Start with a potential non-coding RNA sequence - (Aug/24/2005 )
hi
i am very new in this field. Right now, I have a sequence that is suspected to be related to non-coding RNA, maybe miRNA. How can I start my research with this potential sequence? Use a miRNA prediction software to see if its really related to miRNA? Could you guys give me some suggestions? THanks
Samantha
Hi Samantha,
I would first check if the sequence is conserved across species. Almost all miR sequences are highly conserved. To do so you can paste your sequence into Blat search at UCSC http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Or you can search the miR database by sequence at http://microrna.sanger.ac.uk/sequences/search.shtml
I would first check if the sequence is conserved across species. Almost all miR sequences are highly conserved. To do so you can paste your sequence into Blat search at UCSC http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Or you can search the miR database by sequence at http://microrna.sanger.ac.uk/sequences/search.shtml
hi pcrman,
First, thanks for your reply. i tried to search the miR database, but i couldnt find my sequence in the database.
actually, i just have a few more questions. My sequence is an EST clone, about 600bp long. For miRNA, in my case, should whe whole sequence be highly conserved across species, or just a part of the sequence is enough? Another question is even if my sequence is highly conserved across several species, what can I do next? Thank you so much.
Samantha
For miR gene, only the 60-70 nt stem loop is conserved. To be a miR gene, your sequence should be able to form a stem loop structure. You can use miRscan (http://genes.mit.edu/mirscan/) to predict if your sequence is a miR.