AREsite: a database for the comprehensive investigation of AU-rich elements.
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.
Department of Microbiology and Immunobiology, Institute for Theoretical Chemistry, Max F Perutz Laboratories, University of Vienna, Vienna, Austria. agruber@tbi.univie.ac.at
Andreas R
AR
Gruber
Jörg
J
Fallmann
Franz
F
Kratochvill
Pavel
P
Kovarik
Ivo L
IL
Hofacker
D020413:3' Untranslated Regions; D000225:Adenine / Q000032:analysis*; D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D023281:Genomics; D006801:Humans; D051379:Mice; D016601:RNA-Binding Proteins / Q000378:metabolism; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D014498:Uracil / Q000032:analysis*
D020413:3' Untranslated Regions; D016601:RNA-Binding Proteins; D014498:Uracil; D000225:Adenine