Hey Steve thanks for the reply. It turns out that there is a small list of "official" human mirtron genes in the supplementary information of this paper: http://www.sciencedirect.com/science/article/pii/S1097276507006697 although at 2007 it's a bit dated I'd think and it's a very small list at that!
3 answers
I'm not sure if there is a list of known mirtrons in Hsapiens, but our lab collaborated on this paper:
We've got some code up online for the SVM used to predict these mirtrons along with a tutorial on how you might use it (unfortunately MATLAB is required for this one, I think):
http://cbio.mskcc.org/leslielab/mirtrons/
I didn't work on this project, so I unfortunately can't provide much more information than that.
an update on the topic: http://genome.cshlp.org/content/22/9/1634.long
they used 500 publicly available small RNA seq datasets to identify 240 high confidence mirtrons and 241 lower confidence ones in the human genome http://ericlailab.com/mammalian_mirtrons/hg19/index.html
anyway they didn't study the predicted targets of these mirtrons
To find the microRNA in the Introns, I would extract the intronic regions from the UCSC knownGene table. See Exon Coordinates Of Hg19 Genome Download for extracting the exons ( it should be sightly the same thing for the introns ).
Then, I would find the intersection of those introns with the table wgRna ( snoRNA and miRNA annotations )
http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgRna.txt.gz
I think what you are suggesting would return miRNAs which are coded in introns, as far as I know this is different from a mirtron though, which are specifically debranched introns which have length and hairpin structure of a pre-miRNA and are subsequently incorporated into the miRNA biogenesis at the step after Drosha cleavage.
OK, I didn't know what was an mirton until today :-P
OK, I didn't know what is a mirton until today :-P
Log in to answer this question.