diff test-data/Homo_sapiens.GRCh37_19.71_ensemble.gff3 @ 9:3e436657dcd0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
author iuc
date Fri, 15 Dec 2023 19:39:24 +0000
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Homo_sapiens.GRCh37_19.71_ensemble.gff3	Fri Dec 15 19:39:24 2023 +0000
@@ -0,0 +1,314 @@
+##gff-version 3
+# gffread v0.12.7
+# gffread /tmp/tmpvxc_8nmx/files/9/a/6/dataset_9a6a5831-b7ee-4eee-9b23-08af98672088.dat -L -o /home/berntm/projects/tools-iuc/tools/gffread/test-data/Homo_sapiens.GRCh37_19.71_ensemble.gff3 -t track name
+19	track name	transcript	223158	223261	.	-	.	ID=ENST00000410397;geneID=ENSG00000222329;gene_name=U6;gene_biotype=snRNA;transcript_name=U6.795-201
+19	track name	exon	223158	223261	.	-	.	Parent=ENST00000410397
+19	track name	transcript	229640	230165	.	-	.	ID=ENST00000587910;geneID=ENSG00000267600;gene_name=AC098474.1;gene_biotype=pseudogene;transcript_name=AC098474.1-001
+19	track name	exon	229640	229709	.	-	.	Parent=ENST00000587910
+19	track name	exon	230084	230165	.	-	.	Parent=ENST00000587910
+19	track name	transcript	239145	239247	.	-	.	ID=ENST00000588755;geneID=ENSG00000267305;gene_name=CTD-3113P16.7;gene_biotype=pseudogene;transcript_name=CTD-3113P16.7-001
+19	track name	exon	239145	239247	.	-	.	Parent=ENST00000588755
+19	track name	transcript	279495	280170	.	+	.	ID=ENST00000589981;geneID=ENSG00000267447;gene_name=VN2R11P;gene_biotype=pseudogene;transcript_name=VN2R11P-001
+19	track name	exon	279495	280170	.	+	.	Parent=ENST00000589981
+19	track name	transcript	281043	291386	.	-	.	ID=ENST00000269812;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-001;protein_id=ENSP00000269812
+19	track name	exon	281043	281537	.	-	.	Parent=ENST00000269812
+19	track name	exon	282134	282310	.	-	.	Parent=ENST00000269812
+19	track name	exon	282752	282809	.	-	.	Parent=ENST00000269812
+19	track name	exon	287474	287751	.	-	.	Parent=ENST00000269812
+19	track name	exon	288020	288171	.	-	.	Parent=ENST00000269812
+19	track name	exon	291285	291386	.	-	.	Parent=ENST00000269812
+19	track name	CDS	281388	281537	.	-	0	Parent=ENST00000269812
+19	track name	CDS	282134	282310	.	-	0	Parent=ENST00000269812
+19	track name	CDS	282752	282809	.	-	1	Parent=ENST00000269812
+19	track name	CDS	287474	287751	.	-	0	Parent=ENST00000269812
+19	track name	CDS	288020	288171	.	-	2	Parent=ENST00000269812
+19	track name	CDS	291285	291336	.	-	0	Parent=ENST00000269812
+19	track name	transcript	281345	291393	.	-	.	ID=ENST00000434325;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-003;protein_id=ENSP00000388565
+19	track name	exon	281345	281537	.	-	.	Parent=ENST00000434325
+19	track name	exon	282134	282310	.	-	.	Parent=ENST00000434325
+19	track name	exon	282752	282809	.	-	.	Parent=ENST00000434325
+19	track name	exon	287474	287751	.	-	.	Parent=ENST00000434325
+19	track name	exon	288020	288171	.	-	.	Parent=ENST00000434325
+19	track name	exon	291326	291393	.	-	.	Parent=ENST00000434325
+19	track name	CDS	281388	281537	.	-	0	Parent=ENST00000434325
+19	track name	CDS	282134	282310	.	-	0	Parent=ENST00000434325
+19	track name	CDS	282752	282809	.	-	1	Parent=ENST00000434325
+19	track name	CDS	287474	287751	.	-	0	Parent=ENST00000434325
+19	track name	CDS	288020	288055	.	-	0	Parent=ENST00000434325
