SpliceAid-F: a database of human splicing factors and their binding sites
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 assessed data on 71 human RNA-binding splicing regulatory proteins and organized
them into a database called “SpliceAid-F”. For each splicing factor (SF) the database reports its
functional domains and its protein and chemical interactors. 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,
experimental procedures, 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, 2761 RNA binding sites and 1214 no-binding sites, including information on binding and no-binding specificity in different cellular contexts.
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.
How to cite SpliceAidF
Nucleic Acids Res. 2013 Jan 1;41(D1):D125-31. doi: 10.1093/nar/gks997. Epub 2012 Oct 30.
SpliceAid-F: a database of human splicing factors and their RNA-binding sites.
Giulietti M, Piva F, D'Antonio M, D'Onorio De Meo P, Paoletti D, Castrignanò T, D'Erchia AM, Picardi E, Zambelli F, Principato G, Pavesi G, Pesole G.
Data available for download:Factors database (71 entries)
Binding sites database (2761 entries)
Database of sites without binding activities (1214 entries)
|Number of splicing factors||71|
|Number of binding sites:||2761||Number of sites without binding activities:||1214|
|HIV-1 (Human Immunodeficiency virus 1)||76||Chicken||43|
|SV40 (Simian virus 40)||39||HIV-1 (Human Immunodeficiency virus 1)||32|
|Rat||39||BPV-1 (Bovine Papillomavirus 1)||22|
|PV1 (Human Poliovirus 1)||24||PV1 (Human Poliovirus 1)||18|
|BPV-1 (Bovine Papillomavirus 1)||16||D. melanogaster||9|
|HPV-16 (Human Papillomavirus 16)||11||RSV (Rous Sarcoma virus)||9|
|Ad2 (Human Adenovirus C serotype 2)||9||HPV-16 (Human Papillomavirus 16)||7|
|D. melanogaster||8||S. cerevisiae||7|
|HPV-1 (Human Papillomavirus 1)||7||CVB3 (Coxsackievirus B3)||4|
|RSV (Rous Sarcoma virus)||7||SV40 (Simian virus 40)||3|
|S. cerevisiae||6||HPV-1 (Human Papillomavirus 1)||3|
|HCV (Hepatitis C virus)||5||HCV (Hepatitis C virus)||3|
|CVB3 (Coxsackievirus B3)||3||MVM (Minute virus of Mice)||2|
|MHV (Mouse Hepatitis virus)||2||SeV (Sendai virus)||2|
|MVM (Minute virus of Mice)||2||HCV2 (Hepatitis C virus 2)||1|
|SeV (Sendai virus)||2||Ad2 (Human Adenovirus C serotype 2)||1|
|HCV2 (Hepatitis C virus 2)||1|
|VSV (Vesicular Stomatitis Indiana virus)||1|