Mercurial > repos > iuc > deseq2

annotate test-data/GRCh38_latest_genomic.gff @ 31:9a882d108833 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 469558ddf5bc6249874fe5826637fd6ee81588cf
author iuc
date Tue, 18 Jul 2023 14:58:52 +0000
parents c56e0689e46e
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c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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1 ##gff-version 3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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2 #!gff-spec-version 1.21
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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3 #!processor NCBI annotwriter
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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4 #!genome-build GRCh38.p12
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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5 #!genome-build-accession NCBI_Assembly:GCF_000001405.38
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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6 #!annotation-source NCBI Homo sapiens Annotation Release 109
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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7 # Trimmed version of ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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8 ##sequence-region NC_000005.10 1 181538259
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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9 ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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10 NC_000005.10 RefSeq region 1 181538259 . + . ID=id565344;Dbxref=taxon:9606;Name=5;chromosome=5;gbkey=Src;genome=chromosome;mol_type=genomic DNA
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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11 NC_000005.10 BestRefSeq%2CGnomon gene 36035017 36071358 . - . ID=gene14857;Dbxref=GeneID:167127,HGNC:HGNC:27266,MIM:616384;Name=UGT3A2;description=UDP glycosyltransferase family 3 member A2;gbkey=Gene;gene=UGT3A2;gene_biotype=protein_coding
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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12 NC_000005.10 BestRefSeq mRNA 36035017 36066921 . - . ID=rna45581;Parent=gene14857;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;Name=NM_001168316.1;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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13 NC_000005.10 BestRefSeq exon 36066696 36066921 . - . ID=id576076;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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14 NC_000005.10 BestRefSeq exon 36051870 36051984 . - . ID=id576077;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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15 NC_000005.10 BestRefSeq exon 36048889 36049420 . - . ID=id576078;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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16 NC_000005.10 BestRefSeq exon 36039477 36039708 . - . ID=id576079;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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17 NC_000005.10 BestRefSeq exon 36037797 36038016 . - . ID=id576080;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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18 NC_000005.10 BestRefSeq exon 36035017 36035974 . - . ID=id576081;Parent=rna45581;Dbxref=GeneID:167127,Genbank:NM_001168316.1,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 2;transcript_id=NM_001168316.