Based on literature review and existing sequencing data, we chosen few miRNA, then we over-expressed them in cancer cells using miRNA mimics. We found a gene expression getting down-regulated in qPCR result.
In target scan, we do not found that particular gene as predicted target of of that miRNA.
In this situation, Can i create miRNA-mRNA (3' UTR sequence) alignment??
How to create miRNA-mRNA aligment, which software will be good, Where I will find 3' UTR region. Looking for step-wise-step protocol.
Thanks in advance!!!