GFF ingestion

CoGe visualization of genomic feature from the rice genome

CoGe translates many of the features from a standard GFF file into various genomic features in CoGe's database. For a basic protein coding gene, CoGe tracks three major genomic features:

• gene: the full extent of the transcribed unit including introns
• mRNA: the spliced transcript
• CDS: the regions that code for protein.

From the GFF3 entry below, the gene and mRNA features are collapsed to a gene in CoGe, the exons are combined to make an mRNA in CoGe, and the CDSs are used as a CDS feature in CoGe. The UTRs are skipped as being redundant with the exons.

Example GFF entry for a protein coding gene from the rice genome (v7)

Chr1    MSU_osa1r7      gene    12648   15915   .       +       .       ID=LOC_Os01g01030;Name=LOC_Os01g01030;Note=monocopper%20oxidase%2C%20putative%2C%20expressed
Chr1    MSU_osa1r7      mRNA    12648   15915   .       +       .       ID=LOC_Os01g01030.1;Name=LOC_Os01g01030.1;Parent=LOC_Os01g01030
Chr1    MSU_osa1r7      exon    12648   13813   .       +       .       ID=LOC_Os01g01030.1:exon_1;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      exon    13906   14271   .       +       .       ID=LOC_Os01g01030.1:exon_2;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      exon    14359   14437   .       +       .       ID=LOC_Os01g01030.1:exon_3;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      exon    14969   15171   .       +       .       ID=LOC_Os01g01030.1:exon_4;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      exon    15266   15915   .       +       .       ID=LOC_Os01g01030.1:exon_5;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      five_prime_UTR  12648   12773   .       +       .       ID=LOC_Os01g01030.1:utr_1;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      CDS     12774   13813   .       +       .       ID=LOC_Os01g01030.1:cds_1;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      CDS     13906   14271   .       +       .       ID=LOC_Os01g01030.1:cds_2;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      CDS     14359   14437   .       +       .       ID=LOC_Os01g01030.1:cds_3;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      CDS     14969   15171   .       +       .       ID=LOC_Os01g01030.1:cds_4;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      CDS     15266   15359   .       +       .       ID=LOC_Os01g01030.1:cds_5;Parent=LOC_Os01g01030.1
Chr1    MSU_osa1r7      three_prime_UTR 15360   15915   .       +       .       ID=LOC_Os01g01030.1:utr_2;Parent=LOC_Os01g01030.1

CoGe requires columns 1, 3, 4, 5, 7, and 9 (seqid, type, start, end, strand, and attributes) to have valid values and ignores the other columns. The attributes column must be formatted into key/value pairs delimited by semi-colons and have an ID or Name for each line.