[ensembl-dev] Difference in genomic coordinates between REFSEQ and ENSEMBL

[Andy Yates]

Hi Duarte,

Just to clarify one mis-conception here. Ensembl gene coordinates are the minimum start and maximum end of any transcript from the set linked to a gene (the coordinates which bound all transcripts). A gene's coordinates are not the same as its longest transcript model.

That doesn't explain the discrepancy you've seen between NM_001101426.3 and ENST00000407010. I can see from http://www.ensembl.org/Homo_sapiens/Share/17e6832cf57be0231caa268e919b3da4126347817 that this is caused by a longer 3' UTR in the RefSeq model. I do not know why that's the case. Hopefully someone else on the list will have a better idea.

Andy

On 24 Feb 2014, at 09:09, Duarte Molha <duartemolha at gmail.com> wrote:

> Dear Developers…
> 
>  
> I was wondering if anyone of you could help me with an problem I am having comparing REFSEQ with ENSEMBL transcripts…
> 
> I had assumed that the gene start and end coordinates in ensembl were obtained from the longest transcript model for each gene. However this does not seem to be the case when comparing as list of around 300 genes I have queried
> 
>  
> Take a look at the example for transcript NM_001101426. In refseq this transcript has the coordinates: chr7:16127152-16460947. However if you search for it in Ensembl you get the transcript ENST00000407010 with the coordinates : chr7:16130817-16460947
>  
> If we assume that ensembl would use the longest running transcript to determine the start and end coordinates then the ISPD gene should start at 16127152 and not at 16130817. There is a difference of almost 4KB. I understand the gene models are different and I would expect small differences between the two… but not a 4KB diference. Can you explain the discrepancy? 
> Best regards
> Duarte
> 
> =========================
>      Duarte Miguel Paulo Molha      
>          http://about.me/duarte         
> =========================
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