[ensembl-dev] ApoC3 is missing

[Rishi Nag]

Hi Sebastien

I tried to BLAST the ApoC3 human protein to the Galgal4 genome and had no successful results. There is RNASeq data as well aligning as well as the 
cDNA /EST but without the protein support there wouldn't be an Ensembl gene model at the location.

You can use the Blast tools to see where the sequence aligns to other species,
http://www.ensembl.org/Multi/Tools/Blast?db=core

Regards

Rishi


On 18/03/2015 18:55, Matthieu Muffato wrote:
> 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
>>
>