Question: Identifying miRNA, RNA-binding sites in UTRs
gravatar for EVR
2.4 years ago by
EVR570 wrote:

HI all,

I have UTRs regions of many transcripts of a non-model organism of my interest and I would like to identify the miRNA, RNA binding sites and post transcriptional regulatory elements in the UTRs. Can you suggest a database where can I download the target sequences.

Thanks in advance

utrs rna-binding protein minra • 1.3k views
ADD COMMENTlink modified 2.4 years ago by Russ460 • written 2.4 years ago by EVR570

Just out of curiosity, is it a plant or an animal? The type of organism makes a world of a difference, remember that searching for plant microRNAs is rather easy.

Also, what I get from your question is that you are trying to find microRNAs based on UTRs?

ADD REPLYlink written 2.4 years ago by biofalconch440
gravatar for Kevin Blighe
2.4 years ago by
Kevin Blighe56k
Kevin Blighe56k wrote:

For validated (or predicted) interactions, I would recommend miRWalk2.0 for this. This allows you to search for predicted or validated (via CLASH) mir-to-gene interactions. It has data for gene promotors, 5'UTR, CDS, and 3'UTR.

Alternatively, if you have a list of mirs and want to find in silico predicted gene targets, then miRNAtap is useful and is on Bioconductor. It uses information from 4 databases in order to increase confidence in predictions:

  • PicTar
  • TargetScan
  • miRanda


Finally, if you want to perform functional enrichment via GO and KEGG for each mir's predicted targets (and, thus, each mir), you can again use miRNAtap for GO (which ultimately uses topGO), and KEGGprofile for KEGG pathways.


ADD COMMENTlink modified 19 months ago • written 2.4 years ago by Kevin Blighe56k
gravatar for Russ
2.4 years ago by
Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
Russ460 wrote:

For non-model organisms information can be sparse. miRBase has miRNA sequences from a wide variety of species. You can try combining the sequences obtained from miRBase with TargetScan and miRanda to help predict miRNA binding sites in non-model organisms.

ADD COMMENTlink written 2.4 years ago by Russ460
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