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Both RNA-binding proteins (RBPs) and non-coding RNAs (ncRNAs) bind mRNAs in the so-called cis-elements, found primarily in 5′ and 3′ UTRs. These elements can be represented as recurring RNA sequences or secondary structures shared by a number of transcripts and defined by a pattern, to which the trans factors bind to exert a control over the mRNA.
(Dassi and Quattrone 2012) Tuning the engine: an introduction to resources on post-transcriptional regulation of gene expression. RNA Biol.