• AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements

    • Jörg Fallmann
      Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna
    • Vitaly Sedlyarov
      Centre for Molecular Biology, University of Vienna
    • Andrea Tanzer
      Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna
    • Pavel Kovarik
      Centre for Molecular Biology, University of Vienna
    • Ivo L. Hofacker
      Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna
  • 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

  • PDF

  • http://phaidra.univie.ac.at/o:930760

  • Article

  • Published Version

  • 2015

  • 44

  • D1

  • Oxford University Press (OUP)

  • English

  • Open access

  • CC BY Attribution 4.0 International
    © The Author(s) 2015

  • 323500 – Austrian Science Fund (FWF)

  • SFB F43 – Austrian Science Fund (FWF)

  • 0305-1048