Synonymous SNPs Provide Evidence for Selective Constraint on Human Exonic Splicing Enhancers

No abstract is available for this paper.

• Publication year

  2005

• Venue

  Journal of Molecular Evolution

• Publication date

  Unknown publication date

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1007/s00239-005-0055-xPMID 16320116
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Large-scale Proteomic Analysis of the Human Spliceosome References

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• Linking C5 Deficiency to an Exonic Splicing Enhancer Mutation

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• Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers

  2004influential reference
• Finishing the euchromatic sequence of the human genome

  2004cited by this paper
• Finishing the euchromatic sequence of the human genome

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• A computational and experimental approach toward a priori identification of alternatively spliced exons.

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• The role of common single‐nucleotide polymorphisms on exon 9 and exon 12 skipping in nonmutated CFTR Alleles

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• How did alternative splicing evolve?

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• Variation in sequence and organization of splicing regulatory elements in vertebrate genes.

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• Sequence information for the splicing of human pre-mRNA identified by support vector machine classification.

  2003cited by this paper
• Sequence divergence, functional constraint, and selection in protein evolution.

  2003cited by this paper
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• Listening to silence and understanding nonsense: exonic mutations that affect splicing

  2002influential reference
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• BRCA2 T2722R is a deleterious allele that causes exon skipping.

  2002cited by this paper
• A question of size: the eukaryotic proteome and the problems in defining it.

  2002cited by this paper
• Large-scale proteomic analysis of the human spliceosome.

  2002cited by this paper
• Alternative pre-mRNA splicing and proteome expansion in metazoans

  2002cited by this paper
• Distribution and characterization of regulatory elements in the human genome.

  2002cited by this paper
• Positive and negative selection on the human genome.

  2001influential reference
• Predicting deleterious amino acid substitutions.

  2001cited by this paper
• Alternative splicing: increasing diversity in the proteomic world.

  2001influential reference
• Sorting out the complexity of SR protein functions.

  2000cited by this paper
• Exonic splicing enhancers: mechanism of action, diversity and role in human genetic diseases.

  2000cited by this paper
• Multiple Splicing Defects in an Intronic False Exon

  2000cited by this paper
• Towards a structural basis of human non-synonymous single nucleotide polymorphisms.

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• Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins.

  1998cited by this paper
• Mechanical devices of the spliceosome: motors, clocks, springs, and things.

  1998cited by this paper
• Mechanical Devices of the Spliceosome: Review Motors, Clocks, Springs, and Things

  1998cited by this paper
• The regulation of splice-site selection, and its role in human disease.

  1997influential reference
• Disruption of the splicing enhancer sequence within exon 27 of the dystrophin gene by a nonsense mutation induces partial skipping of the exon and is responsible for Becker muscular dystrophy.

  1997cited by this paper
• Exon Recognition in Vertebrate Splicing (*)

  1995cited by this paper
• The effect of deleterious mutations on neutral molecular variation.

  1993cited by this paper
• In vivo recognition of a vertebrate mini-exon as an exon-intron-exon unit

  1993cited by this paper
• Biometry: The Principles and Practice of Statistics in Biological Research

  1969cited by this paper
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  year unknowninfluential reference
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  2018cites this paper
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  2018cites this paper
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  2018cites this paper
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  2017cites this paper
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  2017cites this paper
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  2016cites this paper
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  2016cites this paper
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  2015influential citation
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  2015cites this paper
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  2015influential citation
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• Cross-Species Characterisation of Alternative Splicing Patterns

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• Common Genetic Variation in KCNH 2 Is Associated With QT Interval Duration The Framingham Heart Study

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• How do synonymous mutations affect fitness?

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• Relating alternative splicing to proteome complexity and genome evolution.

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• Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers.

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• Differentiated evolutionary rates in alternative exons and the implications for splicing regulation

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• The expanding transcriptome: the genome as the ‘Book of Sand’

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• Hearing silence: non-neutral evolution at synonymous sites in mammals

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• Preliminary Assessment of the Impact of MicroRNA-Mediated Regulation on Coding Sequence Evolution in Mammals

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• Regions of extreme synonymous codon selection in mammalian genes

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• Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes

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