[ensembl-dev] Unannotated stop codons

Remo Sanges noncoding at gmail.com
Fri Nov 11 20:02:04 GMT 2016


Hi everybody,

I am working on Ciona savignyi and I noticed that for many transcripts
there is not a stop codon properly annotated even if the stop codon is
present. For these transcripts the stop codon is annotated as the beginning
of the 3'UTR.

Here is an example of a transcript having a stop codon not annotated
http://www.ensembl.org/Ciona_savignyi/Transcript/Sequence_cDNA?db=core;g=ENSCSAVG00000001197;r=reftig_7:323743-332751;t=ENSCSAVT00000002079
As you can see the first nucleotides of the 3'UTR are TGA (a stop codon).

While here is a transcript with a properly annotated stop
http://www.ensembl.org/Ciona_savignyi/Transcript/Sequence_cDNA?db=core;g=ENSCSAVG00000000012;r=reftig_451:111719-120967;t=ENSCSAVT00000000014
Here the TGA are the last nucleotides of the CDS and the stop is correctly
indicated with an asterisk.

In addition to the genome browser, this is affecting both the API and the
fasta of the CDS downloadable from the FTP (from the wrongly annotated
transcript you get a sequence with 3 nucleotide lacking). This error seem
to affect transcripts randomly. I have not checked the other species.

Am I missing something?

Many Thanks

Best Regards

Remo
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