4.8 years ago by
If the software you are using annotated that region as a miRNA (and the software and annotation is reliable) then that means that that region will transcribe the specific miRNA
Which kingdom are you working with here? Whether it is plant or animal, then you are going to get a much different response:
My expertise is with the animal kingdom, so if that is what you are working with:
It depends - is this a known, well-annotated miRNA? Does it exist in miRBase?
If it does, you can use the official TargetScan website to get predicted targets quite easily
If the miRNA is not included already in Targetscan databases, your best bet at the moment would be to use TargetScan. However, this will require a fair bit of work downloading and running the necessary perl scripts (and their dependencies) along with the relevant text files
There are other target prediction algorithms that exist such as miRanda at microrna.org. However, as far as I am aware, Targetscan is the best target prediction software currently out there.
Again, it depends on the specific kingdom and species you are working with.
For animal miRNA, there is something known as the 'seed region' - roughly around nucleotides 1-8 of the miRNA (it is dependent on the specific mRNA target site as well). If any nucleotide in the seed sequence is mutated it will likely have a strong effect on binding. If the mutation is outside the seed region, then it is much less likely to have a great effect on binding.
I guess the only way to know for sure, would be to have clear knowledge of the miRNA targets, then perform some form of experiment and experimental analysis to judge whether there is a significant effect on binding to the target depending on whether the miRNA is mutated or not.
Other than that, I am not sure how you would be able to tell
modified 2.2 years ago
_r_am ♦ 31k
4.8 years ago by
Thomas • 100