ArticleNucleic acids research2006
Aberrant 3' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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54 citing papers in PubMed, 204 citations in OpenAlex.
- Control of 3' splice site selection inRNA (New York, N.Y.) · 2025Article
- Exonic splicing code and coordination of divalent metals in proteins.Nucleic acids research · 2024Article
- Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing.Human mutation · 2022Article
- Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone.HGG advances · 2022Article
- Review
- Interpretation of BRCA2 Splicing Variants: A Case Series of Challenging Variant Interpretations and the Importance of Functional RNA Analysis.Familial cancer · 2022Article
- Evidence for the loss and recovery of SLAMF9 during human evolution: implications on Dollo's law.Immunogenetics · 2021Article
- Transposon clusters as substrates for aberrant splice-site activation.RNA biology · 2021Article
- Article
- AG-exclusion zone revisited: Lessons to learn from 91 intronic NF1 3' splice site mutations outside the canonical AG-dinucleotides.Human mutation · 2020Article
- Insights into the pathophysiology of DFNA10 hearing loss associated with novel EYA4 variants.Scientific reports · 2020Article
- Variation benchmark datasets: update, criteria, quality and applications.Database : the journal of biological databases and curation · 2020Article
- Deep-intronic variants in CNGB3 cause achromatopsia by pseudoexon activation.Human mutation · 2020Article
- A novel CHD7 variant disrupting acceptor splice site in a patient with mild features of CHARGE syndrome: a case report.BMC medical genetics · 2019Article
- Diagnosis, Phenotype, and Molecular Genetics of Congenital Analbuminemia.Frontiers in genetics · 2019Review
- PUF60-activated exons uncover altered 3' splice-site selection by germline missense mutations in a single RRM.Nucleic acids research · 2018Article
- Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes.Nature communications · 2018Article
- Reccurrent F8 Intronic Deletion Found in Mild Hemophilia A Causes Alu Exonization.American journal of human genetics · 2018Article
- CHARGE syndrome: a recurrent hotspot of mutations in CHD7 IVS25 analyzed by bioinformatic tools and minigene assays.European journal of human genetics : EJHG · 2018Article
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1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The frequency distribution of mutation-induced aberrant 3' splice sites (3'ss) in exons and introns is more complex than for 5' splice sites, largely owing to sequence constraints upstream of intron/exon boundaries. As a result, prediction of their localization remains a challenging task. Here, nucleotide sequences of previously reported 218 aberrant 3'ss activated by disease-causing mutations in 131 human genes were compared with their authentic counterparts using currently available splice site prediction tools. Each tested algorithm distinguished authentic 3'ss from cryptic sites more effectively than from de novo sites. The best discrimination between aberrant and authentic 3'ss was achieved by the maximum entropy model. Almost one half of aberrant 3'ss was activated by AG-creating mutations and approximately 95% of the newly created AGs were selected in vivo. The overall nucleotide structure upstream of aberrant 3'ss was characterized by higher purine content than for authentic sites, particularly in position -3, that may be compensated by more stringent requirements for positive and negative nucleotide signatures centred around position -11. A newly developed online database of aberrant 3'ss will facilitate identification of splicing mutations in a gene or phenotype of interest and future optimization of splice site prediction tools.
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