Identifying orthologous exons between human and mouse

Question

[jthomas5062]

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

[GenoMax]

Have you seen this page?

[Sishuo Wang]

and also this one paper1 and this one paper2

[microfuge]

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.

Answer 1

[igor]

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.