SpliceAid 2: a database of human splicing factors expression data and RNA target motifs
Open accessAbstract
Splicing is the most frequently altered biological process by mutations within gene regions. Information for splicing is recognized by several factors that bind pre-mRNA sequence and, through coordinated interaction, yield mature transcripts. Some in silico methods have been developed to predict if a mutation leads to aberrant splicing patterns. We previously created SpliceAid tool that is able to minimize false positive predictions because it adopts strictly experimental RNA target motifs bound by splicing proteins in humans. In order to improve prediction accuracy and better understand the splicing outcome, the tissue specificity of each splicing regulatory factor has to be taken into account. Here, we have developed SpliceAid 2 by adding the expression data related to the splicing factors extracted from the main proteomic and transcriptomic databases, true 5' and 3' splice sites, polypyrimidine tracts, and branch point sequences. The new version collects 2,220 target sites of 62 human splicing proteins and their expression data in 320 tissues per cell. SpliceAid 2 can be useful to foresee the splicing pattern alteration, to guide the identification of the molecular effect due to the mutations and to understand the tissue-specific alternative splicing. SpliceAid 2 is freely accessible at www.introni.it/spliceaid.html.
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Binding sites for several splice factors, including YB-1, SRp20, Sam68, SLM2, SRp40, and multiple hnRNPs, are predicted near the NOCIVA junction site.
“binding sites for many splice factors, including YB-1, SRp20, Sam68, SLM2, SRp40, and multiple hnRNPs (including hnRNP K), were predicted in the near vicinity of the junction site by SpliceAid 2 (30) and SFmap (version 1.8; ref. 31; Fig. 1C).”
From Discovery of a Novel CIP2A Variant (NOCIVA) with Clinical Relevance in Predicting TKI Resistance in Myeloid Leukemias (2021) · cites this paper as [30]
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- Authors
- Piva, F., Giulietti, M., Burini, A. B., & Principato, G.
- Affiliations
- Marche Polytechnic University (IT)
- Corresponding author
- Piva, Francesco
- Venue
- Human Mutation
- Publisher
- Hindawi Limited
- Published
- 2011-10-17
- Volume
- 33
- Issue
- 1
- Pages
- 81-85
- ISSN
- 1059-7794 (ISSN-L)
- OpenAlex
- W2061657172
- Cited by
- 256
- References
- 42
- Citations by year
- 2026: 7 · 2025: 15 · 2024: 18 · 2023: 11 · 2022: 18 · 2021: 36 · 2020: 41 · 2019: 32 · 2018: 16 · 2017: 21 · 2016: 7 · 2015: 11 · 2014: 10 · 2013: 7 · 2012: 6
- FWCI
- 2.98
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- Università Politecnica delle Marche (Università Politecnica delle Marche) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- splicing factors, alternative splicing, tissue-specific gene expression, polypyrimidine tract, pre-mRNA splicing, mutation effect prediction
- MeSH terms
- Exons, Humans, Introns, Mutation, Organ Specificity, RNA Precursors, RNA Splicing, Software, Alternative Splicing, RNA Splice Sites, Genomics, Databases, Genetic, Nucleotide Motifs
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