AREsite: a database for the comprehensive investigation of AU-rich elements
Open Access
- 11 November 2010
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 39 (Databae), D66-D69
- https://doi.org/10.1093/nar/gkq990
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.Keywords
This publication has 23 references indexed in Scilit:
- Deletion of the RNA-binding proteins ZFP36L1 and ZFP36L2 leads to perturbed thymic development and T lymphoblastic leukemiaNature Immunology, 2010
- Essential role of the RNA-binding protein HuR in progenitor cell survival in miceJCI Insight, 2009
- The UCSC Genome Browser database: update 2010Nucleic Acids Research, 2009
- The RNA-Binding Protein Elavl1/HuR Is Essential for Placental Branching Morphogenesis and Embryonic DevelopmentMolecular and Cellular Biology, 2009
- The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory moleculesNature Immunology, 2009
- Gene expression module-based chemical function similarity searchNucleic Acids Research, 2008
- Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processesProceedings of the National Academy of Sciences of the United States of America, 2008
- ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouseNucleic Acids Research, 2007
- Endotoxic shock inAUF1knockout mice mediated by failure to degrade proinflammatory cytokine mRNAsGenes & Development, 2006
- WebLogo: A Sequence Logo Generator: Figure 1Genome Research, 2004