Confusion about miRNA list - (Oct/20/2007 )
I have a quick question....I downloaded the miRNA list for humans from the Sanger database (Ref: http://microrna.sanger.ac.uk/cgi-bin/targets/v4/genome.pl).
The list also contains miRNAs from mmu, gga, etc (eg: mmu-miR-201). Shouldn't it be hsa-miR-201? Does mmu mean that it was identified first in mouse? And a homolog exists in human?
I would appreciate your insights.
Thanks in advance,
If they are conserved across human, mouse, they have the same number. some microRNAs are not conserved and may exist only in human or mouse, in that case, there will be no coresponding microRNA in another specie. for mmu-miR-201, human does not have it.
Thanks pcrman....appreciate your reply.
I just wanted to make sure that I understand it correctly.......when I do a search for miRNAs using Sanger db (http://microrna.sanger.ac.uk/cgi-bin/targets/v4/search.pl) for the following choices:
1. select a genome : H. sapiens
2. gene name: IL2
I get a results including mmu-miR-543, rno-miR-352, etc....does this mean:
1. these miRNAs actually target IL2, but are not present in human?
2. if they are not present in human, then these shouldn't be listed when I select the genome 'H.sapiens', right?
Thanks in advance for your replies.
I have one more question....if mmu-miR-201 does not have a homolog in human, why is it listed in the human mature miRNA list?
Thanks for your reply.
Yes the predicted targets include those from the oganism which is not your choice. I don't know why. Probably it gives you some sense of how a target is conserved. To check whether a miR is conserved in human, you can get the precursor sequence for that miRNA and do a blat search using the UCSC genome browser. Generally if there is no coressponding number for that miR, probably it is not conserved.