A stop codon killed my ORF!

Trond Erik Vee Aune trondaun at biotech.REMOVETHISBEFOREREPLYING.ntnu.no
Mon Mar 14 04:20:26 EST 2005

C.Emilie at gmail.com wrote:

> I have a UGA (opal). Is it (selenocysteine) a frequent occurence. I
> have never heard of it for our fungus...
> I'll read more on that, thanks a lot

Insertion of celenocysteine in eukaryotes is promoted by bSECIS elements 
situated downstream of the opal codon. Close inspection of your gene 
should be able to discover any bSECIS elements. If there's no bSECIS 
element in your sequence, the decoding event must then be of another 
kind than celenocystein insertion, or happening through a novel 
mechanism that doesn't rely on bSECIS elements.

Have you looked at your protein on a protein gel (or western) to see if 
the stop codon is efficient? You could also try to change the tga codon 
to tag codon to see what happens.

Here's a reference to a great review of decoding events in both 
prokaryotes and eukaryotes:

Namy et al. Reprogrammed Genetic Decoding in Cellular Gene Expression. 
Molecular Cell. Vol. 13, 157-168. 2004.

Trond Erik

> Emilie

Trond Erik Vee Aune
Department of Biotechnology
Norwegian University of Science and Technology
Email: trondaun at REMOVETHISBEFOREREPLYING!!biotech.ntnu.no

- Must be sad being a dyslectic, agnostic insomniac, lying
   awake during the night, wondering if there really is a dog

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