[ensembl-dev] ATXN8 gene missing from Ensembl

[Thomas Danhorn]

Hi Kirill,

On the NCBI site for ATXN8 you linked to it says "not in current 
annotation release", so it looks like it may have once been considered a 
valid gene, but not anymore.  I have also looked through a few of the 
older Ensembl releases and none of them have ATXN8 on chromosome 13 (so 
this is not an omission in the new release).  The ones based on the 
GRCh37/hg19 assembly (Ensembl versions 75 and older) have "ATXN8" as a 
synonym of ENSG00000107815, but that is on chromosome 10, so I doubt that 
is what you are looking for.

Hope this helps,

Thomas


On Tue, 5 May 2020, Kirill Tsukanov wrote:

> Hi,
>
> I have a quick question about a data issue. I noticed that Ensembl 100 
> includes ATXN8OS gene 
> <http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000230223;r=13:70107213-70149092> 
> (opposite strand lncRNA), but not the ATXN8 gene itself. The latter is 
> present in NCBI Gene (https://www.ncbi.nlm.nih.gov/gene/724066), but not in 
> Ensembl. This is unfortunate because it means that I can't use it in an Open 
> Targets submission as it does not have an Ensembl gene ID associated with it.
>
> Do you know if there's a specific reason why this gene is missing? Can we 
> expect it to be added in later Ensembl releases?
>
> -- 
> Best,
> Kirill from the European Variation Archive
>