GFF ingestion

How does CoGe ingest GFF annotations

CoGe visualization of genomic feature from the rice genome

Example GFF entry for a protein coding gene

Chr1    MSU_osa1r7      gene    2903    10817   .       +       .       ID=LOC_Os01g01010;Name=LOC_Os01g01010;Note=TBC%20domain%20containing%20protein%2C%20expressed
Chr1    MSU_osa1r7      mRNA    2903    10817   .       +       .       ID=LOC_Os01g01010.1;Name=LOC_Os01g01010.1;Parent=LOC_Os01g01010
Chr1    MSU_osa1r7      exon    2903    3268    .       +       .       ID=LOC_Os01g01010.1:exon_1;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    3354    3616    .       +       .       ID=LOC_Os01g01010.1:exon_2;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    4357    4455    .       +       .       ID=LOC_Os01g01010.1:exon_3;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    5457    5560    .       +       .       ID=LOC_Os01g01010.1:exon_4;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    7136    7944    .       +       .       ID=LOC_Os01g01010.1:exon_5;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    8028    8150    .       +       .       ID=LOC_Os01g01010.1:exon_6;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    8232    8320    .       +       .       ID=LOC_Os01g01010.1:exon_7;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    8408    8608    .       +       .       ID=LOC_Os01g01010.1:exon_8;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    9210    9617    .       +       .       ID=LOC_Os01g01010.1:exon_9;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    10104   10187   .       +       .       ID=LOC_Os01g01010.1:exon_10;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    10274   10430   .       +       .       ID=LOC_Os01g01010.1:exon_11;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      exon    10504   10817   .       +       .       ID=LOC_Os01g01010.1:exon_12;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      five_prime_UTR  2903    3268    .       +       .       ID=LOC_Os01g01010.1:utr_1;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      five_prime_UTR  3354    3448    .       +       .       ID=LOC_Os01g01010.1:utr_2;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     3449    3616    .       +       .       ID=LOC_Os01g01010.1:cds_1;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     4357    4455    .       +       .       ID=LOC_Os01g01010.1:cds_2;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     5457    5560    .       +       .       ID=LOC_Os01g01010.1:cds_3;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     7136    7944    .       +       .       ID=LOC_Os01g01010.1:cds_4;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     8028    8150    .       +       .       ID=LOC_Os01g01010.1:cds_5;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     8232    8320    .       +       .       ID=LOC_Os01g01010.1:cds_6;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     8408    8608    .       +       .       ID=LOC_Os01g01010.1:cds_7;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     9210    9617    .       +       .       ID=LOC_Os01g01010.1:cds_8;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     10104   10187   .       +       .       ID=LOC_Os01g01010.1:cds_9;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      CDS     10274   10297   .       +       .       ID=LOC_Os01g01010.1:cds_10;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      three_prime_UTR 10298   10430   .       +       .       ID=LOC_Os01g01010.1:utr_3;Parent=LOC_Os01g01010.1
Chr1    MSU_osa1r7      three_prime_UTR 10504   10817   .       +       .       ID=LOC_Os01g01010.1:utr_4;Parent=LOC_Os01g01010.1