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RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing.

Cereda, M; Pozzoli, U; Rot, G; Juvan, P; Schweitzer, A; Clark, T; Ule, J; (2014) RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biol , 15 (1) , Article R20. 10.1186/gb-2014-15-1-r20. Green open access

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Abstract

RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. We show that diverse RBPs share basic positional principles, but differ in their propensity to enhance or repress exon inclusion. We assess exons differentially spliced between brain and heart, identifying known and new regulatory motifs, and predict the expression pattern of RBPs that bind these motifs. RNAmotifs is available at https://bitbucket.org/rogrro/rna_motifs.

Type: Article
Title: RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing.
Open access status: An open access version is available from UCL Discovery
DOI: 10.1186/gb-2014-15-1-r20
Publisher version: http:?/dx.doi.org/10.1186/gb-2014-15-1-r20
Language: English
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Brain Sciences > UCL Queen Square Institute of Neurology > Department of Neuromuscular Diseases
URI: https://discovery.ucl.ac.uk/id/eprint/1423429
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