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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19 NC_000005.10 BestRefSeq transcript 36035017 36066921 . - . ID=rna45582;Parent=gene14857;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;Name=NR_031764.1;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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20 NC_000005.10 BestRefSeq exon 36066696 36066921 . - . ID=id576082;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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21 NC_000005.10 BestRefSeq exon 36064249 36064350 . - . ID=id576083;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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22 NC_000005.10 BestRefSeq exon 36051870 36051984 . - . ID=id576084;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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23 NC_000005.10 BestRefSeq exon 36039477 36039708 . - . ID=id576085;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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24 NC_000005.10 BestRefSeq exon 36037797 36038016 . - . ID=id576086;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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25 NC_000005.10 BestRefSeq exon 36035017 36035974 . - . ID=id576087;Parent=rna45582;Dbxref=GeneID:167127,Genbank:NR_031764.1,HGNC:HGNC:27266,MIM:616384;gbkey=misc_RNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 3;transcript_id=NR_031764.1
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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26 NC_000005.10 BestRefSeq mRNA 36035017 36066921 . - . ID=rna45583;Parent=gene14857;Dbxref=GeneID:167127,Genbank:NM_174914.3,HGNC:HGNC:27266,MIM:616384;Name=NM_174914.3;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 1;transcript_id=NM_174914.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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27 NC_000005.10 BestRefSeq exon 36066696 36066921 . - . ID=id576088;Parent=rna45583;Dbxref=GeneID:167127,Genbank:NM_174914.3,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 1;transcript_id=NM_174914.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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28 NC_000005.10 BestRefSeq exon 36064249 36064350 . - . ID=id576089;Parent=rna45583;Dbxref=GeneID:167127,Genbank:NM_174914.3,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 1;transcript_id=NM_174914.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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29 NC_000005.10 BestRefSeq exon 36051870 36051984 . - . ID=id576090;Parent=rna45583;Dbxref=GeneID:167127,Genbank:NM_174914.3,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 1;transcript_id=NM_174914.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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30 NC_000005.10 BestRefSeq exon 36048889 36049420 . - . ID=id576091;Parent=rna45583;Dbxref=GeneID:167127,Genbank:NM_174914.3,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 1;transcript_id=NM_174914.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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31 NC_000005.10 BestRefSeq exon 36039477 36039708 . - . ID=id576092;Parent=rna45583;Dbxref=GeneID:167127,Genbank:NM_174914.3,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 1;transcript_id=NM_174914.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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32 NC_000005.10 BestRefSeq exon 36037797 36038016 . - . ID=id576093;Parent=rna45583;Dbxref=GeneID:167127,Genbank:NM_174914.3,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 1;transcript_id=NM_174914.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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33 NC_000005.10 BestRefSeq exon 36035017 36035974 . - . ID=id576094;Parent=rna45583;Dbxref=GeneID:167127,Genbank:NM_174914.3,HGNC:HGNC:27266,MIM:616384;gbkey=mRNA;gene=UGT3A2;product=UDP glycosyltransferase family 3 member A2%2C transcript variant 1;transcript_id=NM_174914.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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34 ##sequence-region NC_000012.12 1 133275309
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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35 ##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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36 NC_000012.12 RefSeq region 1 133275309 . + . ID=id1163836;Dbxref=taxon:9606;Name=12;chromosome=12;gbkey=Src;genome=chromosome;mol_type=genomic DNA
