[ensembl-dev] Gorilla species

[Southan, Christopher]

Its good to see the updated gorilla in Ensembl Compara system to consolidate the primates and the just published genome.

However, while checking some Gene Tree displays I noticed the BACE1 (ENSGGOG00000014376) outgrouping is instantly suspicious.  

I have confirmed that ENSGGOP00000019139 protein has what appears to be an extensive frameshift. I can't exactly work out what might have happened in annotation pipleline terms (I read the Gorilla page but should this have been zipped up against the UniProt BACE1 at some point?) but there appears to be an insert without matches to anything. 

Yours,  Chris Southan


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-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Bronwen Aken
Sent: den 5 augusti 2011 15:08
To: Sébastien Moretti
Cc: dev
Subject: Re: [ensembl-dev] Gorilla species

Hi Sebastien,

The taxonomy ID will remain as 9593 for gorilla.

Thanks,
Bronwen


On 3 Aug 2011, at 12:58, Sébastien Moretti wrote:

>> Hi Sebastien,
> 
> Hi
> 
>> Yes, the gorilla genome is from Western lowland gorilla. The NCBI taxon id was set at the species level and not at the subspecies level, which is why you see 9593 instead of 9595.
>> 
>> For the coming e64 release, we will be changing the MT sequence from NC_001645 (western gorilla) to NC_011120 (western lowland gorilla).
>> 
>> Cheers,
>> Bronwen
> 
> So, in the next release you should use the subspecies level if all genomic sequences come from the western lowland gorilla ?
> 
>>> Hi
>>> 
>>> The NCBI taxon id for the Western lowland gorilla "Gorilla gorilla gorilla" does not seem to be the right one.
>>> 
>>> You use 9593 which is "Gorilla gorilla" instead of 9595 which belongs to the Western lowland gorilla.
>>> 
>>> 
>>> Is it something wanted because you are not sure of the sequenced species ?
> 
> -- 
> Sébastien Moretti
> Department of Ecology and Evolution,
> Biophore, University of Lausanne,
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4221/4079
> http://bioinfo.unil.ch/