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view test-data/sample.gff3 @ 0:35bcefc9176b draft default tip
planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit dbd9af1e941e35ec9ca2a9f75af02edea67a5981
| author | sanbi-uwc |
|---|---|
| date | Thu, 15 Jun 2017 07:41:38 -0400 |
| parents | |
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##gff-version 3 ##sequence-region Chromosome 1 4410929 #!genome-build European Nucleotide Archive ASM19595v2 #!genome-version GCA_000195955.2 #!genome-date 2015-02 #!genome-build-accession GCA_000195955.2 #!genebuild-last-updated 2015-02 Chromosome ena gene 1 1524 . + . ID=gene:Rv0001;Name=dnaA;biotype=protein_coding;description=Chromosomal replication initiator protein DnaA;gene_id=Rv0001;logic_name=ena;version=1 Chromosome ena transcript 1 1524 . + . ID=transcript:CCP42723;Parent=gene:Rv0001;Name=dnaA-1;biotype=protein_coding;transcript_id=CCP42723;version=1 Chromosome ena exon 1 1524 . + . Parent=transcript:CCP42723;Name=CCP42723-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42723-1;rank=1;version=1 Chromosome ena CDS 1 1524 . + 0 ID=CDS:CCP42723;Parent=transcript:CCP42723;protein_id=CCP42723 ### Chromosome ena gene 2052 3260 . + . ID=gene:Rv0002;Name=dnaN;biotype=protein_coding;description=DNA polymerase III (beta chain) DnaN (DNA nucleotidyltransferase);gene_id=Rv0002;logic_name=ena;version=1 Chromosome ena transcript 2052 3260 . + . ID=transcript:CCP42724;Parent=gene:Rv0002;Name=dnaN-1;biotype=protein_coding;transcript_id=CCP42724;version=1 Chromosome ena exon 2052 3260 . + . Parent=transcript:CCP42724;Name=CCP42724-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42724-1;rank=1;version=1 Chromosome ena CDS 2052 3260 . + 0 ID=CDS:CCP42724;Parent=transcript:CCP42724;protein_id=CCP42724 ### Chromosome ena gene 3280 4437 . + . ID=gene:Rv0003;Name=recF;biotype=protein_coding;description=DNA replication and repair protein RecF (single-strand DNA binding protein);gene_id=Rv0003;logic_name=ena;version=1 Chromosome ena transcript 3280 4437 . + . ID=transcript:CCP42725;Parent=gene:Rv0003;Name=recF-1;biotype=protein_coding;transcript_id=CCP42725;version=1 Chromosome ena exon 3280 4437 . + . Parent=transcript:CCP42725;Name=CCP42725-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42725-1;rank=1;version=1 Chromosome ena CDS 3280 4437 . + 0 ID=CDS:CCP42725;Parent=transcript:CCP42725;protein_id=CCP42725 ### Chromosome ena gene 4434 4997 . + . ID=gene:Rv0004;biotype=protein_coding;description=Conserved hypothetical protein;gene_id=Rv0004;logic_name=ena;version=1 Chromosome ena transcript 4434 4997 . + . ID=transcript:CCP42726;Parent=gene:Rv0004;biotype=protein_coding;transcript_id=CCP42726;version=1 Chromosome ena exon 4434 4997 . + . Parent=transcript:CCP42726;Name=CCP42726-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42726-1;rank=1;version=1 Chromosome ena CDS 4434 4997 . + 0 ID=CDS:CCP42726;Parent=transcript:CCP42726;protein_id=CCP42726 ### Chromosome ena gene 5240 7267 . + . ID=gene:Rv0005;Name=gyrB;biotype=protein_coding;description=DNA gyrase (subunit B) GyrB (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase);gene_id=Rv0005;logic_name=ena;version=1 Chromosome ena transcript 5240 7267 . + . ID=transcript:CCP42727;Parent=gene:Rv0005;Name=gyrB-1;biotype=protein_coding;transcript_id=CCP42727;version=1 Chromosome ena exon 5240 7267 . + . Parent=transcript:CCP42727;Name=CCP42727-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42727-1;rank=1;version=1 Chromosome ena CDS 5240 7267 . + 0 ID=CDS:CCP42727;Parent=transcript:CCP42727;protein_id=CCP42727 ### Chromosome ena gene 7302 9818 . + . ID=gene:Rv0006;Name=gyrA;biotype=protein_coding;description=DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydrolysing)) (DNA topoisomerase II) (type II DNA topoisomerase);gene_id=Rv0006;logic_name=ena;version=1 Chromosome ena transcript 7302 9818 . + . ID=transcript:CCP42728;Parent=gene:Rv0006;Name=gyrA-1;biotype=protein_coding;transcript_id=CCP42728;version=1 