+19	track name	transcript	281388	291200	.	-	.	ID=ENST00000327790;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-004;protein_id=ENSP00000329697
+19	track name	exon	281388	281537	.	-	.	Parent=ENST00000327790
+19	track name	exon	282134	282310	.	-	.	Parent=ENST00000327790
+19	track name	exon	282752	282809	.	-	.	Parent=ENST00000327790
+19	track name	exon	287474	287751	.	-	.	Parent=ENST00000327790
+19	track name	exon	288020	288171	.	-	.	Parent=ENST00000327790
+19	track name	exon	290952	291200	.	-	.	Parent=ENST00000327790
+19	track name	CDS	281388	281537	.	-	0	Parent=ENST00000327790
+19	track name	CDS	282134	282310	.	-	0	Parent=ENST00000327790
+19	track name	CDS	282752	282809	.	-	1	Parent=ENST00000327790
+19	track name	CDS	287474	287751	.	-	0	Parent=ENST00000327790
+19	track name	CDS	288020	288171	.	-	2	Parent=ENST00000327790
+19	track name	CDS	290952	291066	.	-	0	Parent=ENST00000327790
+19	track name	transcript	281991	287636	.	-	.	ID=ENST00000586998;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-007;protein_id=ENSP00000466947
+19	track name	exon	281991	282310	.	-	.	Parent=ENST00000586998
+19	track name	exon	282752	282809	.	-	.	Parent=ENST00000586998
+19	track name	exon	287474	287636	.	-	.	Parent=ENST00000586998
+19	track name	CDS	282122	282310	.	-	0	Parent=ENST00000586998
+19	track name	CDS	282752	282809	.	-	1	Parent=ENST00000586998
+19	track name	CDS	287474	287636	.	-	2	Parent=ENST00000586998
+19	track name	transcript	287161	288530	.	-	.	ID=ENST00000589672;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-006
+19	track name	exon	287161	287751	.	-	.	Parent=ENST00000589672
+19	track name	exon	288020	288530	.	-	.	Parent=ENST00000589672
+19	track name	transcript	287474	291382	.	-	.	ID=ENST00000591572;geneID=ENSG00000141934;gene_name=PPAP2C;gene_biotype=protein_coding;transcript_name=PPAP2C-005;protein_id=ENSP00000466545
+19	track name	exon	287474	287751	.	-	.	Parent=ENST00000591572
+19	track name	exon	288020	288189	.	-	.	Parent=ENST00000591572
+19	track name	exon	291285	291382	.	-	.	Parent=ENST00000591572
+19	track name	CDS	287474	287751	.	-	0	Parent=ENST00000591572
+19	track name	CDS	288020	288189	.	-	2	Parent=ENST00000591572
+19	track name	CDS	291285	291336	.	-	0	Parent=ENST00000591572
+19	track name	transcript	305573	306467	.	+	.	ID=ENST00000591533;geneID=ENSG00000267124;gene_name=CTD-3113P16.5;gene_biotype=antisense;transcript_name=CTD-3113P16.5-002
+19	track name	exon	305573	305703	.	+	.	Parent=ENST00000591533
+19	track name	exon	306057	306467	.	+	.	Parent=ENST00000591533
+19	track name	transcript	305575	344793	.	-	.	ID=ENST00000264819;geneID=ENSG00000105556;gene_name=MIER2;gene_biotype=protein_coding;transcript_name=MIER2-001;protein_id=ENSP00000264819
+19	track name	exon	305575	306711	.	-	.	Parent=ENST00000264819
+19	track name	exon	307119	307536	.	-	.	Parent=ENST00000264819
+19	track name	exon	308577	308665	.	-	.	Parent=ENST00000264819
+19	track name	exon	308801	308925	.	-	.	Parent=ENST00000264819
+19	track name	exon	311845	311939	.	-	.	Parent=ENST00000264819
+19	track name	exon	312191	312272	.	-	.	Parent=ENST00000264819
+19	track name	exon	313492	313643	.	-	.	Parent=ENST00000264819
+19	track name	exon	325635	325704	.	-	.	Parent=ENST00000264819
+19	track name	exon	326507	326598	.	-	.	Parent=ENST00000264819
+19	track name	exon	327133	327256	.	-	.	Parent=ENST00000264819
