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.
PMID: 23118479

Data available for download:

Factors database (71 entries)
Binding sites database (2761 entries)
Database of sites without binding activities (1214 entries)
SpliceAid-F statistics (v1.2 11/2014)
Number of splicing factors71
Number of binding sites:2761Number of sites without binding activities:1214
HIV-1 (Human Immunodeficiency virus 1)76Chicken43
Rat39HIV-1 (Human Immunodeficiency virus 1)32
SV40 (Simian virus 40)39BPV-1 (Bovine Papillomavirus 1)22
PV1 (Human Poliovirus 1)24PV1 (Human Poliovirus 1)18
BPV-1 (Bovine Papillomavirus 1)16Rabbit9
HPV-16 (Human Papillomavirus 16)11D. melanogaster9
Ad2 (Human Adenovirus C serotype 2)9RSV (Rous Sarcoma virus)9
Rabbit9S. cerevisiae7
D. melanogaster8HPV-16 (Human Papillomavirus 16)7
HPV-1 (Human Papillomavirus 1)7CVB3 (Coxsackievirus B3)4
RSV (Rous Sarcoma virus)7HCV (Hepatitis C virus)3
S. cerevisiae6SV40 (Simian virus 40)3
HCV (Hepatitis C virus)5HPV-1 (Human Papillomavirus 1)3
CVB3 (Coxsackievirus B3)3MVM (Minute virus of Mice)2
MHV (Mouse Hepatitis virus)2SeV (Sendai virus)2
MVM (Minute virus of Mice)2HCV2 (Hepatitis C virus 2)1
SeV (Sendai virus)2Ad2 (Human Adenovirus C serotype 2)1
VSV (Vesicular Stomatitis Indiana virus)1
HCV2 (Hepatitis C virus 2)1

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