###################################################### # Ensembl genes in gtf format downloaded from UCSC ###################################################### Downloaded from http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=351513701&clade=mammal&org=Mouse&db=mm10&hgta_group=genes&hgta_track=ensGene&hgta_table=0&hgta_regionType=genome&position=chr12%3A56694976-56714605&hgta_outputType=sequence&hgta_outFileName=ensemblGenes.gtf # First 5 lines (starting after dotted line) ------------------------------------------------------ chr1 mm10_ensGene stop_codon 134202951 134202953 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465"; chr1 mm10_ensGene CDS 134202954 134203590 0.000000 - 1 gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465"; chr1 mm10_ensGene exon 134199223 134203590 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465"; chr1 mm10_ensGene CDS 134234015 134234355 0.000000 - 0 gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465"; chr1 mm10_ensGene start_codon 134234353 134234355 0.000000 - . gene_id "ENSMUST00000086465"; transcript_id "ENSMUST00000086465"; ###################################################### # Following conversion using GFF Toolkit ###################################################### # First 5 lines (starting after dotted line) ------------------------------------------------------ ##gff-version 3 chr1 mm10_ensGene gene 171341329 171345640 . - . ID=Gene:ENSMUST00000141357;Name=Gene:ENSMUST00000141357 chr1 mm10_ensGene transcript 171341329 171345640 0.000000 - . ID=Transcript:ENSMUST00000141357;Parent=Gene:ENSMUST00000141357 chr1 mm10_ensGene exon 171341329 171342797 . - . Parent=Transcript:ENSMUST00000141357 chr1 mm10_ensGene exon 171343438 171343563 . - . Parent=Transcript:ENSMUST00000141357 ###################################################### # GFF files from NCBI ###################################################### ftp://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ # ref_GRCm38.p1_top_level.gff3 # First 10 lines (starting after dotted line): ------------------------------------------------------ ##gff-version 3 #!gff-spec-version 1.20 #!processor NCBI annotwriter ##sequence-region NC_000067.6 1 195471971 ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090 NC_000067.6 RefSeq region 1 195471971 . + . ID=id0;Dbxref=taxon:10090;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=C57BL%2F6J NC_000067.6 RefSeq gene 3214482 3671498 . - . ID=gene0;Name=Xkr4;Dbxref=GeneID:497097,MGI:3528744;description=X Kell blood group precursor related family member 4;gbkey=Gene;gene=Xkr4;gene_synonym=AY534250,Gm210,mKIAA1889,XRG4 NC_000067.6 RefSeq mRNA 3214482 3671498 . - . ID=rna0;Name=NM_001011874.1;Parent=gene0;Dbxref=GeneID:497097,Genbank:NM_001011874.1,MGI:3528744;gbkey=mRNA;gene=Xkr4;product=X Kell blood group precursor related family member 4;transcript_id=NM_001011874.1 NC_000067.6 RefSeq exon 3670552 3671498 . - . ID=id1;Parent=rna0;Dbxref=GeneID:497097,Genbank:NM_001011874.1,MGI:3528744;gbkey=mRNA;gene=Xkr4;product=X Kell blood group precursor related family member 4;transcript_id=NM_001011874.1 NC_000067.6 RefSeq exon 3421702 3421901 . - . ID=id2;Parent=rna0;Dbxref=GeneID:497097,Genbank:NM_001011874.1,MGI:3528744;gbkey=mRNA;gene=Xkr4;product=X Kell blood group precursor related family member 4;transcript_id=NM_001011874.1 # ref_GRCm38.p1_scaffolds.gff3 # First 10 lines (starting after dotted line): ------------------------------------------------------ ##gff-version 3 #!gff-spec-version 1.20 #!processor NCBI annotwriter ##sequence-region NT_039169.8 1 19433268 ##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10090 NT_039169.8 RefSeq region 1 19433268 . + . ID=id0;Dbxref=taxon:10090;chromosome=1;gbkey=Src;genome=genomic;mol_type=genomic DNA;strain=C57BL%2F6J NT_039169.8 RefSeq gene 214482 671498 . - . ID=gene0;Name=Xkr4;Dbxref=GeneID:497097,MGI:3528744;description=X Kell blood group precursor related family member 4;gbkey=Gene;gene=Xkr4;gene_synonym=AY534250,Gm210,mKIAA1889,XRG4 NT_039169.8 RefSeq mRNA 214482 671498 . - . ID=rna0;Name=NM_001011874.1;Parent=gene0;Dbxref=GeneID:497097,Genbank:NM_001011874.1,MGI:3528744;gbkey=mRNA;gene=Xkr4;product=X Kell blood group precursor related family member 4;transcript_id=NM_001011874.1 NT_039169.8 RefSeq exon 670552 671498 . - . ID=id1;Parent=rna0;Dbxref=GeneID:497097,Genbank:NM_001011874.1,MGI:3528744;gbkey=mRNA;gene=Xkr4;product=X Kell blood group precursor related family member 4;transcript_id=NM_001011874.1 NT_039169.8 RefSeq exon 421702 421901 . - . ID=id2;Parent=rna0;Dbxref=GeneID:497097,Genbank:NM_001011874.1,MGI:3528744;gbkey=mRNA;gene=Xkr4;product=X Kell blood group precursor related family member 4;transcript_id=NM_001011874.1