[ensembl-dev] NCBI vs Ensemble

Koul, Sunita sunita at pathology.wustl.edu
Wed Mar 6 17:00:31 GMT 2013

Thanks that was helpful

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Bert Overduin
Sent: Wednesday, March 06, 2013 10:21 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] NCBI vs Ensemble

Hello Sunita,

NCBI and Ensembl generate their gene models in different ways, so they can differ in their coordinates, as is the case for the human DNMT3A gene.

The patches have nothing to do with this as this gene is not located in a patch region.

Just for your information, we indeed annotate at the moment the GRCh37.p10 assembly. The patches themselves however are existing as separate entities from the reference genome assembly. The reference genome itself has not changed between GRCh37 and GRCh37.p10. There are basically two kind of patches, novel patches, which represent alternate loci and fix patches, which represent corrected regions. The fix patches will be incorporated in the reference genome assembly in the next major release (i.e. GRCh38), thus replacing the faulty regions. Until that time genes located in fix patch regions will be annotated both on the reference genome assembly and the fix patch, as you can see for e.g. the human ABO gene:


But again, this does not pertain to the DNMT3A gene, as it is not located in a fix patch region.

Hope this helps.

On Wed, Mar 6, 2013 at 4:03 PM, Koul, Sunita <sunita at pathology.wustl.edu<mailto:sunita at pathology.wustl.edu>> wrote:
I was looking at the Gene DNMT3A (ENSG00000119772)  in the ensemble genome browser
As per the release the ensemble 70 has updated patches for the  human assembly (GRCh37.p10)
In NCBI the genomic location of this gene is (25455830-25565459) http://www.ncbi.nlm.nih.gov/gene?db=gene&cmd=retrieve&dopt=full_report&list_uids=1788

How is that the ensemble still shows the  (25455845-25565459)  in their browser http://useast.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000119772;r=2:25455845-25565459

Am I missing something here?

Basically we are trying to annotate our genes with annotations from Ensemble. We are currently using NCBI build 37.p10 and want to pull in more information from Ensemble
Unless we find the compatibility between these 2 builds we can't proceed
Can someone guide me how we can do this


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Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom


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