Given a protein domain, like a TPR or zinc finger or some other one, can you predict what RNA sequence it binds to?

Question

[Joel Wallenius]

Hello!

Question in the title. I am trying to find out if there is a tool somewhere that takes a protein sequence or structure and predicts what RNA sequence it binds to.

This is about finding out if there are stretches of RNA in some mRNA transcripts that bind to particular transport proteins and travel to some location in the cell before translation takes place.

I suspect that the TPR domain might be relevant, but can't find anything about what sequences it binds to.

Big thanks in advance!

[Russ]

It's not exactly what you're looking for, but CIS-BP has a tool that lets you scan protein sequences to predict DNA binding motifs.

[Joel Wallenius]

That is remarkably close though. I tested it, it couldn't find any significant matches. Perhaps TPR regions are way too diverse for such a tool...