I have identified a miRNA which is assumed to be transcribed from the opposite of mRNA transcribing strand. So the mRNA and miRNA are transcribed from the opposite strand of each other. Thus they are complementary to each other. But the problem is they are parallel, not anti-parallel.
Now my question, is there any possibility that this miRNA can bind with the mRNA? Is it necessary to be anti-parallel for binding a miRNA with mRNA?
I would say that it is not possible, unless the "seed" sequence is palindromic.
however, this miRNA could still act as an endogenous miRNA inhibitor...or sponge for another miRNA binding to you mRNA in that region..
ciao, D.
Actually everything is possible. But what do you mean with parallel and anti-parallel? There are cases in the literature where a miRNA is transcribed from the opposite strand of its target mRNA. In other cases the miRNA is intragenic and it is co-transcribed with its host gene (which can actually be its target also).
Maybe its not a miRNA but another kind of small RNA....there are so many possibilities that you will need to find out more about it, one challenge would be to find out what its true precursor looks like
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