[ensembl-dev] ApoC3 is missing

[Matthieu Muffato]

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. 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 ?

Matthieu

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