Find Mirna Sequences

Question

[esmaeel]

Greeting

I want to study some features of human miRNAs. I need more lengths at 5' & 3' ends for each miRNA concerning the data provided by the miRBasewww.mirbase.org). For example for hsa-mir-6723 the miRBase has provided followed sequence: 5'-AUGCAUCGGGAUAGUCCGAGUAACGUCGGGGCAUUCCGGAUAGGCCGAGAAAGUGUUGUGGGAAGAAAGUUAGAUUUACGCCGAUGAAU-3' As you may know this is called "pre-miRNA" which after some splicing, it produces functional miRNA which is called mature miRNA (From 11-32). I want 100 nucleotides more in upstream and downstream of this pre-miRNA. By use of this miRNA's coordination ,chr1: 567705-567793 [-], and use of the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) I got its DNA sequences (by add 100 nucleotides more in upstream and downstream). Finally I replaced its DNA nucleotide symbols by RNA symbols simply for further analysis. I'm not sure about the accuracy of this method and I'm going to do this for hundreds of miRNAs. Would you please give me some kind advice.

Thanks in advance; Esmaeel

Answer 1

[Richard Smith-Unna]

Your method sounds fine, although I would do this using Ensembl BioMart, simply because the feature is already built in, as follows:

1. Choose homo sapiens dataset
2. Set your list of gene IDs as the filter
3. Choose sequences: upstream flank and downstream flank as attributes.

You can do it either programmatically or using the web interface.

Answer 2

[Matt LaFave]

If you want to stick with the UCSC route, it sounds like the Table Browser should be able to get what you're looking for. My suggestion would be to upload the positions (and orientations) of your miRNAs of interest as a BED file (via "manage custom tracks"), and use the Table Browser to fetch the sequence of the miRNAs and the flanking 100 bp, as you did before.