[ensembl-dev] Question regarding gene Annotations discrepancies between GRCh38 and 37 on the latest API.

mag mr6 at ebi.ac.uk
Wed Jul 1 11:58:20 BST 2015

Dear Duarte,

The gene set in the GRCh37 database is a freeze from release 75.
The variation and regulation annotation is updated when major data sets 
are released.

The gene set however is not updated given our major evidence sources are 
updated to GRCh38.


On 01/07/2015 11:03, Duarte Molha wrote:
> Dear developers
> It was my understanding that ensembl would be keeping 2 databases 
> running in parallel for both GRCh38 and GRCh37 and so all genes would 
> be receiving annotation updates and both databases could be queried 
> with the latest and greatest ensembl perl api.
> However I am finding inconsistencies in gene annotation what have left 
> me puzzled.
> Take for example gene DNAAF5
> http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=26013
> If you query ensembl GRCh38 V80, the gene is there properly annotated
> http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000164818;r=7:726701-786475
> However, on GRCh37 V80, the gene is still annotated with the previous 
> HGNC symbol HEATR2
> http://grch37.ensembl.org/Multi/Search/Results?q=HEATR2;site=ensembl;page=1
> the ENSEMBL gene ID is the same in both cases :
> ENSG00000164818
> Is my thinking flawed? What is the reason for the out-of-date gene 
> annotation for this gene?
> Many thanks
> Duarte
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