+19	track name	exon	327864	327989	.	-	.	Parent=ENST00000264819
+19	track name	exon	334400	334542	.	-	.	Parent=ENST00000264819
+19	track name	exon	336083	336173	.	-	.	Parent=ENST00000264819
+19	track name	exon	344774	344793	.	-	.	Parent=ENST00000264819
+19	track name	CDS	306690	306711	.	-	1	Parent=ENST00000264819
+19	track name	CDS	307119	307536	.	-	2	Parent=ENST00000264819
+19	track name	CDS	308577	308665	.	-	1	Parent=ENST00000264819
+19	track name	CDS	308801	308925	.	-	0	Parent=ENST00000264819
+19	track name	CDS	311845	311939	.	-	2	Parent=ENST00000264819
+19	track name	CDS	312191	312272	.	-	0	Parent=ENST00000264819
+19	track name	CDS	313492	313643	.	-	2	Parent=ENST00000264819
+19	track name	CDS	325635	325704	.	-	0	Parent=ENST00000264819
+19	track name	CDS	326507	326598	.	-	2	Parent=ENST00000264819
+19	track name	CDS	327133	327256	.	-	0	Parent=ENST00000264819
+19	track name	CDS	327864	327989	.	-	0	Parent=ENST00000264819
+19	track name	CDS	334400	334542	.	-	2	Parent=ENST00000264819
+19	track name	CDS	336083	336173	.	-	0	Parent=ENST00000264819
+19	track name	CDS	344774	344782	.	-	0	Parent=ENST00000264819
+19	track name	transcript	305579	325706	.	+	.	ID=ENST00000589092;geneID=ENSG00000267124;gene_name=CTD-3113P16.5;gene_biotype=antisense;transcript_name=CTD-3113P16.5-001
+19	track name	exon	305579	305934	.	+	.	Parent=ENST00000589092
+19	track name	exon	325624	325706	.	+	.	Parent=ENST00000589092
+19	track name	transcript	326607	336178	.	-	.	ID=ENST00000586994;geneID=ENSG00000105556;gene_name=MIER2;gene_biotype=protein_coding;transcript_name=MIER2-004
+19	track name	exon	326607	327256	.	-	.	Parent=ENST00000586994
+19	track name	exon	327864	327989	.	-	.	Parent=ENST00000586994
+19	track name	exon	334400	334542	.	-	.	Parent=ENST00000586994
+19	track name	exon	336083	336178	.	-	.	Parent=ENST00000586994
+19	track name	transcript	327864	340599	.	-	.	ID=ENST00000592722;geneID=ENSG00000105556;gene_name=MIER2;gene_biotype=protein_coding;transcript_name=MIER2-003
+19	track name	exon	327864	327989	.	-	.	Parent=ENST00000592722
+19	track name	exon	330264	330380	.	-	.	Parent=ENST00000592722
+19	track name	exon	334400	334542	.	-	.	Parent=ENST00000592722
+19	track name	exon	336083	336173	.	-	.	Parent=ENST00000592722
+19	track name	exon	340514	340599	.	-	.	Parent=ENST00000592722
+19	track name	transcript	334115	344798	.	-	.	ID=ENST00000587966;geneID=ENSG00000105556;gene_name=MIER2;gene_biotype=protein_coding;transcript_name=MIER2-002
+19	track name	exon	334115	334542	.	-	.	Parent=ENST00000587966
+19	track name	exon	344774	344798	.	-	.	Parent=ENST00000587966
+19	track name	transcript	361750	376013	.	-	.	ID=ENST00000342640;geneID=ENSG00000105549;gene_name=THEG;gene_biotype=protein_coding;transcript_name=THEG-001;protein_id=ENSP00000340088
+19	track name	exon	361750	362426	.	-	.	Parent=ENST00000342640
+19	track name	exon	367065	367224	.	-	.	Parent=ENST00000342640
+19	track name	exon	371205	371322	.	-	.	Parent=ENST00000342640
+19	track name	exon	372631	372700	.	-	.	Parent=ENST00000342640
+19	track name	exon	373470	373531	.	-	.	Parent=ENST00000342640
+19	track name	exon	373940	374011	.	-	.	Parent=ENST00000342640
+19	track name	exon	374299	374421	.	-	.	Parent=ENST00000342640
+19	track name	exon	375663	376013	.	-	.	Parent=ENST00000342640
