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two or more ENS IDs for SNORA2 #187

Closed ElaineMcA closed 4 years ago

ElaineMcA commented 6 years ago

@gkos-bio commented on Thu Jan 05 2017

Nice to see that we also incorporate the ncRNA gene trees from Ensembl described by Pignatelli et al. :) in the Platform.

I may have spotted some inconsistencies. When I searched for SNORA2, I get to https://www.targetvalidation.org/target/ENSG00000202343 but the ID of the chimp orthologue did not match to the one in Ensembl:

http://www.ensembl.org/Homo_sapiens/Gene/Compara_Tree?db=core;g=ENSG00000199959;r=1:84277321-84277457;t=ENST00000363089

Then I realised the ENS ID of SNORA2 did not agree either. So we also have:

https://www.targetvalidation.org/target/ENSG00000199959 and also

https://www.targetvalidation.org/target/ENSG00000206647

This seems to happen to other SNORAs such as SNORA22:

https://www.targetvalidation.org/search?src=q:SNORA2

When searching for the Ensembl gene ID (from Ensembl) for both SNORA2 and 22, there are no diseases associated with them. But for the other IDs (that we link to SNORA2 and SNORA22), there seems to be associations...

@ckongEbi commented on Tue Jul 10 2018

@gkos-bio should this be a Ensembl issue? helpdesk@ensembl.org

@ElaineMcA commented on Mon Oct 15 2018

@gkos-bio - can I close this or is this still valid and needs Ensembl f-up? Thanks,

Elaine

deniseOme commented 5 years ago

This is no longer an issue as per 18.12 release. However it may be useful to monitor this over the new releases. Worth including this on our manual QC, @ElaineMcA ?

The reason for two or more ENS gene IDs for SNORA2 is that there are in fact not only one SNORA2 but rather several SNORA2 (or paralogs).

Here they are (plus their chimp orthologues taken from our target profile page):

ENSG00000221491 aka SNORA2C (chimp orthologue is ENSPTRG00000036232) ENSG00000206612 aka SNORA2A (chimp orthologue is ENSPTRG00000026103) ENSG00000207313 aka SNORA2B (chimp orthologue is ENSPTRG00000027302) ENSG00000199959 (chimp orthologue is ENSPTRG00000024630) ENSG00000206647 (chimp orthologue is ENSPTRG00000046783) ENSG00000202343 (chimp orthologue is ENSPTRG00000027059)

Summary:

note: investigation done using 18.12 release and Ensembl 94

Same behaviour can be extended to other members of the SNORA family including SNORA22 (ENSG00000206634, with 3 chimp orthologues: ENSPTRG00000043447, ENSPTRG00000042700, ENSPTRG00000045851). SNORA22 paralogues: