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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. <br>
<br>
Kind regards<br>
Vang <br>
<br>
<div class="moz-cite-prefix">On 05/11/2016 12:05 PM, Luke Goodsell wrote:<br>
</div>
<blockquote cite="mid:59C49FE16E416F46873F86D530DA80521BD87B@ExchangeServer.internal.ogtip.com" type="cite">
Hi,<br>
<br>
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)?<br>
<br>
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.<br>
<br>
Kind regards,<br>
Luke<br>
<br>
<br>
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