You may go to this site:

STarMir Tools for Prediction of microRNA binding sites - NCBI - NIH

Dear Victoria,

Please be careful in using these sites as there are many of them, however the predictions are less than 50% accurate. The presence of a miR binding sites does not equate to functional regulation. We have used every site available and none of them have been reliable. What we have done is to use new technology to inhibit miR function in cells and animals to understand miR function. This new system is extremely efficient, specific, non-toxic and has no off target effects. With this system you can truly identify genes regulated by specific miRs, even within a cluster. You can either transiently transfect cells, transform cells with lentivirus contracts or make animal models, and this is the only system that can do this level of specificity. Please see https://naturemiri.com.

Dear Dr. Victoria

In my opinion, use of only one algorithm to predict potential binding sites of microRNA is not a good choice as there are several target sites of miRNA even within a single target gene. What I would like to suggest you is, use three to four algorithm for prediction and select only those common sites which are predicted by at least three algorithm. I am not familiar with the new system described by Dr. Brad. However, I would also like to try if I get more information about this system.

Best of luck

Thanks all. We all ready have significant functional evidence that our miRNA is inhibiting our gene of interest. We have used the PITA algorithm, along with others, in our prediction analysis in the past and for consistency I would like to use it to analyze subsequent data. Cheers!