Hi everyone
I did the 25 bp deletion as series in my 3'UTR region for observing which regions are important for miRNA regulation. Now I got the region that may be regulated by miRNAs but I don't know how to predict the miRNA binding site from my region. Can anyone suggest me the way that I can know the miRNA binding sites in my expected region.
Many thanks
You must identify the seed sequence of your microRNA using "http://www.mirbase.org/" .
There are many bioinformatic tools for validation of microRNA and their targets. I would like to suggest , you can use “targetscan” and flow their instructions.
Or simply,
click their "http://www.targetscan.org/vert_50/" then
write your target gene name or Enter a human Entrez Gene symbol(e.g-smad4) then write your microRNA name(e.g-has-miR-145) and submit and you will get your target gene 3’UTR sequence with target microRNA seed sequence.
Best of luck, Pannapa pinweha
Perhaps take the consensus of multiple target prediction programs to be conservative.
http://mirnablog.com/microrna-target-prediction-tools/
Targetscan is a good resource.
http://www.targetscan.org/vert_71/
it will only give you annotations of binding sites over your 'gene" 5'UTR though.
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