ArticleNucleic acids research2005
Biased exon/intron distribution of cryptic and de novo 3' splice sites.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU.European journal of human genetics : EJHG · 2019Trial
- ThreeFrontiers in immunology · 2026Article
- Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone.HGG advances · 2022Article
- Genome-wide identification of exon extension/shrinkage events induced by splice-site-creating mutations.RNA biology · 2022Article
- Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites.Cellular and molecular life sciences : CMLS · 2021Article
- Restriction of an intron size en route to endothermy.Nucleic acids research · 2021Article
- Splicing of long non-coding RNAs primarily depends on polypyrimidine tract and 5' splice-site sequences due to weak interactions with SR proteins.Nucleic acids research · 2019Article
- Predicting gene structure changes resulting from genetic variants via exon definition features.Bioinformatics (Oxford, England) · 2018Article
- Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes.Nature communications · 2018Article
- An intronic mutation in Chd7 creates a cryptic splice site, causing aberrant splicing in a mouse model of CHARGE syndrome.Scientific reports · 2018Article
- Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons.Nucleic acids research · 2017Article
- Spliceosomal gene mutations in myelodysplasia: molecular links to clonal abnormalities of hematopoiesis.Genes & development · 2016Review
- Identification of U2AF(35)-dependent exons by RNA-Seq reveals a link between 3' splice-site organization and activity of U2AF-related proteins.Nucleic acids research · 2015Article
- Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers.PLoS computational biology · 2015Article
- Trafficking protein particle complex 6A delta (TRAPPC6AΔ) is an extracellular plaque-forming protein in the brain.Oncotarget · 2015Article
- A novel mutation in the β-spectrin gene causes the activation of a cryptic 5'-splice site and the creation of a de novo 3'-splice site.Human genome variation · 2015Article
- Compensatory signals associated with the activation of human GC 5' splice sites.Nucleic acids research · 2011Article
- Identification of a MIP mutation that activates a cryptic acceptor splice site in the 3' untranslated region.Molecular vision · 2010Article
- Dual effect of a single nucleotide polymorphism in the first intron of the porcine secreted phosphoprotein 1 gene: allele-specific binding of C/EBP beta and activation of aberrant splicing.BMC molecular biology · 2009Article
- A single-base substitution within an intronic repetitive element causes dominant retinitis pigmentosa with reduced penetrance.Human mutation · 2009Article
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3 authors.
Funding
Abstract
We compiled sequences of previously published aberrant 3' splice sites (3'ss) that were generated by mutations in human disease genes. Cryptic 3'ss, defined here as those resulting from a mutation of the 3'YAG consensus, were more frequent in exons than in introns. They clustered in approximately 20 nt region adjacent to authentic 3'ss, suggesting that their under-representation in introns is due to a depletion of AG dinucleotides in the polypyrimidine tract (PPT). In contrast, most aberrant 3'ss that were induced by mutations outside the 3'YAG consensus (designated 'de novo') were in introns. The activation of intronic de novo 3'ss was largely due to AG-creating mutations in the PPT. In contrast, exonic de novo 3'ss were more often induced by mutations improving the PPT, branchpoint sequence (BPS) or distant auxiliary signals, rather than by direct AG creation. The Shapiro-Senapathy matrix scores had a good prognostic value for cryptic, but not de novo 3'ss. Finally, AG-creating mutations in the PPT that produced aberrant 3'ss upstream of the predicted BPS in vivo shared a similar 'BPS-new AG' distance. Reduction of this distance and/or the strength of the new AG PPT in splicing reporter pre-mRNAs improved utilization of authentic 3'ss, suggesting that AG-creating mutations that are located closer to the BPS and are preceded by weaker PPT may result in less severe splicing defects.
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