[ensembl-dev] Transcripts with stop codon ?

Moretti Sébastien sebastien.moretti at unil.ch
Wed Feb 1 14:54:07 GMT 2012

>> Hi
>> I have just noticed that some transcripts have stop codon(s) in their
>> sequence. E.g. ENSCJAT00000065209
>> Is it normal ?
>> These stop codons and, more problematic, the "fake" codons next after
>> the stop are included in compara alignments.
> you mean translations?
> Due to the case that the translation also doesn't have a start, I would
> put that down as a prediction artefact, similar to what you can see on a
> lot of low-coverage gene sets where you get fragments of genes and
> in-frame-stops.

I fully agree about prediction artefacts.
But in the case of ENSCJAT00000065209, there are 2 predicted amino acids 
after the stop codon. Those ones are included in your alignment and tree 
building processes.
Two aa should not disturb the phylogeny too much but what happens if 
this is 40 untranslated aa ?

> M

Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/

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