[ensembl-dev] Discrepancies for rat gene Hps1

[Daniel Barrell]

Dear Man Chun John Ma,

Currently we are running our gene annotation system on the new rat 
assembly, Rnor_6.0. I've checked and the cDNA BC099744.1 has aligned in 
the correct position on chromosome 1 (as it was in e69). This was also 
the case in Rnor_5.0, however, when choosing one evidence set over 
another it seems our choice meant that Hps1 was removed and we ended up 
with ENSRNOT00000021278. What we'll do is attach a flag to the 
BC099744.1 alignment so that the Hps1 gene returns in the gene set for 
Rnor_6.0, which we hope to release in e80.

Incidentally, we also now merge rat with manual annotation from the 
HAVANA team. Manual annotation is favoured over automatic gene 
annotation, therefore if the gene is manually annotated it will always 
be displayed. I'll forward your email to the HAVANA team separately so 
that they are aware of your interest in Hps1.

Regards,

Daniel Barrell




On 09/01/15 10:19, Man Chun John MA wrote:
> Hi all,
>
> Before e70, when Ensembl changed the genome assembly used for rats 
> from rn4 to rn5, the rat Hps1 gene was located at ENSRNOG00000015891. 
> After that point Ensembl seems to have retired that ID in favour of 
> ENSRNOG00000045838 (HPS), the annotation of which sounds like it's a 
> different gene. On the other hand, the Hps1 gene has been continued in 
> the rn5 in RGD (69193) and EntrezGene (114638).
>
> While I understand different annotation pipeline would generate 
> different results as gene annotation is concerned, do you think this 
> is a discrepancy that you may fix?
>
> Thanks for the reply in advance!
>
> Regards,
>
> Man Chun John Ma, PhD
> manchunjohn-ma at uiowa.edu
>
>
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