Chromosome ena exon 7302 9818 . + . Parent=transcript:CCP42728;Name=CCP42728-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42728-1;rank=1;version=1 Chromosome ena CDS 7302 9818 . + 0 ID=CDS:CCP42728;Parent=transcript:CCP42728;protein_id=CCP42728 ### Chromosome ena gene 9914 10828 . + . ID=gene:Rv0007;biotype=protein_coding;description=Possible conserved membrane protein;gene_id=Rv0007;logic_name=ena;version=1 Chromosome ena transcript 9914 10828 . + . ID=transcript:CCP42729;Parent=gene:Rv0007;biotype=protein_coding;transcript_id=CCP42729;version=1 Chromosome ena exon 9914 10828 . + . Parent=transcript:CCP42729;Name=CCP42729-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42729-1;rank=1;version=1 Chromosome ena CDS 9914 10828 . + 0 ID=CDS:CCP42729;Parent=transcript:CCP42729;protein_id=CCP42729 ### Chromosome ena tRNA_gene 10887 10960 . + . ID=gene:EBG00000313329;Name=ileT;biotype=tRNA;gene_id=EBG00000313329;logic_name=ena_rna;version=1 Chromosome ena transcript 10887 10960 . + . ID=transcript:EBG00000313329-1;Parent=gene:EBG00000313329;Name=ileT;biotype=tRNA;transcript_id=EBG00000313329-1;version=1 Chromosome ena exon 10887 10960 . + . Parent=transcript:EBG00000313329-1;Name=EBG00000313329-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=EBG00000313329-1;rank=1;version=1 ### Chromosome ena_gene biological_region 10887 10960 . + . external_name=AL123456.3:gene:10887..10960;logic_name=ena_gene Chromosome ena tRNA_gene 11112 11184 . + . ID=gene:EBG00000313365;Name=alaT;biotype=tRNA;gene_id=EBG00000313365;logic_name=ena_rna;version=1 Chromosome ena transcript 11112 11184 . + . ID=transcript:EBG00000313365-1;Parent=gene:EBG00000313365;Name=alaT;biotype=tRNA;transcript_id=EBG00000313365-1;version=1 Chromosome ena exon 11112 11184 . + . Parent=transcript:EBG00000313365-1;Name=EBG00000313365-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=EBG00000313365-1;rank=1;version=1 ### Chromosome ena_gene biological_region 11112 11184 . + . external_name=AL123456.3:gene:11112..11184;logic_name=ena_gene Chromosome ena gene 11874 12311 . - . ID=gene:Rv0008c;biotype=protein_coding;description=Possible membrane protein;gene_id=Rv0008c;logic_name=ena;version=1 Chromosome ena transcript 11874 12311 . - . ID=transcript:CCP42730;Parent=gene:Rv0008c;biotype=protein_coding;transcript_id=CCP42730;version=1 Chromosome ena exon 11874 12311 . - . Parent=transcript:CCP42730;Name=CCP42730-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42730-1;rank=1;version=1 Chromosome ena CDS 11874 12311 . - 0 ID=CDS:CCP42730;Parent=transcript:CCP42730;protein_id=CCP42730 ### Chromosome ena gene 12468 13016 . + . ID=gene:Rv0009;Name=ppiA;biotype=protein_coding;description=Probable iron-regulated peptidyl-prolyl cis-trans isomerase A PpiA (PPIase A) (rotamase A);gene_id=Rv0009;logic_name=ena;version=1 Chromosome ena transcript 12468 13016 . + . ID=transcript:CCP42731;Parent=gene:Rv0009;Name=ppiA-1;biotype=protein_coding;transcript_id=CCP42731;version=1 Chromosome ena exon 12468 13016 . + . Parent=transcript:CCP42731;Name=CCP42731-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42731-1;rank=1;version=1 Chromosome ena CDS 12468 13016 . + 0 ID=CDS:CCP42731;Parent=transcript:CCP42731;protein_id=CCP42731 ### Chromosome ena gene 13133 13558 . - . ID=gene:Rv0010c;biotype=protein_coding;description=Probable conserved membrane protein;gene_id=Rv0010c;logic_name=ena;version=1 Chromosome ena transcript 13133 13558 . - . ID=transcript:CCP42732;Parent=gene:Rv0010c;biotype=protein_coding;transcript_id=CCP42732;version=1 Chromosome ena exon 13133 13558 . - . Parent=transcript:CCP42732;Name=CCP42732-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42732-1;rank=1;version=1 Chromosome ena CDS 13133 13558 . - 0 ID=CDS:CCP42732;Parent=transcript:CCP42732;protein_id=CCP42732 ### Chromosome ena gene 13714 13995 . - . ID=gene:Rv0011c;biotype=protein_coding;description=Probable conserved transmembrane protein;gene_id=Rv0011c;logic_name=ena;version=1 