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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37 NC_000012.12 BestRefSeq gene 53938792 53946544 . + . ID=gene33473;Dbxref=GeneID:3229,HGNC:HGNC:5125,MIM:142976;Name=HOXC13;description=homeobox C13;gbkey=Gene;gene=HOXC13;gene_biotype=protein_coding;gene_synonym=ECTD9,HOX3,HOX3G
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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38 NC_000012.12 BestRefSeq mRNA 53938792 53946544 . + . ID=rna100330;Parent=gene33473;Dbxref=GeneID:3229,Genbank:NM_017410.2,HGNC:HGNC:5125,MIM:142976;Name=NM_017410.2;gbkey=mRNA;gene=HOXC13;product=homeobox C13;transcript_id=NM_017410.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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39 NC_000012.12 BestRefSeq exon 53938792 53939642 . + . ID=id1209110;Parent=rna100330;Dbxref=GeneID:3229,Genbank:NM_017410.2,HGNC:HGNC:5125,MIM:142976;gbkey=mRNA;gene=HOXC13;product=homeobox C13;transcript_id=NM_017410.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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40 NC_000012.12 BestRefSeq exon 53945000 53946544 . + . ID=id1209111;Parent=rna100330;Dbxref=GeneID:3229,Genbank:NM_017410.2,HGNC:HGNC:5125,MIM:142976;gbkey=mRNA;gene=HOXC13;product=homeobox C13;transcript_id=NM_017410.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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41 NC_000012.12 BestRefSeq gene 53954868 53956606 . + . ID=gene33475;Dbxref=GeneID:3228,HGNC:HGNC:5124,MIM:142975;Name=HOXC12;description=homeobox C12;gbkey=Gene;gene=HOXC12;gene_biotype=protein_coding;gene_synonym=HOC3F,HOX3,HOX3F
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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42 NC_000012.12 BestRefSeq mRNA 53954868 53956606 . + . ID=rna100332;Parent=gene33475;Dbxref=GeneID:3228,Genbank:NM_173860.2,HGNC:HGNC:5124,MIM:142975;Name=NM_173860.2;gbkey=mRNA;gene=HOXC12;product=homeobox C12;transcript_id=NM_173860.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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43 NC_000012.12 BestRefSeq exon 53954868 53955539 . + . ID=id1209115;Parent=rna100332;Dbxref=GeneID:3228,Genbank:NM_173860.2,HGNC:HGNC:5124,MIM:142975;gbkey=mRNA;gene=HOXC12;product=homeobox C12;transcript_id=NM_173860.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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44 NC_000012.12 BestRefSeq exon 53956328 53956606 . + . ID=id1209116;Parent=rna100332;Dbxref=GeneID:3228,Genbank:NM_173860.2,HGNC:HGNC:5124,MIM:142975;gbkey=mRNA;gene=HOXC12;product=homeobox C12;transcript_id=NM_173860.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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45 NC_000012.12 BestRefSeq gene 53973126 53976419 . + . ID=gene33477;Dbxref=GeneID:3227,HGNC:HGNC:5123,MIM:605559;Name=HOXC11;description=homeobox C11;gbkey=Gene;gene=HOXC11;gene_biotype=protein_coding;gene_synonym=HOX3H
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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46 NC_000012.12 BestRefSeq mRNA 53973126 53976419 . + . ID=rna100336;Parent=gene33477;Dbxref=GeneID:3227,Genbank:NM_014212.3,HGNC:HGNC:5123,MIM:605559;Name=NM_014212.3;Note=The RefSeq transcript has 1 non-frameshifting indel compared to this genomic sequence;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=HOXC11;inference=similar to RNA sequence%2C mRNA (same species):RefSeq:NM_014212.3;product=homeobox C11;transcript_id=NM_014212.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
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47 NC_000012.12 BestRefSeq exon 53973126 53973923 . + . ID=id1209133;Parent=rna100336;Dbxref=GeneID:3227,Genbank:NM_014212.3,HGNC:HGNC:5123,MIM:605559;Note=The RefSeq transcript has 1 non-frameshifting indel compared to this genomic sequence;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=HOXC11;inference=similar to RNA sequence%2C mRNA (same species):RefSeq:NM_014212.3;product=homeobox C11;transcript_id=NM_014212.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
