Identifying microRNA computationally? - (Sep/06/2005 )

I have some short murine transcribed sequences identified by exon trapping. I am
wondering if they could possibly be microRNAs but am unsure how to go about
investigating this computationally. Any info/help would be gratefully
appreciated.
Thanks
Anthea

Hi Anthea,

Please check this post

http://www.protocol-online.org/forums/inde...?showtopic=9014

Also this page http://www.rnaiweb.com/RNAi/MicroRNA/Micro...ware/index.html

Thanks very much PCRman. My sequences dont appear to be MiRNA based on folding,sequence similarity or searching the known MiRNA databases.

I am wondering if they could possibly be siRNA. How would I go about finding this out? How do MiRNA and siRNA differ?

Thanks
Anthea

Hi Anthea,

I am not sure if there are naturally occuring siRNAs in animal cells. In plants, siRNA may be generated from double-stranded RNA via dicer processing. Double-stranded RNA can be formed in three ways such as bidirectional transcription of the same gene, from a transcript that contains inverted repeat so that it can form hairpin structure. I couldn't remember the third situation.

miRNA and siRNA don't differ much in terms of function, but differ a lot regarding biogenesis.