Question: Convert mouse amino acid location to genomic location
0
gravatar for angrypigeon
27 days ago by
angrypigeon120
angrypigeon120 wrote:

I have amino acid positions for a number of mouse mutations, for example DNMT3a R878H. Is there a way to convert this to a genome coordinate such aschr12:12345?

The Ensembl Rest API seems to be capable of such a task, and when I make a call for a human change it works as shown here:

https://rest.ensembl.org/map/translation/ENSP00000288602/100..300?content-type=application/json

But when trying to change the gene to mouse the call no longer works.

gene genome • 164 views
ADD COMMENTlink modified 26 days ago • written 27 days ago by angrypigeon120
2

duplicate Amino Acid Change To Genomic Location ; Convert Amino Acid Change To Chromosomal Snp Coordinate ; Finding A Mutation Coordinate From Mutation Nomenclature And Gene Name ; ...

ADD REPLYlink written 27 days ago by Pierre Lindenbaum121k

Thanks Pierre, I did have a look at this but it is unclear how to perform such an analysis for mouse. It looks like the Ensembl API might be able to do it as illustrated here, but how to switch from human to mouse is not clear to me.

ADD REPLYlink written 27 days ago by angrypigeon120
1

Give VEP a shot

ADD REPLYlink written 26 days ago by RamRS22k

This doesn't seem to work for me either. I am trying to get the coordinates for the mouse DNMT3a R878H mutation in the question like this:

https://rest.ensembl.org/vep/human/hgvs/ENSMUSG00000020661:p.Arg878His?content-type=application/json

But this will not return anything.

ADD REPLYlink written 26 days ago by angrypigeon120
4
  1. Your URL contains human, not mouse/mus_musculus
  2. The URL contains gene id followed by protein change, which is an entity mismatch.

This works:

https://rest.ensembl.org/vep/mus_musculus/hgvs/ENSMUSP00000020991:p.Arg878His?content-type=application/json

ADD REPLYlink modified 26 days ago • written 26 days ago by RamRS22k

"ENSMUSP00000020991" is actually protein id of "ENSMUSG00000020661".

ADD REPLYlink written 26 days ago by arup1.5k

Indeed. That's how I built the working URL from the "broken" URL

ADD REPLYlink written 26 days ago by RamRS22k

This works great! But how did you find the protein id instead of the gene id?

ADD REPLYlink modified 26 days ago • written 26 days ago by angrypigeon120
2
  1. Google the gene id to get to the ENSG entry
  2. Expand the transcript table and ensure the "Translation ID" column is displayed
  3. Everything is now available in a single view:

ADD REPLYlink written 26 days ago by RamRS22k
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