Do I need to consider strand information in searching microRNA binding sites ?

Question

[camelbbs]

Hi all,

I want to ask when we extract genomic sequences to predict the microRNA binding sites, do we need to consider the strand information for it? I know the sequences from plus and minus strand are complementary. So which strand I can use for the prediction of microRNA binding sites, or it is not necessary to consider that? On the other hand, do use sense or anitsense sequence affect the prediction result?

Thanks very much, Camel

Answer 1

[Emily]

MiRNAs generally bind to the 3' end of the mRNA therefore they must be complimentary to the target mRNA.