[ensembl-dev] Mouse Genomes Project gene symbols missing in Ensembl release 114

[Leanne Haggerty]

Hi Eric,

Just to add to Jorge’s response, in case it’s useful, you can find the genomes and Ensembl annotations for the latest Mouse Genome Project on the Ensembl project page:
https://projects.ensembl.org/mouse_genomes/

From this page, you can download the GFF files. Gene symbols have been added using a machine learning approach that closely replicates traditional Ensembl assignment methods with high accuracy. You can read more about this approach here:
https://www.embl.org/news/science/a-machine-learning-approach-for-allocating-gene-function/, and more on Ensembl’s conventional gene naming methods here: https://www.ensembl.org/info/genome/genebuild/gene_names.html

I hope this is helpful while we await the release of these genomes in the new website.

All the best
Leanne


> On 4 Jul 2025, at 16:47, Jorge Batista da Rocha <jrocha at ebi.ac.uk> wrote:
> 
> Hi Eric, 
> 
> Hope you are well, and thank you for reaching out. 
> 
> I’m sorry to say that the gene symbols are missing due to an error in our external references pipeline. Our data teams are looking into it. 
> 
> It will not be fixed for the upcoming 115 release in the autumn. Any fixes would be incorporated into the subsequent 116 release.
> 
> We expect the updated builds to become available in our new site, beta.ensembl.org <http://beta.ensembl.org/> within the next few months. 
> 
> Thanks and best wishes
> Jorge 
> 
> 
> 
> 
> 
> Dr Jorge Batista da Rocha
> Ensembl Outreach Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> 
>> On 1 Jul 2025, at 14:58, Eric Engelhard <eric.engelhard at regeneron.com> wrote:
>> 
>> Ensembl release 114 includes new genome builds and annotations for the non-canonical Mouse Genome Project strains (https://www.ensembl.info/2025/05/07/ensembl-114-has-been-released/). I recently noticed, however, that new gene annotations now lack gene symbols for both the web service and within the MySQL sources. Additionally, BioMart sources are no longer synchronized to the new gene identifiers, all of which have been replaced.
>>  
>> Are gene symbol annotations and a BioMart update planned for the next release?
>>  
>> Thank you,
>> Eric
>> 
>> Regeneron - Internal
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