parent=ENST00000269812 19 protein_coding exon 282134 282310 . - . Parent=ENST00000269812 19 protein_coding exon 282752 282809 . - . Parent=ENST00000269812 19 protein_coding exon 287474 287751 . - . Parent=ENST00000269812 19 protein_coding exon 288020 288171 . - . Parent=ENST00000269812 19 protein_coding exon 291285 291386 . - . Parent=ENST00000269812 -19 protein_coding CDS 281391 281537 . - 0 Parent=ENST00000269812 +19 protein_coding CDS 281388 281537 . - 0 Parent=ENST00000269812 19 protein_coding CDS 282134 282310 . - 0 Parent=ENST00000269812 19 protein_coding CDS 282752 282809 . - 1 Parent=ENST00000269812 19 protein_coding CDS 287474 287751 . - 0 Parent=ENST00000269812 19 protein_coding CDS 288020 288171 . - 2 Parent=ENST00000269812 19 protein_coding CDS 291285 291336 . - 0 Parent=ENST00000269812 -19 protein_coding mRNA 281345 291393 . - . ID=ENST00000434325;geneID=ENSG00000141934;gene_name=PPAP2C +19 protein_coding transcript 281345 291393 . - . ID=ENST00000434325;geneID=ENSG00000141934;gene_name=PPAP2C 19 protein_coding exon 281345 281537 . - . Parent=ENST00000434325 19 protein_coding exon 282134 282310 . - . Parent=ENST00000434325 19 protein_coding exon 282752 282809 . - . Parent=ENST00000434325 19 protein_coding exon 287474 287751 . - . Parent=ENST00000434325 19 protein_coding exon 288020 288171 . - . Parent=ENST00000434325 19 protein_coding exon 291326 291393 . - . Parent=ENST00000434325 -19 protein_coding CDS 281391 281537 . - 0 Parent=ENST00000434325 +19 protein_coding CDS 281388 281537 . - 0 Parent=ENST00000434325 19 protein_coding CDS 282134 282310 . - 0 Parent=ENST00000434325 19 protein_coding CDS 282752 282809 . - 1 Parent=ENST00000434325 19 protein_coding CDS 287474 287751 . - 0 Parent=ENST00000434325 19 protein_coding CDS 288020 288055 . - 0 Parent=ENST00000434325 -19 protein_coding mRNA 281388 291200 . - . ID=ENST00000327790;geneID=ENSG00000141934;gene_name=PPAP2C +19 protein_coding transcript 281388 291200 . - . ID=ENST00000327790;geneID=ENSG00000141934;gene_name=PPAP2C 19 protein_coding exon 281388 281537 . - . Parent=ENST00000327790 19 protein_coding exon 282134 282310 . - . Parent=ENST00000327790 19 protein_coding exon 282752 282809 . - . Parent=ENST00000327790 19 protein_coding exon 287474 287751 . - . Parent=ENST00000327790 19 protein_coding exon 288020 288171 . - . Parent=ENST00000327790 19 protein_coding exon 290952 291200 . - . Parent=ENST00000327790 -19 protein_coding CDS 281391 281537 . - 0 Parent=ENST00000327790 +19 protein_coding CDS 281388 281537 . - 0 Parent=ENST00000327790 19 protein_coding CDS 282134 282310 . - 0 Parent=ENST00000327790 19 protein_coding CDS 282752 282809 . - 1 Parent=ENST00000327790 19 protein_coding CDS 287474 287751 . - 0 Parent=ENST00000327790 19 protein_coding CDS 288020 288171 . - 2 Parent=ENST00000327790 19 protein_coding CDS 290952 291066 . - 0 Parent=ENST00000327790 -19 protein_coding mRNA 281991 287636 . - . ID=ENST00000586998;geneID=ENSG00000141934;gene_name=PPAP2C +19 protein_coding transcript 281991 287636 . - . ID=ENST00000586998;geneID=ENSG00000141934;gene_name=PPAP2C 19 protein_coding exon 281991 282310 . - . Parent=ENST00000586998 19 protein_coding exon 282752 282809 . - . Parent=ENST00000586998 19 protein_coding exon 287474 287636 . - . Parent=ENST00000586998 -19 protein_coding CDS 282125 282310 . - 0 Parent=ENST00000586998 +19 protein_coding CDS 282122 282310 . - 0 Parent=ENST00000586998 19 protein_coding CDS 282752 282809 . - 1 Parent=ENST00000586998 19 protein_coding CDS 287474 