Identify target miRNA for a mRNA

Question

[Bioinformatist Newbie]

I have the mRNA of PARK7 gene, the wild type contain 8 exons. It undergo a mis-splicing and new mRNA has exon number 3 deleted (no frame shift but 7 exons). The question here is if the skipping of exon 3 or the ligation of exon 2 and exon 4 leads to new miRNA binding sites. I have queried that gene to TargetScan, miranda, microT and many other miRNA binding site prediction tools but all they predict are the binding sites in 3' UTR region which is in range of exon 4-8. I am interested in finding binding sites for miRNAs at the end of 4th exon which is not in the 3' UTR. Can anyone guide me how I can do that?

Thanks

Answer 1

[Asaf]

I know it sounds not very sophisticated but it might be that your best chance is looking for a simple seed matching 7-mer with a trailing A in that region. You might want to look at the folding of the mRNA - it might change when there is exon skipping and open the region for binding the miRNA.