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Obtaining 3'UTR and perform microRNA target prediction


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#1 Baars01

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Posted 26 August 2010 - 06:44 AM

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

#2 pcrman

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Posted 26 August 2010 - 05:52 PM

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...ocs/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.co...rget-prediction

Good luck!

#3 Baars01

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Posted 27 August 2010 - 01:20 AM

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...ocs/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.co...rget-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.




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