287636 . - 2 Parent=ENST00000586998 19 retained_intron transcript 287161 288530 . - . ID=ENST00000589672;geneID=ENSG00000141934;gene_name=PPAP2C 19 retained_intron exon 287161 287751 . - . Parent=ENST00000589672 19 retained_intron exon 288020 288530 . - . Parent=ENST00000589672 -19 protein_coding mRNA 287474 291382 . - . ID=ENST00000591572;geneID=ENSG00000141934;gene_name=PPAP2C +19 protein_coding transcript 287474 291382 . - . ID=ENST00000591572;geneID=ENSG00000141934;gene_name=PPAP2C 19 protein_coding exon 287474 287751 . - . Parent=ENST00000591572 19 protein_coding exon 288020 288189 . - . Parent=ENST00000591572 19 protein_coding exon 291285 291382 . - . Parent=ENST00000591572 @@ -67,7 +68,7 @@ 19 antisense transcript 305573 306467 . + . ID=ENST00000591533;geneID=ENSG00000267124;gene_name=CTD-3113P16.5 19 antisense exon 305573 305703 . + . Parent=ENST00000591533 19 antisense exon 306057 306467 . + . Parent=ENST00000591533 -19 protein_coding mRNA 305575 344793 . - . ID=ENST00000264819;geneID=ENSG00000105556;gene_name=MIER2 +19 protein_coding transcript 305575 344793 . - . ID=ENST00000264819;geneID=ENSG00000105556;gene_name=MIER2 19 protein_coding exon 305575 306711 . - . Parent=ENST00000264819 19 protein_coding exon 307119 307536 . - . Parent=ENST00000264819 19 protein_coding exon 308577 308665 . - . Parent=ENST00000264819 @@ -82,7 +83,7 @@ 19 protein_coding exon 334400 334542 . - . Parent=ENST00000264819 19 protein_coding exon 336083 336173 . - . Parent=ENST00000264819 19 protein_coding exon 344774 344793 . - . Parent=ENST00000264819 -19 protein_coding CDS 306693 306711 . - 1 Parent=ENST00000264819 +19 protein_coding CDS 306690 306711 . - 1 Parent=ENST00000264819 19 protein_coding CDS 307119 307536 . - 2 Parent=ENST00000264819 19 protein_coding CDS 308577 308665 . - 1 Parent=ENST00000264819 19 protein_coding CDS 308801 308925 . - 0 Parent=ENST00000264819 @@ -113,7 +114,7 @@ 19 retained_intron transcript 334115 344798 . - . ID=ENST00000587966;geneID=ENSG00000105556;gene_name=MIER2 19 retained_intron exon 334115 334542 . - . Parent=ENST00000587966 19 retained_intron exon 344774 344798 . - . Parent=ENST00000587966 -19 protein_coding mRNA 361750 376013 . - . ID=ENST00000342640;geneID=ENSG00000105549;gene_name=THEG +19 protein_coding transcript 361750 376013 . - . ID=ENST00000342640;geneID=ENSG00000105549;gene_name=THEG 19 protein_coding exon 361750 362426 . - . Parent=ENST00000342640 19 protein_coding exon 367065 367224 . - . Parent=ENST00000342640 19 protein_coding exon 371205 371322 . - . Parent=ENST00000342640 @@ -122,7 +123,7 @@ 19 protein_coding exon 373940 374011 . - . Parent=ENST00000342640 19 protein_coding exon 374299 374421 . - . Parent=ENST00000342640 19 protein_coding exon 375663 376013 . - . Parent=ENST00000342640 -19 protein_coding CDS 362203 362426 . - 2 Parent=ENST00000342640 +19 protein_coding CDS 362200 362426 . - 2 Parent=ENST00000342640 19 protein_coding CDS 367065 367224 . - 0 Parent=ENST00000342640 19 protein_coding CDS 371205 371322 . - 1 Parent=ENST00000342640 19 protein_coding CDS 372631 372700 . - 2 Parent=ENST00000342640 @@ -134,7 +135,7 @@ 19 retained_intron exon 362058 362426 . - . Parent=ENST00000530711 19 retained_intron exon 367065 367224 . - . Parent=ENST00000530711 19 retained_intron exon 374299 374620 . - . Parent=ENST00000530711 -19 protein_coding mRNA 362200 375970 . - . ID=ENST00000346878;geneID=ENSG00000105549;gene_name=THEG +19 protein_coding transcript 362200 375970 . - . ID=ENST00000346878;geneID=ENSG00000105549;gene_name=THEG 