Chromosome ena transcript 13714 13995 . - . ID=transcript:CCP42733;Parent=gene:Rv0011c;biotype=protein_coding;transcript_id=CCP42733;version=1 Chromosome ena exon 13714 13995 . - . Parent=transcript:CCP42733;Name=CCP42733-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42733-1;rank=1;version=1 Chromosome ena CDS 13714 13995 . - 0 ID=CDS:CCP42733;Parent=transcript:CCP42733;protein_id=CCP42733 ### Chromosome ena gene 14089 14877 . + . ID=gene:Rv0012;biotype=protein_coding;description=Probable conserved membrane protein;gene_id=Rv0012;logic_name=ena;version=1 Chromosome ena transcript 14089 14877 . + . ID=transcript:CCP42734;Parent=gene:Rv0012;biotype=protein_coding;transcript_id=CCP42734;version=1 Chromosome ena exon 14089 14877 . + . Parent=transcript:CCP42734;Name=CCP42734-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42734-1;rank=1;version=1 Chromosome ena CDS 14089 14877 . + 0 ID=CDS:CCP42734;Parent=transcript:CCP42734;protein_id=CCP42734 ### Chromosome ena gene 14914 15612 . + . ID=gene:Rv0013;Name=trpG;biotype=protein_coding;description=Possible anthranilate synthase component II TrpG (glutamine amidotransferase);gene_id=Rv0013;logic_name=ena;version=1 Chromosome ena transcript 14914 15612 . + . ID=transcript:CCP42735;Parent=gene:Rv0013;Name=trpG-1;biotype=protein_coding;transcript_id=CCP42735;version=1 Chromosome ena exon 14914 15612 . + . Parent=transcript:CCP42735;Name=CCP42735-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42735-1;rank=1;version=1 Chromosome ena CDS 14914 15612 . + 0 ID=CDS:CCP42735;Parent=transcript:CCP42735;protein_id=CCP42735 ### Chromosome ena gene 15590 17470 . - . ID=gene:Rv0014c;Name=pknB;biotype=protein_coding;description=Transmembrane serine/threonine-protein kinase B PknB (protein kinase B) (STPK B);gene_id=Rv0014c;logic_name=ena;version=1 Chromosome ena transcript 15590 17470 . - . ID=transcript:CCP42736;Parent=gene:Rv0014c;Name=pknB-1;biotype=protein_coding;transcript_id=CCP42736;version=1 Chromosome ena exon 15590 17470 . - . Parent=transcript:CCP42736;Name=CCP42736-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42736-1;rank=1;version=1 Chromosome ena CDS 15590 17470 . - 0 ID=CDS:CCP42736;Parent=transcript:CCP42736;protein_id=CCP42736 ### Chromosome ena gene 17467 18762 . - . ID=gene:Rv0015c;Name=pknA;biotype=protein_coding;description=Transmembrane serine/threonine-protein kinase A PknA (protein kinase A) (STPK A);gene_id=Rv0015c;logic_name=ena;version=1 Chromosome ena transcript 17467 18762 . - . ID=transcript:CCP42737;Parent=gene:Rv0015c;Name=pknA-1;biotype=protein_coding;transcript_id=CCP42737;version=1 Chromosome ena exon 17467 18762 . - . Parent=transcript:CCP42737;Name=CCP42737-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42737-1;rank=1;version=1 Chromosome ena CDS 17467 18762 . - 0 ID=CDS:CCP42737;Parent=transcript:CCP42737;protein_id=CCP42737 ### Chromosome ena gene 18759 20234 . - . ID=gene:Rv0016c;Name=pbpA;biotype=protein_coding;description=Probable penicillin-binding protein PbpA;gene_id=Rv0016c;logic_name=ena;version=1 Chromosome ena transcript 18759 20234 . - . ID=transcript:CCP42738;Parent=gene:Rv0016c;Name=pbpA-1;biotype=protein_coding;transcript_id=CCP42738;version=1 Chromosome ena exon 18759 20234 . - . Parent=transcript:CCP42738;Name=CCP42738-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42738-1;rank=1;version=1 Chromosome ena CDS 18759 20234 . - 0 ID=CDS:CCP42738;Parent=transcript:CCP42738;protein_id=CCP42738 ### Chromosome ena gene 20231 21640 . - . ID=gene:Rv0017c;Name=rodA;biotype=protein_coding;description=Probable cell division protein RodA;gene_id=Rv0017c;logic_name=ena;version=1 Chromosome ena transcript 20231 21640 . - . ID=transcript:CCP42739;Parent=gene:Rv0017c;Name=rodA-1;biotype=protein_coding;transcript_id=CCP42739;version=1 Chromosome ena exon 20231 21640 . - . Parent=transcript:CCP42739;Name=CCP42739-1;constitutive=1;ensembl_end_phase=0;ensembl_phase=0;exon_id=CCP42739-1;rank=1;version=1