+19	track name	CDS	362200	362426	.	-	2	Parent=ENST00000342640
+19	track name	CDS	367065	367224	.	-	0	Parent=ENST00000342640
+19	track name	CDS	371205	371322	.	-	1	Parent=ENST00000342640
+19	track name	CDS	372631	372700	.	-	2	Parent=ENST00000342640
+19	track name	CDS	373470	373531	.	-	1	Parent=ENST00000342640
+19	track name	CDS	373940	374011	.	-	1	Parent=ENST00000342640
+19	track name	CDS	374299	374421	.	-	1	Parent=ENST00000342640
+19	track name	CDS	375663	375970	.	-	0	Parent=ENST00000342640
+19	track name	transcript	362058	374620	.	-	.	ID=ENST00000530711;geneID=ENSG00000105549;gene_name=THEG;gene_biotype=protein_coding;transcript_name=THEG-002
+19	track name	exon	362058	362426	.	-	.	Parent=ENST00000530711
+19	track name	exon	367065	367224	.	-	.	Parent=ENST00000530711
+19	track name	exon	374299	374620	.	-	.	Parent=ENST00000530711
+19	track name	transcript	362200	375970	.	-	.	ID=ENST00000346878;geneID=ENSG00000105549;gene_name=THEG;gene_biotype=protein_coding;transcript_name=THEG-004;protein_id=ENSP00000264820
+19	track name	exon	362200	362426	.	-	.	Parent=ENST00000346878
+19	track name	exon	367065	367224	.	-	.	Parent=ENST00000346878
+19	track name	exon	371205	371322	.	-	.	Parent=ENST00000346878
+19	track name	exon	372631	372700	.	-	.	Parent=ENST00000346878
+19	track name	exon	373470	373531	.	-	.	Parent=ENST00000346878
+19	track name	exon	374299	374421	.	-	.	Parent=ENST00000346878
+19	track name	exon	375663	375970	.	-	.	Parent=ENST00000346878
+19	track name	CDS	362200	362426	.	-	2	Parent=ENST00000346878
+19	track name	CDS	367065	367224	.	-	0	Parent=ENST00000346878
+19	track name	CDS	371205	371322	.	-	1	Parent=ENST00000346878
+19	track name	CDS	372631	372700	.	-	2	Parent=ENST00000346878
+19	track name	CDS	373470	373531	.	-	1	Parent=ENST00000346878
+19	track name	CDS	374299	374421	.	-	1	Parent=ENST00000346878
+19	track name	CDS	375663	375970	.	-	0	Parent=ENST00000346878
+19	track name	transcript	367202	374249	.	-	.	ID=ENST00000528213;geneID=ENSG00000105549;gene_name=THEG;gene_biotype=protein_coding;transcript_name=THEG-003
+19	track name	exon	367202	367224	.	-	.	Parent=ENST00000528213
+19	track name	exon	371205	371322	.	-	.	Parent=ENST00000528213
+19	track name	exon	372631	372700	.	-	.	Parent=ENST00000528213
+19	track name	exon	373470	373531	.	-	.	Parent=ENST00000528213
+19	track name	exon	373940	374249	.	-	.	Parent=ENST00000528213
+19	track name	transcript	397589	398941	.	+	.	ID=ENST00000591757;geneID=ENSG00000267443;gene_name=AC010641.1;gene_biotype=processed_transcript;transcript_name=AC010641.1-001
+19	track name	exon	397589	397633	.	+	.	Parent=ENST00000591757
+19	track name	exon	398690	398941	.	+	.	Parent=ENST00000591757
+19	track name	transcript	405445	409139	.	-	.	ID=ENST00000332235;geneID=ENSG00000183186;gene_name=C2CD4C;gene_biotype=protein_coding;transcript_name=C2CD4C-001;protein_id=ENSP00000328677
+19	track name	exon	405445	408401	.	-	.	Parent=ENST00000332235
+19	track name	exon	409006	409139	.	-	.	Parent=ENST00000332235
+19	track name	CDS	407096	408361	.	-	0	Parent=ENST00000332235
+19	track name	transcript	416583	419879	.	-	.	ID=ENST00000587423;geneID=ENSG00000129946;gene_name=SHC2;gene_biotype=protein_coding;transcript_name=SHC2-004
+19	track name	exon	416583	417322	.	-	.	Parent=ENST00000587423
+19	track name	exon	418923	419879	.	-	.	Parent=ENST00000587423
