This section describes the representation of a protein-coding gene in GFF3. To illustrate how a canonical gene is represented, consider Figure 1 (figure1.png). This indicates a gene named EDEN extending from position 1000 to position 9000. It encodes three alternatively-spliced transcripts named EDEN.1, EDEN.2 and EDEN.3, the last of which has two alternative translational start sites leading to the generation of two protein coding sequences.
There is also an identified transcriptional factor binding site located 50 bp upstream from the transcriptional start site of EDEN.1 and EDEN2.
Here is how this gene should be described using GFF3:
0 ##gff-version 3.2.1 1 ##sequence-region ctg123 1 1497228 2 ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN 3 ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001 4 ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1 5 ctg123 . mRNA 1050 9000 . + . ID=mRNA00002;Parent=gene00001;Name=EDEN.2 6 ctg123 . mRNA 1300 9000 . + . ID=mRNA00003;Parent=gene00001;Name=EDEN.3 7 ctg123 . exon 1300 1500 . + . ID=exon00001;Parent=mRNA00003 8 ctg123 . exon 1050 1500 . + . ID=exon00002;Parent=mRNA00001,mRNA00002 9 ctg123 . exon 3000 3902 . + . ID=exon00003;Parent=mRNA00001,mRNA00003 10 ctg123 . exon 5000 5500 . + . ID=exon00004;Parent=mRNA00001,mRNA00002,mRNA00003 11 ctg123 . exon 7000 9000 . + . ID=exon00005;Parent=mRNA00001,mRNA00002,mRNA00003 12 ctg123 . CDS 1201 1500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1 13 ctg123 . CDS 3000 3902 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1 14 ctg123 . CDS 5000 5500 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1 15 ctg123 . CDS 7000 7600 . + 0 ID=cds00001;Parent=mRNA00001;Name=edenprotein.1 16 ctg123 . CDS 1201 1500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2 17 ctg123 . CDS 5000 5500 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2 18 ctg123 . CDS 7000 7600 . + 0 ID=cds00002;Parent=mRNA00002;Name=edenprotein.2 19 ctg123 . CDS 3301 3902 . + 0 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3 20 ctg123 . CDS 5000 5500 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3 21 ctg123 . CDS 7000 7600 . + 1 ID=cds00003;Parent=mRNA00003;Name=edenprotein.3 22 ctg123 . CDS 3391 3902 . + 0 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4 23 ctg123 . CDS 5000 5500 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4 24 ctg123 . CDS 7000 7600 . + 1 ID=cds00004;Parent=mRNA00003;Name=edenprotein.4
Lines beginning with ‘##’ are directives (sometimes called pragmas or meta-data) and provide meta-information about the document as a whole. Blank lines should be ignored by parsers and lines beginning with a single ‘#’ are used for human-readable comments and can be ignored by parsers. End-of-line comments (comments preceeded by # at the end of and on the same line as a feature or directive line) are not allowed.
Line 0 gives the GFF version using the ##gff-version pragma. Line 1 indicates the boundaries of the region being annotated (a 1,497,228 bp region named “ctg123”) using the ##sequence-region pragma.
Line 2 defines the boundaries of the gene. Column 9 of this line assigns the gene an ID of gene00001, and a human-readable name of EDEN. Because the gene is not part of a larger feature, it has no Parent.
Line 3 annotates the transcriptional factor binding site. Since it is logically part of the gene, its Parent attribute is gene00001.
Lines 4–6 define this gene’s three spliced transcripts, one line for the full extent of each of the mRNAs. These features are necessary to act as parents for the four CDSs which derive from them, as well as the structural parents of the five exons in the alternative splicing set.
Lines 7–11 identify the five exons. The Parent attributes indicate which mRNAs the exons belong to. Notice that several of the exons share the same parents, using the comma symbol to indicate multiple parentage.
Lines 12–24 denote this gene’s four CDSs. Each CDS belongs to one of the mRNAs. cds00003 and cds00004, which correspond to alternative start codons, belong to the same mRNA.
Note that several of the features, including the gene, its mRNAs and the CDSs, all have Name attributes. This attributes assigns those features a public name, but is not mandatory. The ID attributes are only mandatory for those features that have children (the gene and mRNAs), or for those that span multiple lines. The IDs do not have meaning outside the file in which they reside. Hence, a slightly simplified version of this file would look like this:
Find more at this link: https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md