19 protein_coding exon 362200 362426 . - . Parent=ENST00000346878 19 protein_coding exon 367065 367224 . - . Parent=ENST00000346878 19 protein_coding exon 371205 371322 . - . Parent=ENST00000346878 @@ -142,7 +143,7 @@ 19 protein_coding exon 373470 373531 . - . Parent=ENST00000346878 19 protein_coding exon 374299 374421 . - . Parent=ENST00000346878 19 protein_coding exon 375663 375970 . - . Parent=ENST00000346878 -19 protein_coding CDS 362203 362426 . - 2 Parent=ENST00000346878 +19 protein_coding CDS 362200 362426 . - 2 Parent=ENST00000346878 19 protein_coding CDS 367065 367224 . - 0 Parent=ENST00000346878 19 protein_coding CDS 371205 371322 . - 1 Parent=ENST00000346878 19 protein_coding CDS 372631 372700 . - 2 Parent=ENST00000346878 @@ -158,10 +159,10 @@ 19 processed_transcript transcript 397589 398941 . + . ID=ENST00000591757;geneID=ENSG00000267443;gene_name=AC010641.1 19 processed_transcript exon 397589 397633 . + . Parent=ENST00000591757 19 processed_transcript exon 398690 398941 . + . Parent=ENST00000591757 -19 protein_coding mRNA 405445 409139 . - . ID=ENST00000332235;geneID=ENSG00000183186;gene_name=C2CD4C +19 protein_coding transcript 405445 409139 . - . ID=ENST00000332235;geneID=ENSG00000183186;gene_name=C2CD4C 19 protein_coding exon 405445 408401 . - . Parent=ENST00000332235 19 protein_coding exon 409006 409139 . - . Parent=ENST00000332235 -19 protein_coding CDS 407099 408361 . - 0 Parent=ENST00000332235 +19 protein_coding CDS 407096 408361 . - 0 Parent=ENST00000332235 19 retained_intron transcript 416583 419879 . - . ID=ENST00000587423;geneID=ENSG00000129946;gene_name=SHC2 19 retained_intron exon 416583 417322 . - . Parent=ENST00000587423 19 retained_intron exon 418923 419879 . - . Parent=ENST00000587423 @@ -169,7 +170,7 @@ 19 retained_intron exon 416583 417322 . - . Parent=ENST00000588376 19 retained_intron exon 418923 419056 . - . Parent=ENST00000588376 19 retained_intron exon 422146 422828 . - . Parent=ENST00000588376 -19 protein_coding mRNA 416593 460996 . - . ID=ENST00000264554;geneID=ENSG00000129946;gene_name=SHC2 +19 protein_coding transcript 416593 460996 . - . ID=ENST00000264554;geneID=ENSG00000129946;gene_name=SHC2 19 protein_coding exon 416593 417322 . - . Parent=ENST00000264554 19 protein_coding exon 418923 419056 . - . Parent=ENST00000264554 19 protein_coding exon 422146 422456 . - . Parent=ENST00000264554 @@ -183,7 +184,7 @@ 19 protein_coding exon 438970 439030 . - . Parent=ENST00000264554 19 protein_coding exon 440862 440932 . - . Parent=ENST00000264554 19 protein_coding exon 460529 460996 . - . Parent=ENST00000264554 -19 protein_coding CDS 418931 419056 . - 0 Parent=ENST00000264554 +19 protein_coding CDS 418928 419056 . - 0 Parent=ENST00000264554 19 protein_coding CDS 422146 422456 . - 2 Parent=ENST00000264554 19 protein_coding CDS 425097 425231 . - 2 Parent=ENST00000264554 19 protein_coding CDS 430684 430747 . - 0 Parent=ENST00000264554 @@ -207,14 +208,14 @@ 19 retained_intron exon 438718 438837 . - . Parent=ENST00000589922 19 retained_intron exon 438970 439030 . - . Parent=ENST00000589922 19 retained_intron exon 440862 441384 . - . Parent=ENST00000589922 -19 nonsense_mediated_decay mRNA 417200 436258 . - . ID=ENST00000590170;geneID=ENSG00000129946;gene_name=SHC2 +19 nonsense_mediated_decay transcript 417200 436258 . - . ID=ENST00000590170;geneID=ENSG00000129946;gene_name=SHC2 19 nonsense_mediated_decay exon 417200 417322 . - . Parent=ENST00000590170 19 nonsense_mediated_decay exon 418923 419056 . - . Parent=ENST00000590170 19 nonsense_mediated_decay exon 422146 422379 . - . Parent=ENST00000590170 19 nonsense_mediated_decay exon 430684 430747 . - . Parent=ENST00000590170 19 nonsense_mediated_decay exon 434709 434865 . - . Parent=ENST00000590170 19 nonsense_mediated_decay exon 436165 436258 . - . Parent=ENST00000590170 -19 nonsense_mediated_decay CDS 434765 434865 . - 2 Parent=ENST00000590170 +19 nonsense_mediated_decay CDS 434762 434865 . - 2 Parent=ENST00000590170 19 nonsense_mediated_decay CDS 436165 436258 . - 0 Parent=ENST00000590170 19 processed_transcript transcript 417200 436258 . - . ID=ENST00000591948;geneID=ENSG00000129946;gene_name=SHC2 19 processed_transcript exon 417200 417322 . - . Parent=ENST00000591948 @@ -223,7 +224,7 @@ 19 processed_transcript exon 430684 430747 . - . Parent=ENST00000591948 19 processed_transcript exon 434709 434865 . - . Parent=ENST00000591948 19 processed_transcript exon 436165 436258 . - . Parent=ENST00000591948 -19 nonsense_mediated_decay mRNA 434702 460571 . - . ID=ENST00000590222;geneID=ENSG00000129946;gene_name=SHC2 +19 nonsense_mediated_decay transcript 434702 460571 . - . ID=ENST00000590222;geneID=ENSG00000129946;gene_name=SHC2 19 nonsense_mediated_decay exon 434702 434865 . - . Parent=ENST00000590222 19 nonsense_mediated_decay exon 436165 436291 . - . Parent=ENST00000590222 19 nonsense_mediated_decay exon 436380 436431 . - . Parent=ENST00000590222 @@ -233,7 +234,7 @@ 19 nonsense_mediated_decay exon 439233 439491 . - . Parent=ENST00000590222 19 nonsense_mediated_decay exon 440862 440932 . - . Parent=ENST00000590222 19 nonsense_mediated_decay exon 460529 460571 . - . Parent=ENST00000590222 -19 nonsense_mediated_decay CDS 439401 439491 . - 1 Parent=ENST00000590222 +19 nonsense_mediated_decay CDS 439398 439491 . - 1 Parent=ENST00000590222 19 nonsense_mediated_decay CDS 440862 440932 . - 0 Parent=ENST00000590222 19 nonsense_mediated_decay CDS 460529 460571 . - 1 Parent=ENST00000590222 19 retained_intron transcript 435771 436534 . - . ID=ENST00000591388;geneID=ENSG00000129946;gene_name=SHC2 @@ -249,20 +250,20 @@ 19 processed_transcript exon 438970 439031 . - . Parent=ENST00000590113 19 rRNA transcript 453134 453245 . + . ID=ENST00000516730;geneID=ENSG00000252539;gene_name=RNA5SP462 19 rRNA exon 453134 453245 . + . Parent=ENST00000516730 -19 protein_coding mRNA 463346 474983 . - . ID=ENST00000315489;geneID=ENSG00000181781;gene_name=ODF3L2 +19 protein_coding transcript 463346 474983 . - . ID=ENST00000315489;geneID=ENSG00000181781;gene_name=ODF3L2 19 protein_coding exon 463346 464364 . - . Parent=ENST00000315489 19 protein_coding exon 467649 467762 . - . Parent=ENST00000315489 19 protein_coding exon 472394 472501 . - . Parent=ENST00000315489 19 protein_coding exon 474621 474983 . - . Parent=ENST00000315489 -19 protein_coding CDS 463847 464364 . - 2 Parent=ENST00000315489 +19 protein_coding CDS 463844 464364 . - 2 Parent=ENST00000315489 19 protein_coding CDS 467649 467762 . - 2 Parent=ENST00000315489 19 protein_coding CDS 472394 472501 . - 2 Parent=ENST00000315489 19 protein_coding CDS 474621 474747 . - 0 Parent=ENST00000315489 -19 protein_coding mRNA 463467 474880 . - . ID=ENST00000382696;geneID=ENSG00000181781;gene_name=ODF3L2 +19 protein_coding transcript 463467 474880 . - . ID=ENST00000382696;geneID=ENSG00000181781;gene_name=ODF3L2 19 protein_coding exon 463467 464364 . - . Parent=ENST00000382696 19 protein_coding exon 467649 467762 . - . Parent=ENST00000382696 19 protein_coding exon 474621 474880 . - . Parent=ENST00000382696 -19 protein_coding CDS 463847 464364 . - 2 Parent=ENST00000382696 +19 protein_coding CDS 463844 464364 . - 2 Parent=ENST00000382696 19 protein_coding CDS 467649 467762 . - 2 Parent=ENST00000382696 19 protein_coding CDS 474621 474747 . - 0 Parent=ENST00000382696 19 retained_intron transcript 464146 472631 . - . ID=ENST00000591681;geneID=ENSG00000181781;gene_name=ODF3L2 @@ -277,7 +278,7 @@ 19 antisense exon 490046 490353 . - . Parent=ENST00000592413 19 antisense exon 501541 501624 . - . Parent=ENST00000592413 19 antisense exon 507376 507813 . - . Parent=ENST00000592413 -19 protein_coding mRNA 496454 505207 . + . ID=ENST00000346144;geneID=ENSG00000099866;gene_name=MADCAM1 +19 protein_coding transcript 496454 505207 . + . ID=ENST00000346144;geneID=ENSG00000099866;gene_name=MADCAM1 19 protein_coding exon 496454 496551 . + . Parent=ENST00000346144 19 protein_coding exon 497833 498117 . + . Parent=ENST00000346144 19 protein_coding exon 498496 498825 . + . Parent=ENST00000346144 @@ -285,8 +286,8 @@ 19 protein_coding CDS 496500 496551 . + 0 Parent=ENST00000346144 19 protein_coding CDS 497833 498117 . + 2 Parent=ENST00000346144 19 protein_coding CDS 498496 498825 . + 2 Parent=ENST00000346144 -19 protein_coding CDS 504745 504963 . + 2 Parent=ENST00000346144 -19 protein_coding mRNA 496454 505347 . + . ID=ENST00000215637;geneID=ENSG00000099866;gene_name=MADCAM1 +19 protein_coding CDS 504745 504965 . + 2 Parent=ENST00000346144 +19 protein_coding transcript 496454 505347 . + . ID=ENST00000215637;geneID=ENSG00000099866;gene_name=MADCAM1 19 protein_coding exon 496454 496551 . + . Parent=ENST00000215637 19 protein_coding exon 497833 498117 . + . Parent=ENST00000215637 19 protein_coding exon 498496 498825 . + . Parent=ENST00000215637 @@ -296,18 +297,18 @@ 19 protein_coding CDS 497833 498117 . + 2 Parent=ENST00000215637 19 protein_coding CDS 498496 498825 . + 2 Parent=ENST00000215637 19 protein_coding CDS 501669 501929 . + 2 Parent=ENST00000215637 -19 protein_coding CDS 504745 504963 . + 2 Parent=ENST00000215637 -19 protein_coding mRNA 496500 504965 . + . ID=ENST00000382683;geneID=ENSG00000099866;gene_name=MADCAM1 +19 protein_coding CDS 504745 504965 . + 2 Parent=ENST00000215637 +19 protein_coding transcript 496500 504965 . + . ID=ENST00000382683;geneID=ENSG00000099866;gene_name=MADCAM1 19 protein_coding exon 496500 496551 . + . Parent=ENST00000382683 19 protein_coding exon 498496 498825 . + . Parent=ENST00000382683 19 protein_coding exon 504745 504965 . + . Parent=ENST00000382683 19 protein_coding CDS 496500 496551 . + 0 Parent=ENST00000382683 19 protein_coding CDS 498496 498825 . + 2 Parent=ENST00000382683 -19 protein_coding CDS 504745 504963 . + 2 Parent=ENST00000382683 -19 protein_coding mRNA 507299 519654 . + . ID=ENST00000359315;geneID=ENSG00000141933;gene_name=TPGS1 +19 protein_coding CDS 504745 504965 . + 2 Parent=ENST00000382683 +19 protein_coding transcript 507299 519654 . + . ID=ENST00000359315;geneID=ENSG00000141933;gene_name=TPGS1 19 protein_coding exon 507299 507844 . + . Parent=ENST00000359315 19 protein_coding exon 518889 519654 . + . Parent=ENST00000359315 19 protein_coding CDS 507507 507844 . + 0 Parent=ENST00000359315 -19 protein_coding CDS 518889 519421 . + 1 Parent=ENST00000359315 +19 protein_coding CDS 518889 519423 . + 1 Parent=ENST00000359315 19 retained_intron transcript 507500 510372 . + . ID=ENST00000588278;geneID=ENSG00000141933;gene_name=TPGS1 19 retained_intron exon 507500 510372 . + . Parent=ENST00000588278