I'd like to figure out the difference between validated miRNAs whose identifiers only differ by a "*". 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! [[alternative HTML version deleted]]

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! > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Dr. med. Peter N. Robinson, MSc. Institut f?r Medizinische Genetik Universit?tsklinikum Charite Humboldt-Universit?t 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