[ensembl-dev] NCBI vs Ensemble

Bert Overduin bert at ebi.ac.uk
Wed Mar 6 16:20:30 GMT 2013

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>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
> Thanks
> Sunita
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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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