Obtaining 3'UTR and perform microRNA target prediction - How to commence? (Aug/26/2010 )
Hi,
How would one go about finding the 3'UTR of the mRNA of relatively unknown genes? I have a set of genes which are definitely transcribed, but I don't know their 3'UTR. Furthermore, I would like to see which microRNAs have the potential to target these genes. What would be the best software for this?
Many thanks
There are a number of databases that already have done the prediction on 3 UTR of all protein coding genes, so chances are high that you can search your gene to find potential miRNA targets.
Here is a few database:
MicroSosm at http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ It is my favrite one. To use it, click Search and then choose the organism of your interest and gene name.
Targetscan at http://www.targetscan.org/. TargetScan put much weight on seed conservation
There are additional databases listed here http://www.exiqon.com/microrna-target-prediction
Good luck!
pcrman on Fri Aug 27 01:52:03 2010 said:
There are a number of databases that already have done the prediction on 3 UTR of all protein coding genes, so chances are high that you can search your gene to find potential miRNA targets.
Here is a few database:
MicroSosm at http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ It is my favrite one. To use it, click Search and then choose the organism of your interest and gene name.
Targetscan at http://www.targetscan.org/. TargetScan put much weight on seed conservation
There are additional databases listed here http://www.exiqon.com/microrna-target-prediction
Good luck!
Thanks for the tips, but I have tried those databases before, but unfortunately they do not contain the genes I'm looking at.