[ensembl-dev] Do pseudogenes' have a "parent gene" annotation?

[Thibaut Hourlier]

Hi Luke and Vang,
No we don't store this information. One way to do it would be to get the supporting evidence for your pseudogene, I would expect one protein evidence. Then search for protein coding transcripts which also have this protein as supporting evidence. I don't know how reliable it would be.

Regards
Thibaut

> On 18 May 2016, at 10:26, Vang Quy Le / Region Nordjylland <vql at rn.dk> wrote:
> 
> I was looking for something like this as well. Haven't found anything in the web-bases Biomart or R-based biomaRt. It seems ENSEMBL does not output this information. I think if I have time or someone at ENSEML can do faster, it is possible to check the pseudogene prediction/annoation process and extract information from there. 
> 
> Kind regards
> Vang 
> 
> On 05/11/2016 12:05 PM, Luke Goodsell wrote:
>> Hi,
>> 
>> For a given pseudogene in EnsEMBL API, is there an annotation to access the parent gene from which it is derived? For example, if I get PMS2P2 (PMS2P2), is there a link to PMS2 (parent gene)?
>> 
>> I'd like to be able to get a list of all pseudogenes and, where applicable, get a list of "parent genes" from which they are derived. I've already written a script that works for pseudogenes like PMS2, where the pseudogene's official symbol is the parent's gene symbol + some other characters, excluding splits in the middle of multi-digit numbers. However, this does not capture all parent genes, and will have some false positives, too.
>> 
>> Kind regards,
>> Luke
>> 
>> 
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