ArticleJournal of molecular evolution2006
Synonymous SNPs provide evidence for selective constraint on human exonic splicing enhancers.
Article in Journal of molecular evolution, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Selection on synonymous sites: the unwanted transcript hypothesis.Nature reviews. Genetics · 2024Review
- Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption.Nucleic acids research · 2021Article
- Selection Shapes Synonymous Stop Codon Use in Mammals.Journal of molecular evolution · 2020Article
- Mutational bias and the protein code shape the evolution of splicing enhancers.Nature communications · 2020Article
- A Depletion of Stop Codons in lincRNA is Owing to Transfer of Selective Constraint from Coding Sequences.Molecular biology and evolution · 2020Article
- Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices.G3 (Bethesda, Md.) · 2018Article
- Exonic splice regulation imposes strong selection at synonymous sites.Genome research · 2018Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- Depletion of somatic mutations in splicing-associated sequences in cancer genomes.Genome biology · 2017Article
- Analysis of Newly Identified and Rare Synonymous Genetic Variants in the RET Gene in Patients with Medullary Thyroid Carcinoma in Polish Population.Endocrine pathology · 2017Article
- Estimating the prevalence of functional exonic splice regulatory information.Human genetics · 2017Review
- Both Maintenance and Avoidance of RNA-Binding Protein Interactions Constrain Coding Sequence Evolution.Molecular biology and evolution · 2017Article
- DNA sequence diversity and the efficiency of natural selection in animal mitochondrial DNA.Heredity · 2017Article
- Purifying Selection on Exonic Splice Enhancers in Intronless Genes.Molecular biology and evolution · 2016Article
- Determinants of the Usage of Splice-Associated cis-Motifs Predict the Distribution of Human Pathogenic SNPs.Molecular biology and evolution · 2016Article
- The functional relevance of somatic synonymous mutations in melanoma and other cancers.Pigment cell & melanoma research · 2015Review
- Why Selection Might Be Stronger When Populations Are Small: Intron Size and Density Predict within and between-Species Usage of Exonic Splice Associated cis-Motifs.Molecular biology and evolution · 2015Article
- Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana.Molecular ecology · 2015Article
- Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry.BMC evolutionary biology · 2015Article
- Identification of common genetic variants controlling transcript isoform variation in human whole blood.Nature genetics · 2015Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The human SNP database was used to detect selection on 238 hexamers previously identified as exonic splicing enhancers (ESEs). We compared the distribution of the 238 putative ESEs in biallelic and triallelic SNPs within five different functional categories of the SNP database: synonymous, nonsynonymous, introns, UTRs, and nongenic SNPs. Since true ESEs do not function outside of exons, SNPs that disrupt ESE motifs were expected to be more common in nonexonic portions of the genome. Our results supported this expectation: ESEs were least prevalent within synonymous SNPs and most common in nongenic SNPs. There were approximately 11% fewer ESEs within synonymous biallelic SNPs than expected under no selective constraint. We also compared the frequency of neutral SNPs, those where neither allele was an ESE, with deleterious SNPs, those where one or more alleles was an ESE, across the five different functional classes of SNPs. In comparison with the other functional classes of SNPs, synonymous SNPs contained an excess of neutral variants (+1.64% and +6.04% for biallelic and triallelic SNPs, respectively) and a dearth of deleterious variants (-13.11% and -52.39% for biallelic and triallelic SNPs, respectively). The observed patterns were consistent with purifying selection on the 238 hexamers to maintain their function as ESEs. However, in contrast to previous work, we did not find evidence for selection to maintain ESE function at nonsynonymous SNPs because selection at the protein level probably obscured any difference at the level of ESE function.
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