title: uORFdb--a comprehensive literature database on eukaryotic uORF biology.
abstract: Approximately half of all human transcripts contain at least one upstream translational initiation site that precedes the main coding sequence (CDS) and gives rise to an upstream open reading frame (uORF). We generated uORFdb, publicly available at http://cbdm.mdc-berlin.de/tools/uorfdb, to serve as a comprehensive literature database on eukaryotic uORF biology. Upstream ORFs affect downstream translation by interfering with the unrestrained progression of ribosomes across the transcript leader sequence. Although the first uORF-related translational activity was observed >30 years ago, and an increasing number of studies link defective uORF-mediated translational control to the development of human diseases, the features that determine uORF-mediated regulation of downstream translation are not well understood. The uORFdb was manually curated from all uORF-related literature listed at the PubMed database. It categorizes individual publications by a variety of denominators including taxon, gene and type of study. Furthermore, the database can be filtered for multiple structural and functional uORF-related properties to allow convenient and targeted access to the complex field of eukaryotic uORF biology.
authors.affiliation: Max Delbrück Center for Molecular Medicine (MDC), Cell Differentiation and Tumorigenesis, Robert-Rössle-Strasse 10, D-13092 Berlin, Germany, Hematology, Oncology and Tumor Immunology, Helios Klinikum Berlin-Buch, Schwanebecker Chaussee 50, D-13125 Berlin, Germany, Max Delbrück Center for Molecular Medicine (MDC), Computational Biology and Data Mining, Robert-Rössle-Strasse 10, D-13092 Berlin, Germany and Humoldt-University, Department of Biology, Invalidenstrasse 43, D-10115 Berlin, Germany.
authors.forename: Klaus
authors.initials: K
authors.lastname: Wethmar
authors.forename: Adriano
authors.initials: A
authors.lastname: Barbosa-Silva
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
authors.forename: Achim
authors.initials: A
authors.lastname: Leutz
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D030561:Databases, Nucleic Acid; D004194:Disease / Q000235:genetics; D014644:Genetic Variation; D006801:Humans; D020407:Internet; D051379:Mice; D059365:Nonsense Mediated mRNA Decay; D016366:Open Reading Frames; D011401:Promoter Regions, Genetic; D014176:Protein Biosynthesis; D020871:RNA Stability; D012333:RNA, Messenger / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism
chemical_list: D012333:RNA, Messenger