I am not biologist and just work in Bioinformatics field. Does anyone know what is the meaning of conservation in the context of miRNAs and their pairings to mRNAs?


Each of these duplexes has a region called the “seed”, a site located at 5’ part of miRNA (positions 2-7) which is characterized by a strict or almost strict Watson-Crick pairing between miRNA and its target site and shows the best conservation among the miRNA sequence.

(from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3182075/)

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    $\begingroup$ As far as I know this is unknown. Binding sequences for miRNA where empirically found to be more conserved overall (this is actually used by and very important for algorithms to predict miRNA binding sites) than the rest of the transcriptome but the actual reasons behind it are still unclear. For the meaning, well the seed in particular is very conserved which means that this information can be used to better predict where miRNA will bind and therefore which genes they will silence, i.e. mismatches in the seed regions are more heavily penalized than mismatches in non-seed regions. $\endgroup$ – cagliari2005 Jun 27 '15 at 6:08
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    $\begingroup$ What the conservation scores denote is how well is the miRNA binding site conserved between different organisms (orthologs). PicTar uses an HMM based methodology to do that. TargetScan and miRanda also provide conservation scores. I shall give you a detailed answer in a while. $\endgroup$ – WYSIWYG Jun 27 '15 at 6:37

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