[ensembl-dev] Discrepancies for rat gene Hps1

[Daniel Barrell]

Hi Again,

I thought I should also add that the contig (AC096317.6) that this gene 
lies on in the Rnor_6.0 assembly has been flipped so the gene will now 
be on the reverse strand.

Dan

On 09/01/15 11:07, Daniel Barrell wrote:
>
> 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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