last codon codes just for a stop codon

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pgupta
Posts: 13
Joined: Sat Aug 18, 2012 9:59 pm

last codon codes just for a stop codon

Post by pgupta » Thu Aug 30, 2012 7:31 pm

Hi

I am working with a gene whose ortholog has 9 predicted exons.However the last exon is three bases long and codes for the stop codon only.Since we need to specify the stop codon position separately I entered the positions for only 8 exons in the gene checker.I get a pass sign for all the exons but I also get an orange warning sign which says that "gene model has 8 CDS's,ortholog has 9 CDS's.Do I need to recheck the gene model?

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

Re: last codon codes just for a stop codon

Post by wleung » Thu Aug 30, 2012 8:15 pm

> Do I need to recheck the gene model?

No, you can ignore the warning from the Gene Model Checker in this case. Having a stop codon at the beginning of the last coding exon is unusual and it merits additional explanations in the GEP Annotation Report. However, the explanation in the Annotation Report could be that the last exon in the orthologous D. melanogaster isoform consists of only 3 bases that correspond to the stop codon.

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