title: AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.
abstract: AREsite2 represents an update for AREsite, an on-line resource for the investigation of AU-rich elements (ARE) in human and mouse mRNA 3'UTR sequences. The new updated and enhanced version allows detailed investigation of AU, GU and U-rich elements (ARE, GRE, URE) in the transcriptome of Homo sapiens, Mus musculus, Danio rerio, Caenorhabditis elegans and Drosophila melanogaster. It contains information on genomic location, genic context, RNA secondary structure context and conservation of annotated motifs. Improvements include annotation of motifs not only in 3'UTRs but in the whole gene body including introns, additional genomes, and locally stable secondary structures from genome wide scans. Furthermore, we include data from CLIP-Seq experiments in order to highlight motifs with validated protein interaction. Additionally, we provide a REST interface for experienced users to interact with the database in a semi-automated manner. The database is publicly available at: http://rna.tbi.univie.ac.at/AREsite.
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria.
authors.forename: Jörg
authors.identifier: http://orcid.org/0000-0002-4573-9939
authors.initials: J
authors.lastname: Fallmann
authors.affiliation: Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
authors.forename: Vitaly
authors.identifier: http://orcid.org/0000-0002-9872-3535
authors.initials: V
authors.lastname: Sedlyarov
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria at@tbi.univie.ac.at.
authors.forename: Andrea
authors.initials: A
authors.lastname: Tanzer
authors.affiliation: Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
authors.forename: Pavel
authors.identifier: http://orcid.org/0000-0003-2956-0944
authors.initials: P
authors.lastname: Kovarik
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, A-1090 Vienna, Austria Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.
authors.forename: Ivo L
authors.identifier: http://orcid.org/0000-0001-7132-0800
authors.initials: IL
authors.lastname: Hofacker
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D030561:Databases, Nucleic Acid; D023281:Genomics; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*
chemical_list: D020413:3' Untranslated Regions; D012313:RNA