[ensembl-dev] ApoC3 is missing

[p.pierre419 at laposte.net]

Hello Matthieu, 

----- Mail original -----

De: "Matthieu Muffato" <muffato at ebi.ac.uk> 
À: "Ensembl developers list" <dev at ensembl.org> 
Envoyé: Mercredi 18 Mars 2015 19:55:42 
Objet: Re: [ensembl-dev] ApoC3 is missing 

Dear Sébastien, 

It looks like ApoC3 has not been annotated by the Ensembl pipeline. You 
can have a look at the region with most of the evidence switched on: 
http://www.ensembl.org/Gallus_gallus/Share/6ce226669bc7414392cd55e837dc1982178952913 
(it is the same location as on the NCBI browser) 

Some ESTs and cDNAs mapping there, and there even is a Genscan 
prediction, but no proteins are aligned to this locus. 
Yes, it is very strange because Apoc3 protein seems to exists : 
http://www.ncbi.nlm.nih.gov/protein/NP_001289056.1 

This could be the 
reason why the Genescan gene model was not retained by the Ensembl 
pipeline. Perhaps a genebuilder can shed some light on the situation ? 
Excuse my naive question but how can I do a genebuilder ? 
Thanks, 
Sébastien 


On 18/03/15 17:50, p.pierre419 at laposte.net wrote: 
> Good morning, 
> 
> I am working on phylogeny beetween species and more particulary 
> gain/loss genes between homo sapiens and gallus gallus. 
> 
> So, using "Gene tree" (via Ensembl!) --> "view fully expanded tree", we 
> can note that none gallus gallus gene for ApoC3 is present : 
> http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?collapse=none;db=core;g=ENSG00000110245;r=11:116829706-116833072 
> 
> while ApoC3 exists in map viewer for gallus gallus : 
> http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031&chr=24&MAPS=genes-r&cmd=focus&fill=40&query=uid%28-1586510584%29&QSTR=apoc3 
> 
> My question is : 
> Is it possible to know, from Gene tree or Ensembl! site web, that ApoC3 
> is present in gallus gallus and may be others species ? 
> 
> Thanks, 
> Sébastien 
> 

-- 
Matthieu Muffato, Ph.D. 
Ensembl Compara Project Leader 
European Bioinformatics Institute (EMBL-EBI) 
European Molecular Biology Laboratory 
Wellcome Trust Genome Campus, Hinxton 
Cambridge, CB10 1SD, United Kingdom 
Room A3-145 
Phone + 44 (0) 1223 49 4631 
Fax + 44 (0) 1223 49 4468 

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