Hi all,
I want to find a homolog for a single mouse SNP (not a gene) in humans. Is this even possible ? I am only aware of ways to compare longer sequences ....
Thanks!
If you search for the variant in Ensembl it will take you to a variant page. From there you can click on Phylogenetic context to get an alignment between multiple species. Choose your alignment from the drop down (the 17 and 39 mammals set both include both human and mouse). If there's an alignment at that locus, you'll see the variant plus 10bp up- and downstream. Any variants in the other species will also be highlighted, so if there's a mouse one at the same locus, you can click on it and find out more.
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version 2.3.6
Hi Emily, thanks for the tip! I tried this and unfortunately this SNP is not available on Ensembl (sorry I mistakenly said it is a mouse SNP when it is actually a Prairie Vole SNP). In that case, do you have any suggestion for alternative strategies ?
We don't have Prairie vole in Ensembl yet, but we will in the next release, due next month. Unfortunately, we won't have a variation database, which makes this a bit more faffy. If you know the location of the SNP you can search for that locus then go to the alignments on the left to get a page like this (I've chosen Guinea Pig as a random example). From there you can click on the locus in human and identify if there are any known SNPs at that locus.