[Genome] UCSC table for both 5p and 3p miRNAs?

[Anjuska Kyllönen]

Hello,

I can find only one table (sno/miRNA) for microRNAs and I have used it
for looking at miRNA expression in my NGS data. However for my
research it is critical to get the expression differences between 5p
and 3p miRNAs. What table should I use?

Thank you in advance,
Anjuska Kyll��nen

--
B.Sc. Anjuska Kyll��nen
University of Helsinki
Department of Biosciences, Genetics
Finland
Phone: +358405930986
Email: anjuska....@helsinki.fi

[Greg Roe]

Hi Anjuska,

Sorry for the delayed reply...

One of our engineers had these comments:
" In the snoMiRna (a.k.a. wgRna) table, we have some pre-miRNAs (don't
be confused by the fact that the type column says that they're miRNAs.
miRNAs are actually the mature miRNAs chopped out of pre-miRNAs, and are
approximately 22 nucleotides in length. The 'miRNAs' in the wgRna table
are 138 nts in length). FWIW, this table is a few years old now. Given
the rate at which miRNA data is accumulating, that makes it "old".

To my knowledge, we don't have any tracks of mature miRNAs.

There are also /some/ pre-miRNAs in UCSC Genes, via Rfam. The way to
spot them is that in the kgXref table, rfamAcc is not "" and geneSymbol
matches 'Mir*'.

So unfortunately, we don't have a direct way to distinguish 3' and 5'
miRNAs. The best we can do is the pre-miRNAs that they came from.

Alternatively, the user could download the miRNA coordinate data from
miRBase ( http://www.mirbase.org/ftp.shtml) and load it as a custom
track. The coordinates are in GFF3 format, so we should be able to read
them. The miRBase coordinate data contains both pre-miRNAs and mature
miRNAs, but they're easily distinguished by the contents of the type field."

Please let us know if you have any additional questions or need help
with anything suggested above: gen...@soe.ucsc.edu

-
Greg Roe
UCSC Genome Bioinformatics Group