48 NC_000012.12 BestRefSeq exon 53975181 53976419 . + . ID=id1209134;Parent=rna100336;Dbxref=GeneID:3227,Genbank:NM_014212.3,HGNC:HGNC:5123,MIM:605559;Note=The RefSeq transcript has 1 non-frameshifting indel compared to this genomic sequence;exception=annotated by transcript or proteomic data;gbkey=mRNA;gene=HOXC11;inference=similar to RNA sequence%2C mRNA (same species):RefSeq:NM_014212.3;product=homeobox C11;transcript_id=NM_014212.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
49 NC_000012.12 BestRefSeq gene 53985162 53990279 . + . ID=gene33479;Dbxref=GeneID:3226,HGNC:HGNC:5122,MIM:605560;Name=HOXC10;description=homeobox C10;gbkey=Gene;gene=HOXC10;gene_biotype=protein_coding;gene_synonym=HOX3I
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
50 NC_000012.12 BestRefSeq mRNA 53985162 53990279 . + . ID=rna100338;Parent=gene33479;Dbxref=GeneID:3226,Genbank:NM_017409.3,HGNC:HGNC:5122,MIM:605560;Name=NM_017409.3;gbkey=mRNA;gene=HOXC10;product=homeobox C10;transcript_id=NM_017409.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
51 NC_000012.12 BestRefSeq exon 53985162 53986010 . + . ID=id1209144;Parent=rna100338;Dbxref=GeneID:3226,Genbank:NM_017409.3,HGNC:HGNC:5122,MIM:605560;gbkey=mRNA;gene=HOXC10;product=homeobox C10;transcript_id=NM_017409.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
52 NC_000012.12 BestRefSeq exon 53989169 53990279 . + . ID=id1209145;Parent=rna100338;Dbxref=GeneID:3226,Genbank:NM_017409.3,HGNC:HGNC:5122,MIM:605560;gbkey=mRNA;gene=HOXC10;product=homeobox C10;transcript_id=NM_017409.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
53 NC_000012.12 BestRefSeq gene 54000119 54003337 . + . ID=gene33483;Dbxref=GeneID:3225,HGNC:HGNC:5130,MIM:142971;Name=HOXC9;description=homeobox C9;gbkey=Gene;gene=HOXC9;gene_biotype=protein_coding;gene_synonym=HOX3,HOX3B
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
54 NC_000012.12 BestRefSeq mRNA 54000119 54003337 . + . ID=rna100344;Parent=gene33483;Dbxref=GeneID:3225,Genbank:NM_006897.2,HGNC:HGNC:5130,MIM:142971;Name=NM_006897.2;gbkey=mRNA;gene=HOXC9;product=homeobox C9;transcript_id=NM_006897.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
55 NC_000012.12 BestRefSeq exon 54000119 54000726 . + . ID=id1209154;Parent=rna100344;Dbxref=GeneID:3225,Genbank:NM_006897.2,HGNC:HGNC:5130,MIM:142971;gbkey=mRNA;gene=HOXC9;product=homeobox C9;transcript_id=NM_006897.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
56 NC_000012.12 BestRefSeq exon 54002430 54003337 . + . ID=id1209155;Parent=rna100344;Dbxref=GeneID:3225,Genbank:NM_006897.2,HGNC:HGNC:5130,MIM:142971;gbkey=mRNA;gene=HOXC9;product=homeobox C9;transcript_id=NM_006897.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
57 NC_000012.12 BestRefSeq gene 54009106 54012763 . + . ID=gene33485;Dbxref=GeneID:3224,HGNC:HGNC:5129,MIM:142970;Name=HOXC8;description=homeobox C8;gbkey=Gene;gene=HOXC8;gene_biotype=protein_coding;gene_synonym=HOX3,HOX3A
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
58 NC_000012.12 BestRefSeq mRNA 54009106 54012763 . + . ID=rna100346;Parent=gene33485;Dbxref=GeneID:3224,Genbank:NM_022658.3,HGNC:HGNC:5129,MIM:142970;Name=NM_022658.3;gbkey=mRNA;gene=HOXC8;product=homeobox C8;transcript_id=NM_022658.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
59 NC_000012.12 BestRefSeq exon 54009106 54009720 . + . ID=id1209158;Parent=rna100346;Dbxref=GeneID:3224,Genbank:NM_022658.3,HGNC:HGNC:5129,MIM:142970;gbkey=mRNA;gene=HOXC8;product=homeobox C8;transcript_id=NM_022658.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
60 NC_000012.12 BestRefSeq exon 54011089 54012763 . + . ID=id1209159;Parent=rna100346;Dbxref=GeneID:3224,Genbank:NM_022658.3,HGNC:HGNC:5129,MIM:142970;gbkey=mRNA;gene=HOXC8;product=homeobox C8;transcript_id=NM_022658.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
61 NC_000012.12 BestRefSeq gene 54016852 54056030 . + . ID=gene33486;Dbxref=GeneID:3221,HGNC:HGNC:5126,MIM:142974;Name=HOXC4;description=homeobox C4;gbkey=Gene;gene=HOXC4;gene_biotype=protein_coding;gene_synonym=cp19,HOX3,HOX3E
