Monday, October 10, 2011

How to scan a 3'UTR of gene of interest for conserved miRNA homologies

Another great tool for miRNA analysis,

http://www.targetscan.org/

TargetScan is searching the 3'UTR region for the presence of conserved 8-mer and 7-mer sites that match the miRNA seed regions. As an option, nonconserved sites are also predicted.

The additional strength of such analysis is that by searching for the conservation among species we increase the chance of finding functionally relevant miRNA matches in the 3'UTR of a gene.

This is how the output of the TargetScanHuman looks like when NFIC human gene was scanned for conserved miRNAs.





The resulting output shows conserved (and poorly conserved) miRNAs that potentially regulate the 3'UTR region of the gene of interest. Bellow the sequence comparison of different species there is a list of conserved and poorly conserved miRNA matches. For the NFIC gene there are 3 conserved miRNA that could be accessed by clicking on their respective names under the gene depiction.

To view poorly conserved miRNAs, in addition to conserved ones, click on Show poorly conserved sites and sites for poorly conserved miRNA families. It is possible also to show only poorly conserved miRNAs by hiding the conserved miRNAs.

To download all results as a table click View table of miRNA sites.

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