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Nucleic Acids Res. 2011 Jan;39(Database issue):D66-9. doi: 10.1093/nar/gkq990. Epub 2010 Nov 11.

AREsite: a database for the comprehensive investigation of AU-rich elements.

Author information

1
Department of Microbiology and Immunobiology, Institute for Theoretical Chemistry, Max F Perutz Laboratories, University of Vienna, Vienna, Austria. agruber@tbi.univie.ac.at

Abstract

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREs are one of the most prominent cis-acting regulatory elements found in 3'-UTRs of mRNAs. Various ARE-binding proteins that possess RNA stabilizing or destabilizing functions are recruited by sequence-specific motifs. Recent findings suggest an essential role of the structural mRNA context in which these sequence motifs are embedded. AREsite is the first database that allows to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. Moreover, we also provide a detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite.

PMID:
21071424
PMCID:
PMC3013810
DOI:
10.1093/nar/gkq990
[Indexed for MEDLINE]
Free PMC Article

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