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?