Question: some questions on GFF3
0
gravatar for prasundutta87
2.0 years ago by
prasundutta87360
prasundutta87360 wrote:

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 annotation gtf • 591 views
ADD COMMENTlink written 2.0 years ago by prasundutta87360
1
gravatar for h.mon
2.0 years ago by
h.mon30k
Brazil
h.mon30k wrote:

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

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by h.mon30k

Thanks a lot h.mon..

ADD REPLYlink written 2.0 years ago by prasundutta87360
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1684 users visited in the last hour