+19	track name	transcript	416583	422828	.	-	.	ID=ENST00000588376;geneID=ENSG00000129946;gene_name=SHC2;gene_biotype=protein_coding;transcript_name=SHC2-003
+19	track name	exon	416583	417322	.	-	.	Parent=ENST00000588376
+19	track name	exon	418923	419056	.	-	.	Parent=ENST00000588376
+19	track name	exon	422146	422828	.	-	.	Parent=ENST00000588376
+19	track name	transcript	416593	460996	.	-	.	ID=ENST00000264554;geneID=ENSG00000129946;gene_name=SHC2;gene_biotype=protein_coding;transcript_name=SHC2-001;protein_id=ENSP00000264554
+19	track name	exon	416593	417322	.	-	.	Parent=ENST00000264554
+19	track name	exon	418923	419056	.	-	.	Parent=ENST00000264554
+19	track name	exon	422146	422456	.	-	.	Parent=ENST00000264554
+19	track name	exon	425097	425231	.	-	.	Parent=ENST00000264554
+19	track name	exon	430684	430747	.	-	.	Parent=ENST00000264554
+19	track name	exon	434709	434865	.	-	.	Parent=ENST00000264554
+19	track name	exon	436165	436291	.	-	.	Parent=ENST00000264554
+19	track name	exon	436380	436431	.	-	.	Parent=ENST00000264554
+19	track name	exon	436630	436683	.	-	.	Parent=ENST00000264554
+19	track name	exon	438718	438837	.	-	.	Parent=ENST00000264554
+19	track name	exon	438970	439030	.	-	.	Parent=ENST00000264554
+19	track name	exon	440862	440932	.	-	.	Parent=ENST00000264554
+19	track name	exon	460529	460996	.	-	.	Parent=ENST00000264554
+19	track name	CDS	418928	419056	.	-	0	Parent=ENST00000264554
+19	track name	CDS	422146	422456	.	-	2	Parent=ENST00000264554
+19	track name	CDS	425097	425231	.	-	2	Parent=ENST00000264554
+19	track name	CDS	430684	430747	.	-	0	Parent=ENST00000264554
+19	track name	CDS	434709	434865	.	-	1	Parent=ENST00000264554
+19	track name	CDS	436165	436291	.	-	2	Parent=ENST00000264554
+19	track name	CDS	436380	436431	.	-	0	Parent=ENST00000264554
+19	track name	CDS	436630	436683	.	-	0	Parent=ENST00000264554
+19	track name	CDS	438718	438837	.	-	0	Parent=ENST00000264554
+19	track name	CDS	438970	439030	.	-	1	Parent=ENST00000264554
+19	track name	CDS	440862	440932	.	-	0	Parent=ENST00000264554
+19	track name	CDS	460529	460996	.	-	0	Parent=ENST00000264554
+19	track name	transcript	416609	441384	.	-	.	ID=ENST00000589922;geneID=ENSG00000129946;gene_name=SHC2;gene_biotype=protein_coding;transcript_name=SHC2-002
+19	track name	exon	416609	417322	.	-	.	Parent=ENST00000589922
+19	track name	exon	418923	419056	.	-	.	Parent=ENST00000589922
+19	track name	exon	422146	422456	.	-	.	Parent=ENST00000589922
+19	track name	exon	425097	425231	.	-	.	Parent=ENST00000589922
+19	track name	exon	430684	430747	.	-	.	Parent=ENST00000589922
+19	track name	exon	434709	434865	.	-	.	Parent=ENST00000589922
+19	track name	exon	436165	436291	.	-	.	Parent=ENST00000589922
+19	track name	exon	436380	436683	.	-	.	Parent=ENST00000589922
+19	track name	exon	438718	438837	.	-	.	Parent=ENST00000589922
+19	track name	exon	438970	439030	.	-	.	Parent=ENST00000589922
+19	track name	exon	440862	441384	.	-	.	Parent=ENST00000589922
+19	track name	transcript	417200	436258	.	-	.	ID=ENST00000590170;geneID=ENSG00000129946;gene_name=SHC2;gene_biotype=protein_coding;transcript_name=SHC2-009;protein_id=ENSP00000465764
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+19	track name	exon	418923	419056	.	-	.	Parent=ENST00000590170
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