Predicting targets from 3-UTR of novel splice variants

Question

[sayantanibhowmik15]

Hello Everyone,

I am trying to predict microRNAs that could target the 3ÚTR of a novel variant of SCARB1. It's better for me if I get a software where I can put the 3ÚTR sequence and it gives me a list of microRNAs that could target. Please help.

Answer 1

[Erin Haskell]

Tarbase is a database of predicted mRNA target positions. You can find your gene in Ensembl and add the Tarbase track (click on Configure this page > Regulation > Other Regulatory regions > Tarbase > close window) in the location page, zoom into the 3' UTR and see where they are predicted to bind - for example. You can click on the green boxes representing the miRNA binding to see info and links to mirBase. I don't think you'll be able to download the data from Ensembl though, you may need to do that from tar base.