[BioC] difference between "hsa-miR-xxx" and "hsa-miR-xxx*"

[Peter Robinson]

mauede at alice.it wrote:
> I'd like to figure out the difference between validated miRNAs whose identifiers only differ by a "*".

See the following from miRbase 
(http://www.mirbase.org/help/nomenclature.shtml):

When the relative abundancies clearly indicate which is the 
predominantly expressed miRNA, the mature sequences are assigned names 
of the form miR-56 (the predominant product) and miR-56* (from the 
opposite arm of the precursor).


Note that the targets of the *-version are generally different from that 
of the predominant product.

-Peter



> 
> I downloaded the miRNA  datasets "hsSeqs" and "hsTargets" and noticed  that none of the miRNA identifiers
>  in dataset "hsSeqs" contains the character "*"  whereas many miRNA identifiers in dataset  "hsTargets" end with
>  the character "*". I checked a couple of them and found out that the set of Ensembl-Transcript_Identifiers for 
> "hsa-miR-18a" and the set of Ensembl-Transcript_Identifiers for "hsa-miR-18a*" are disjoined.
> Therefore "hsa-miR-18a"  and  "hsa-miR-18a*" seem to be two different entities. I wonder whether 
>   "hsa-miR-18a"  and  "hsa-miR-18a*" share the same sequence even if apparently they bind to different
> gene transcripts.  
> 
> My naive question is: 
> how can I find the sequence of those miRNAs whose identifier ends with a "*" given that none of the miRNA identifiers in dataset "hsSeqs" contain a "*" ?
> In short, I kind of realized that  "hsa-miR-xxx*"  is an evolution of  "hsa-miR-xxx". 
> But when  it comes to dig out the 3UTR sequences of the relative targets which one of the two versions ( "hsa-miR-xxx"  or  "hsa-miR-xxx*" ) shall I ascribe them to ?
> 
> Thank you in advance for your attention.
> Maura 
> 
> 
> 
> tutti i telefonini TIM!
> 
> 
> 
> 
> 
> tutti i telefonini TIM!
> 
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-- 
Dr. med. Peter N. Robinson, MSc.
Institut für Medizinische Genetik
Universitätsklinikum Charite
Humboldt-Universität
Augustenburger Platz 1
13353 Berlin
Germany
voice: 49-30-450569124
fax:   49-30-450569915
email: peter.robinson at charite.de
http://compbio.charite.de/
http://www.human-phenotype-ontology.org