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
62 NC_000012.12 BestRefSeq mRNA 54016852 54056030 . + . ID=rna100347;Parent=gene33486;Dbxref=GeneID:3221,Genbank:NM_014620.5,HGNC:HGNC:5126,MIM:142974;Name=NM_014620.5;gbkey=mRNA;gene=HOXC4;product=homeobox C4%2C transcript variant 1;transcript_id=NM_014620.5
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
63 NC_000012.12 BestRefSeq exon 54016852 54017414 . + . ID=id1209160;Parent=rna100347;Dbxref=GeneID:3221,Genbank:NM_014620.5,HGNC:HGNC:5126,MIM:142974;gbkey=mRNA;gene=HOXC4;product=homeobox C4%2C transcript variant 1;transcript_id=NM_014620.5
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
64 NC_000012.12 BestRefSeq exon 54053160 54053276 . + . ID=id1209161;Parent=rna100347;Dbxref=GeneID:3221,Genbank:NM_014620.5,HGNC:HGNC:5126,MIM:142974;gbkey=mRNA;gene=HOXC4;product=homeobox C4%2C transcript variant 1;transcript_id=NM_014620.5
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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diff changeset
65 NC_000012.12 BestRefSeq exon 54053917 54054361 . + . ID=id1209162;Parent=rna100347;Dbxref=GeneID:3221,Genbank:NM_014620.5,HGNC:HGNC:5126,MIM:142974;gbkey=mRNA;gene=HOXC4;product=homeobox C4%2C transcript variant 1;transcript_id=NM_014620.5
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
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diff changeset
66 NC_000012.12 BestRefSeq exon 54054850 54056030 . + . ID=id1209163;Parent=rna100347;Dbxref=GeneID:3221,Genbank:NM_014620.5,HGNC:HGNC:5126,MIM:142974;gbkey=mRNA;gene=HOXC4;product=homeobox C4%2C transcript variant 1;transcript_id=NM_014620.5
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
67 NC_000012.12 BestRefSeq mRNA 54053877 54056030 . + . ID=rna100348;Parent=gene33486;Dbxref=GeneID:3221,Genbank:NM_153633.2,HGNC:HGNC:5126,MIM:142974;Name=NM_153633.2;gbkey=mRNA;gene=HOXC4;product=homeobox C4%2C transcript variant 2;transcript_id=NM_153633.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
68 NC_000012.12 BestRefSeq exon 54053877 54054361 . + . ID=id1209164;Parent=rna100348;Dbxref=GeneID:3221,Genbank:NM_153633.2,HGNC:HGNC:5126,MIM:142974;gbkey=mRNA;gene=HOXC4;product=homeobox C4%2C transcript variant 2;transcript_id=NM_153633.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
69 NC_000012.12 BestRefSeq exon 54054850 54056030 . + . ID=id1209165;Parent=rna100348;Dbxref=GeneID:3221,Genbank:NM_153633.2,HGNC:HGNC:5126,MIM:142974;gbkey=mRNA;gene=HOXC4;product=homeobox C4%2C transcript variant 2;transcript_id=NM_153633.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
70 NC_000012.12 BestRefSeq gene 54016852 54035361 . + . ID=gene33487;Dbxref=GeneID:3222,HGNC:HGNC:5127,MIM:142973;Name=HOXC5;description=homeobox C5;gbkey=Gene;gene=HOXC5;gene_biotype=protein_coding;gene_synonym=CP11,HOX3,HOX3D
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
71 NC_000012.12 BestRefSeq transcript 54016852 54035361 . + . ID=rna100349;Parent=gene33487;Dbxref=GeneID:3222,Genbank:NR_003084.2,HGNC:HGNC:5127,MIM:142973;Name=NR_003084.2;gbkey=misc_RNA;gene=HOXC5;product=homeobox C5%2C transcript variant 2;transcript_id=NR_003084.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
72 NC_000012.12 BestRefSeq exon 54016852 54017414 . + . ID=id1209166;Parent=rna100349;Dbxref=GeneID:3222,Genbank:NR_003084.2,HGNC:HGNC:5127,MIM:142973;gbkey=misc_RNA;gene=HOXC5;product=homeobox C5%2C transcript variant 2;transcript_id=NR_003084.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
73 NC_000012.12 BestRefSeq exon 54034278 54035361 . + . ID=id1209167;Parent=rna100349;Dbxref=GeneID:3222,Genbank:NR_003084.2,HGNC:HGNC:5127,MIM:142973;gbkey=misc_RNA;gene=HOXC5;product=homeobox C5%2C transcript variant 2;transcript_id=NR_003084.2
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
74 NC_000012.12 BestRefSeq mRNA 54033048 54035361 . + . ID=rna100350;Parent=gene33487;Dbxref=GeneID:3222,Genbank:NM_018953.3,HGNC:HGNC:5127,MIM:142973;Name=NM_018953.3;gbkey=mRNA;gene=HOXC5;product=homeobox C5%2C transcript variant 1;transcript_id=NM_018953.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
