[ensembl-dev] Assembly Coverter incorrect for CHD2 GRCh38 ->GRCh37

[Andrew Yates]

Hi Luke,

I think there are a few things going on here to explain that will hopefully resolve your issue.

Firstly the annotation for CHD2 against GRCh38 was from a re-annotation of the genome. That gene was not simply lifted over from the previous assembly but was a fresh call (supported by NM_001271.3 as detailed for the longest transcript from [1]). The line "This gene maps to 93,443,419-93,571,235 in GRCh37 coordinates" is created by lifting over the coordinates from GRCh38 to GRCh37. It is not saying you can find the same gene in GRCh37 at this position. That's why we have the additional link to ENSG00000173575 in GRCh37 to ensure we can send you to the correct locus.

Does that help?

All the best,

Andy

1 - http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000173575;r=15:92900189-93028005;t=ENST00000394196 <http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000173575;r=15:92900189-93028005;t=ENST00000394196>

------------
Andrew Yates - Genomics Technology Infrastructure Team Leader
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
Skype: andy.yates.ebi
http://www.ebi.ac.uk/
http://www.ensembl.org/

> On 22 Apr 2016, at 09:55, Luke Goodsell <Luke.Goodsell at ogt.com> wrote:
> 
> Hi,
>  
> Are misconversions by the Assembly Converter being fixed?
>  
> On the GRCh38 EnsEMBL browser page for CHD2 (http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575 <http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575>), it states “This gene maps to 93,443,419-93,571,235 in GRCh37 coordinates.” However, the GRCh37 page (http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575 <http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000173575>) shows the co-ordinates as “Chromosome 15: 93,426,526-93,571,237”.
>  
> These co-ordinates are the same as the “Assembly Converter” conversion, from which I assume the browser takes its data.
>  
> Kind regards,
> Luke
>  
> 
> 
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