unconventional start codons

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dbarnard
Posts: 2
Joined: Sun Feb 04, 2007 10:09 pm

unconventional start codons

Post by dbarnard » Thu Mar 05, 2015 3:13 pm

Question about unconventional start codons - we have a student trying to annotate Wnk in D. biarmipies. There are 5 isoforms in melanogaster Wnk - four of them use AUU to code for Met. In the AA sequence there is a Met, but we kept stumbling on the Isoleucine (which is what comes up in the gene model). There is a comment that it is believed that this is a unconventional start. Has this gene turned up the same problems in other species (I haven't encountered this before)? I am having the student proceed with the gene model checker with the fail for the Start codon - is there anything else that we should do?
Thanks

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

Re: unconventional start codons

Post by wleung » Thu Mar 05, 2015 4:36 pm

As you have mentioned, the FlyBase comments for the Wnk gene models indicate that this gene uses a non-canonical start codon (AUU). The comment also indicates that this non-canonical start codon is conserved in other Drosophila species.
alternate_start_codon_comment.png
alternate_start_codon_comment.png (58.81 KiB) Viewed 6657 times
Examination of the "Conservation" track (under the "Comparative Genomics" section) shows the AUU (ATT) start codon is conserved in all seven Drosophila species that are part of the multiz alignment. Hence the available evidence suggest that the D. elegans ortholog also likely uses this non-canonical start codon.
alternate_start_conservation.png
alternate_start_conservation.png (104.18 KiB) Viewed 6657 times
The Gene Model Checker checklist will report an issue with the non-canonical start codon. However, you can explain the reason for using the non-canonical start codon in the GEP Annotation Report. Please include a screenshot of the FlyBase comments for the D. melanogaster Wnk gene models in the GEP Annotation Report in order to justify the use of the unusual start codon.

dbarnard
Posts: 2
Joined: Sun Feb 04, 2007 10:09 pm

Re: unconventional start codons

Post by dbarnard » Thu Mar 05, 2015 4:37 pm

Thanks! I saw the "conservation in other species" comment after I posted. We will include a screen shot of the comments as evidence. Thanks again.
Daron

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