Gene model checker, in frame stop codons

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etucker
Posts: 1
Joined: Tue Jun 19, 2012 9:29 pm

Gene model checker, in frame stop codons

Post by etucker » Sun Oct 14, 2012 11:44 pm

When checking a gene with GMC it tells me that the proposed gene model has in-frame stop codons almost in each CDS, however none of these sequences have stop codons. Is it possible that GMC is reading frames different from those proposed by blast search?

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Gene model checker, in frame stop codons

Post by wleung » Mon Oct 15, 2012 2:41 pm

Yes, in frame stop codons in the gene model is typically caused by incompatible splice donor and acceptor sites. When the sum of the donor and acceptor phases is not either 0 or 3, it will introduce a frame shift in the translation. In most cases, translating in the incorrect reading frame would result in stop codons in the translation.

Therefore, I will suggest checking the "Extracted Coding Exons" tab in the Gene Model Checker to determine the first exon where stop codons are found (it should also be listed in the checklist). Then I will check the acceptor site in that exon and the donor site from the previous exon to make sure that the donor and acceptor phases are compatible with each other.

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