75 NC_000012.12 BestRefSeq exon 54033048 54033576 . + . ID=id1209168;Parent=rna100350;Dbxref=GeneID:3222,Genbank:NM_018953.3,HGNC:HGNC:5127,MIM:142973;gbkey=mRNA;gene=HOXC5;product=homeobox C5%2C transcript variant 1;transcript_id=NM_018953.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
76 NC_000012.12 BestRefSeq exon 54034278 54035361 . + . ID=id1209169;Parent=rna100350;Dbxref=GeneID:3222,Genbank:NM_018953.3,HGNC:HGNC:5127,MIM:142973;gbkey=mRNA;gene=HOXC5;product=homeobox C5%2C transcript variant 1;transcript_id=NM_018953.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
77 NC_000012.12 BestRefSeq gene 54016852 54030823 . + . ID=gene33488;Dbxref=GeneID:3223,HGNC:HGNC:5128,MIM:142972;Name=HOXC6;description=homeobox C6;gbkey=Gene;gene=HOXC6;gene_biotype=protein_coding;gene_synonym=CP25,HHO.C8,HOX3,HOX3C
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
78 NC_000012.12 BestRefSeq mRNA 54016852 54030823 . + . ID=rna100351;Parent=gene33488;Dbxref=GeneID:3223,Genbank:NM_153693.4,HGNC:HGNC:5128,MIM:142972;Name=NM_153693.4;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 2;transcript_id=NM_153693.4
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
79 NC_000012.12 BestRefSeq exon 54016852 54017414 . + . ID=id1209172;Parent=rna100351;Dbxref=GeneID:3223,Genbank:NM_153693.4,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 2;transcript_id=NM_153693.4
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
80 NC_000012.12 BestRefSeq exon 54028576 54028921 . + . ID=id1209173;Parent=rna100351;Dbxref=GeneID:3223,Genbank:NM_153693.4,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 2;transcript_id=NM_153693.4
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
81 NC_000012.12 BestRefSeq exon 54029655 54030823 . + . ID=id1209174;Parent=rna100351;Dbxref=GeneID:3223,Genbank:NM_153693.4,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 2;transcript_id=NM_153693.4
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
82 NC_000012.12 BestRefSeq mRNA 54028410 54030823 . + . ID=rna100352;Parent=gene33488;Dbxref=GeneID:3223,Genbank:NM_004503.3,HGNC:HGNC:5128,MIM:142972;Name=NM_004503.3;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 1;transcript_id=NM_004503.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
83 NC_000012.12 BestRefSeq exon 54028410 54028921 . + . ID=id1209175;Parent=rna100352;Dbxref=GeneID:3223,Genbank:NM_004503.3,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 1;transcript_id=NM_004503.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
84 NC_000012.12 BestRefSeq exon 54029655 54030823 . + . ID=id1209176;Parent=rna100352;Dbxref=GeneID:3223,Genbank:NM_004503.3,HGNC:HGNC:5128,MIM:142972;gbkey=mRNA;gene=HOXC6;product=homeobox C6%2C transcript variant 1;transcript_id=NM_004503.3
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
85 NC_000012.12 RefSeq cDNA_match 53973126 53973923 798 + . ID=46c4f9c5-f2cf-415e-a892-fbd053a8f7eb;Target=NM_014212.3 1 798 +;assembly_bases_aln=152;assembly_bases_seq=152;consensus_splices=2;exon_identity=0.991241;for_remapping=2;gap_count=1;identity=0.991241;idty=1;matches=2037;num_ident=2037;num_mismatch=0;pct_coverage=99.1241;pct_coverage_hiqual=99.1241;pct_identity_gap=99.1241;pct_identity_ungap=100;product_coverage=1;rank=1;splices=2;weighted_identity=0.991461
c56e0689e46e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 5b6dc96c6e14582d5bb1dc213ac8d26dc7b2829e
iuc
parents:
diff changeset
86 NC_000012.12 RefSeq cDNA_match 53975181 53976419 1232.82 + . ID=46c4f9c5-f2cf-415e-a892-fbd053a8f7eb;Target=NM_014212.3 799 2055 +;assembly_bases_aln=152;assembly_bases_seq=152;consensus_splices=2;exon_identity=0.991241;for_remapping=2;gap_count=1;identity=0.991241;idty=0.98568;matches=2037;num_ident=2037;num_mismatch=0;pct_coverage=99.1241;pct_coverage_hiqual=99.1241;pct_identity_gap=99.1241;pct_identity_ungap=100;product_coverage=1;rank=1;splices=2;weighted_identity=0.991461;Gap=M705 I18 M534