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last codon codes just for a stop codon

Posted: Thu Aug 30, 2012 7:31 pm
by pgupta
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?

Re: last codon codes just for a stop codon

Posted: Thu Aug 30, 2012 8:15 pm
by wleung
> 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.