Question: Identifying orthologous exons between human and mouse
2
gravatar for jthomas5062
3.5 years ago by
jthomas506220
jthomas506220 wrote:

Hello,

I have been using MISO to identify mis-spliced exons in a human dataset and now I am trying to compare these mis-spliced human exons to another dataset from a mouse model with similar splicing events. Does anyone know of a resource to identify orthologous exons between human and mouse? I've searched through Biomart many times and can't seem to find this. I have also been "blat-ing" the human sequence against a query of mouse exon sequences but this seems to be giving many false negatives.

Thanks a lot!

James

rna-seq sequence gene • 1.3k views
ADD COMMENTlink modified 21 months ago by igor9.6k • written 3.5 years ago by jthomas506220
1

Have you seen this page?

ADD REPLYlink written 3.5 years ago by genomax78k
1

and also this one paper1 and this one paper2

ADD REPLYlink written 21 months ago by Sishuo Wang190

A presumably bad solution would be to have bed file of all exons and use intersection with the conservation track of the UCSC browser via table browser. I am also waiting for someone here to suggest a more direct solution/resource for this.

ADD REPLYlink written 3.5 years ago by microfuge1.5k
0
gravatar for igor
21 months ago by
igor9.6k
United States
igor9.6k wrote:

This is probably not the optimal solution, but it should technically work. You could extract the exon coordinates and run LiftOver on them, which can be done cross-species. Then you could match the new species coordinates to the exons that fall there.

ADD COMMENTlink written 21 months ago by igor9.6k
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