[ensembl-dev] Biomart Genomic Coding Start/End

[Rhoda Kinsella]

Hi Simon
Yes this is likely to be related to the issue below. Can you send me a  
specific example so that I can check that this? We have rerun the  
calculations and are in the process of testing to make sure all id  
okay before copying the fixed mart to the live site. I will send an  
email once the fix has been made live.
Regards
Rhoda

On 23 May 2012, at 18:06, Simon Chan wrote:

> Hello,
>
> I'm using BioMart to fetch all protein coding portions of all exons  
> of all transcripts of my favourite gene (Ensembl Genes 67, Homo  
> sapiens genes GRCh37.p7).  In the past, 'Genomic coding start' and  
> 'Genomic coding end' would give me all exon coordinates minus UTRs.   
> However, now it seems to return the UTR coordinates as well.   
> Perhaps this is related to the UTR issue reported by Beat below?
>
> Thank you.
> Simon.
>
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On  
> Behalf Of Rhoda Kinsella
> Sent: Tuesday, May 22, 2012 3:38 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Ensembl release 67 is out!
>
> Hi Beat
> We are currently looking into why this has occurred but it is  
> certainly a bug in our mart databases. I will respond as soon as we  
> have a fix in place. Thank you for reporting this and apologies for  
> any inconvenience.
> Regards
> Rhoda
>
> On 19 May 2012, at 15:55, Beat Wolf wrote:
>
>
> Hi,
>
> i'm a computer scientist and not a biologist, so perhaps i missed  
> something about the DMD gene changing recently.
> I have an automated unit test for my application that uses biomart.  
> It happens to test the DMD-001 transcript of the DMD gene.
> In the 66 version of enembl, the UTR3 coordinates of the exon number  
> 79 where:
>
> 31137345
> to 31140035
> which was correct. Now with the version 67 of ensembl, the UTR3  
> region in the same exon is:
>
> 31137345 to
> 31137344
> Which can not be correct, because that means that UTR3 has a length  
> of 1. The other numbers don't match up either.
>
> Did the DMD gene change? Is the information stored differently in  
> ensembl? What values do i need to reconstruct the true UTR3 region?  
> Or is this a bug in the new ensembl version. If yes, how many other  
> genes are affected? Currently i will stay on the 66 version thanks  
> to the archives, but i have some connection issues with it, it seems  
> to be much less stable than the 67 version.
>
> Greetings
>
> Beat Wolf
>
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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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