some questions on GFF3

Question

[prasundutta87]

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?

Answer 1

[h.mon]

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

[prasundutta87]

Thanks a lot h.mon..