ArticleProceedings of the National Academy of Sciences of the United States of America2011
Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 159 papers.
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Who cites it
159 citing papers in PubMed, 283 citations in OpenAlex.
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- RNA-based discovery and correction of splicing defects caused byMolecular therapy. Nucleic acids · 2026Article
- The exon junction complex coordinates the cotranscriptional inclusion of blocks of neighboring exons.Genes & development · 2026Article
- Cell modeling and rescue of a novel noncoding genetic cause of glycogen storage disease IX.Genetics in medicine open · 2026Article
- RNA Splicing as a Therapeutic Target in Cancer.Annual review of pharmacology and toxicology · 2026Review
- Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions.medRxiv : the preprint server for health sciences · 2025Article
- KATMAP infers splicing factor activity and regulatory targets from knockdown data.Nature biotechnology · 2025Article
- Alternative Splicing Regulation in Metabolic Disorders.Obesity reviews : an official journal of the International Association for the Study of Obesity · 2025Review
- OpenASO: RNA Rescue-designing splice-modulating antisense oligonucleotides through community science.RNA (New York, N.Y.) · 2025Article
- Genetic and functional analyses of CTBP2 in anorexia nervosa and body weight regulation.Molecular psychiatry · 2025Article
- ncRNA Editing: Functional Characterization and Computational Resources.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Pre-mRNA Splicing Modulation by Antisense Oligonucleotides.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Integrating next-generation sequencing and artificial intelligence for the identification and validation of pathogenic variants in colorectal cancer.Frontiers in oncology · 2025Article
- Case Report: Evaluation ofFrontiers in medicine · 2025Article
- In silico splicing analysis of the PMS2 gene: exploring alternative molecular mechanisms in PMS2-associated Lynch syndrome.BMC genomic data · 2024Article
- Splicing-specific transcriptome-wide association uncovers genetic mechanisms for schizophrenia.American journal of human genetics · 2024Article
- Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis.Nature communications · 2024Article
- SpliceAPP: an interactive web server to predict splicing errors arising from human mutations.BMC genomics · 2024Article
99 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
We present an intuitive strategy for predicting the effect of sequence variation on splicing. In contrast to transcriptional elements, splicing elements appear to be strongly position dependent. We demonstrated that exonic binding of the normally intronic splicing factor, U2AF65, inhibits splicing. Reasoning that the positional distribution of a splicing element is a signature of its function, we developed a method for organizing all possible sequence motifs into clusters based on the genomic profile of their positional distribution around splice sites. Binding sites for serine/arginine rich (SR) proteins tended to be exonic whereas heterogeneous ribonucleoprotein (hnRNP) recognition elements were mostly intronic. In addition to the known elements, novel motifs were returned and validated. This method was also predictive of splicing mutations. A mutation in a motif creates a new motif that sometimes has a similar distribution shape to the original motif and sometimes has a different distribution. We created an intraallelic distance measure to capture this property and found that mutations that created large intraallelic distances disrupted splicing in vivo whereas mutations with small distances did not alter splicing. Analyzing the dataset of human disease alleles revealed known splicing mutants to have high intraallelic distances and suggested that 22% of disease alleles that were originally classified as missense mutations may also affect splicing. This category together with mutations in the canonical splicing signals suggest that approximately one third of all disease-causing mutations alter pre-mRNA splicing.
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Registered trials
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