How to map miRNA to transcripts of targeting genes ?

Question

[jack]

Hi,

I have set of experimentally validated miRNA-gene interactions. I jut have information about the miRNA-Gene binding. but I want to know that miRNA to which transcripts or isoforms of targeting gene binds.

Would someone help me in this case?

[Manvendra Singh]

I am just guessing that once you have found anti-correlation between the expression levels of miRNA and target genes, and seed is also pairing on 3'UTR then you might see whether , there is any specific isoform which is anticorrelated in sharp contrast with other isoforms of same gene.

PS: This is just a guess.

Answer 1

[Renesh]

Refer to this link

It provides several tool for miRNA target prediction.

Answer 2

[Bade]

You can try sPARTA, if working on plants. It's very fast and sensitive to secondary structures that miRNA and target form

Link to paper

Bade