title: SpliceAid-F: a database of human splicing factors and their RNA-binding sites.
abstract: A comprehensive knowledge of all the factors involved in splicing, both proteins and RNAs, and of their interaction network is crucial for reaching a better understanding of this process and its functions. A large part of relevant information is buried in the literature or collected in various different databases. By hand-curated screenings of literature and databases, we retrieved experimentally validated data on 71 human RNA-binding splicing regulatory proteins and organized them into a database called 'SpliceAid-F' (http://www.caspur.it/SpliceAidF/). For each splicing factor (SF), the database reports its functional domains, its protein and chemical interactors and its expression data. Furthermore, we collected experimentally validated RNA-SF interactions, including relevant information on the RNA-binding sites, such as the genes where these sites lie, their genomic coordinates, the splicing effects, the experimental procedures used, as well as the corresponding bibliographic references. We also collected information from experiments showing no RNA-SF binding, at least in the assayed conditions. In total, SpliceAid-F contains 4227 interactions, 2590 RNA-binding sites and 1141 'no-binding' sites, including information on cellular contexts and conditions where binding was tested. The data collected in SpliceAid-F can provide significant information to explain an observed splicing pattern as well as the effect of mutations in functional regulatory elements.
authors.affiliation: Department of Biosciences, University of Bari, Bari, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Giulietti
authors.forename: Francesco
authors.initials: F
authors.lastname: Piva
authors.forename: Mattia
authors.initials: M
authors.lastname: D'Antonio
authors.forename: Paolo
authors.initials: P
authors.lastname: D'Onorio De Meo
authors.forename: Daniele
authors.initials: D
authors.lastname: Paoletti
authors.forename: Tiziana
authors.initials: T
authors.lastname: Castrignanò
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: D'Erchia
authors.forename: Ernesto
authors.initials: E
authors.lastname: Picardi
authors.forename: Federico
authors.initials: F
authors.lastname: Zambelli
authors.forename: Giovanni
authors.initials: G
authors.lastname: Principato
authors.forename: Giulio
authors.initials: G
authors.lastname: Pavesi
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
mesh_terms: D001665:Binding Sites; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D017434:Protein Structure, Tertiary; D012322:RNA Precursors / Q000378:metabolism; D012326:RNA Splicing; D012333:RNA, Messenger / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D012322:RNA Precursors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins