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some questions on GFF3

Hi,

Can someone explain me in a little more detail these gff3 annotations?

NW_020229148.1  Gnomon  exon    23509   23858   .   -   .   ID=id836183;Parent=id836181;Dbxref=GeneID:112582887;gbkey=V_segment;gene=LOC112582887;model_evidence=Supporting evidence includes similarity to: 83%25 coverage of the annotated genomic feature by RNAseq alignments%2C including 22 samples with support for all annotated introns;standard_name=T cell receptor alpha variable 8-3-like
NW_020229148.1  Gnomon  CDS 23989   24034   .   -   0   ID=cds58507;Parent=id836181;Dbxref=GeneID:112582887;exception=rearrangement required for product;gbkey=CDS;gene=LOC112582887;product=T cell receptor alpha variable 8-3-like
NW_020229148.1  Gnomon  CDS 23509   23858   .   -   2   ID=cds58507;Parent=id836181;Dbxref=GeneID:112582887;exception=rearrangement required for product;gbkey=CDS;gene=LOC112582887;product=T cell receptor alpha variable 8-3-like

I have read about them here:http://biomirror.aarnet.edu.au/biomirror/ncbigenomes/README_GFF3.txt

It is not very clear to me what is V_segment and what exactly does 'rearrangement required for product' mean? They don't seem to be an important feature? Or the NCBI annotation pipeline could not find suitable annotation?

gff gtf annotation
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written by prasundutta87 prasundutta87

1 answer

V_segment: https://www.ebi.ac.uk/ena/WebFeat/V_segment_s.html

Rearrangement required for product: https://www.ebi.ac.uk/ena/WebFeat/qualifiers/exception.html

An intro to the biology behind this: https://en.m.wikipedia.org/wiki/V(D)J_recombination

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written by h.mon h.mon

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