[ensembl-dev] Gene with multiple personality disorder?

Magali mr6 at ebi.ac.uk
Wed Sep 25 12:11:40 BST 2013


Hi Duarte,

The NCBI entry you are referring to was updated on the 14th September
this year, so 10 days ago.
The Ensembl gene set displayed on the browser was last updated in June.

It could be that additional biological evidence as been made available
since, which could be incorporated in our next gene set update.

Additionally, there is a vega annotation for that gene.
http://vega.sanger.ac.uk/Homo_sapiens/Gene/Summary?db=core;g=OTTHUMG00000151665;r=19-COX_2:194318-203659;t=OTTHUMT00000323417
The annotation says that there is no ungapped mapping available for this
gene in GRCh37.
This would prevent us from annotating a full length model.

Hopefully this will be fixed with the new assembly GRCh38 and will allow
us to annotate the full gene model, as well as assign it its correct name.


Regards,
Magali

On 25/09/13 12:01, Duarte Molha wrote:
> Dear Magali
>
> I am still confused... if you look in this gene KIR2DL5A in NCBI:
>
> http://www.ncbi.nlm.nih.gov/gene/57292
>
> In the section "Links to other resources" there are links to several
> other services.
>
> If you click on the UCSC link it takes you to the gene with the same name:
> http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=NM_020535
>
> However if you click on the ensembl link
>
> http://www.ensembl.org/Homo_sapiens/geneview?gene=NM_020535
>
> it redirects you automatically to this other gene:
>
> http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000215764;r=GL000209.1:7891-96246
>
> So both NCBI and UCSC agree on the existence of this gene but not ensembl?
>
> My apologies to insist on this but I want to understand Ensembl
> disagrees with these other sources and the gene simply is missing from
> ENSEMBL because it has merged it into KIR2DL2 -  ENSG00000215764
>
> Best regards
>
> Duarte
>
>
> =========================
>      Duarte Miguel Paulo Molha      
>          http://about.me/duarte         
> =========================
>
>
> On Wed, Sep 25, 2013 at 11:46 AM, Magali <mr6 at ebi.ac.uk
> <mailto:mr6 at ebi.ac.uk>> wrote:
>
>     Hi Duarte,
>
>     Looking at the HGNC entry for KIR2DL5A, there is no link there to
>     any Ensembl annotation.
>     If there was, we would be able to assign the HGNC name directly to
>     the Ensembl gene.
>
>     For ENSG00000215764, we were able to align a refseq entry, NM_014219.2
>     http://www.ncbi.nlm.nih.gov/nuccore/NM_014219.2
>
>     This entry in turn links back to the HGNC entry for KIR2DL2, which
>     is where the Ensembl gene gets its name from.
>
>     If you have any biological evidence that ENSG00000215764
>     corresponds to KIR2DL5A, we would be most grateful if you could
>     submit it to HGNC.
>     This would allow them to update their records regarding KIR2DL5A
>     and in turn we would be able to assign the correct name.
>
>
>     Regards,
>     Magali
>
>
>     On 25/09/13 11:32, Duarte Molha wrote:
>>
>>     Dear developers
>>
>>      I have a question regarding a gene that I would like your help
>>     with  
>>
>>      I have a Gene called KIR2DL5A.. This is the most up-to-date
>>      name in HGNC for this gene:
>>
>>      http://www.genenames.org/data/hgnc_data.php?hgnc_id=16345
>>
>>      However, ensembl calls it: KIR2DL2
>>
>>     http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000215764;r=GL000209.1:7891-96246
>>
>>
>>        This is not the correct name, and it is not even an alias of
>>       the gene of interest.... What is going on here?
>>
>>
>>        Best regards
>>
>>      Duarte
>>
>>
>>
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>
>

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