Computational definition of sequence motifs governing constitutive exon splicing.
Identifieur interne : 002279 ( PubMed/Checkpoint ); précédent : 002278; suivant : 002280Computational definition of sequence motifs governing constitutive exon splicing.
Auteurs : Xiang H-F Zhang [États-Unis] ; Lawrence A. ChasinSource :
- Genes & development [ 0890-9369 ] ; 2004.
Descripteurs français
- KwdFr :
- Animaux, Cellules cultivées, Données de séquences moléculaires, Exons, Gènes, Humains, I-kappa B Kinase, Introns, Mammifères, Modèles génétiques, Mutation, Protein-Serine-Threonine Kinases (génétique), Régions 5' non traduites, Simulation numérique, Séquence nucléotidique, Séquences régulatrices de l'acide ribonucléique, Transfection, Éléments activateurs (génétique), Éléments silenceurs transcriptionnels, Épissage des ARN.
- MESH :
- génétique : Protein-Serine-Threonine Kinases.
- Animaux, Cellules cultivées, Données de séquences moléculaires, Exons, Gènes, Humains, I-kappa B Kinase, Introns, Mammifères, Modèles génétiques, Mutation, Régions 5' non traduites, Simulation numérique, Séquence nucléotidique, Séquences régulatrices de l'acide ribonucléique, Transfection, Éléments activateurs (génétique), Éléments silenceurs transcriptionnels, Épissage des ARN.
English descriptors
- KwdEn :
- 5' Untranslated Regions, Animals, Base Sequence, Cells, Cultured, Computer Simulation, Enhancer Elements, Genetic, Exons, Genes, Humans, I-kappa B Kinase, Introns, Mammals, Models, Genetic, Molecular Sequence Data, Mutation, Protein-Serine-Threonine Kinases (genetics), RNA Splicing, Regulatory Sequences, Ribonucleic Acid, Silencer Elements, Transcriptional, Transfection.
- MESH :
- chemical , genetics : Protein-Serine-Threonine Kinases.
- chemical : 5' Untranslated Regions, I-kappa B Kinase, Regulatory Sequences, Ribonucleic Acid.
- Animals, Base Sequence, Cells, Cultured, Computer Simulation, Enhancer Elements, Genetic, Exons, Genes, Humans, Introns, Mammals, Models, Genetic, Molecular Sequence Data, Mutation, RNA Splicing, Silencer Elements, Transcriptional, Transfection.
Abstract
We have searched for sequence motifs that contribute to the recognition of human pre-mRNA splice sites by comparing the frequency of 8-mers in internal noncoding exons versus unspliced pseudo exons and 5' untranslated regions (5' untranslated regions [UTRs]) of transcripts of intronless genes. This type of comparison avoids the isolation of sequences that are distinguished by their protein-coding information. We classified sequence families comprising 2069 putative exonic enhancers and 974 putative exonic silencers. Representatives of each class functioned as enhancers or silencers when inserted into a test exon and assayed in transfected mammalian cells. As a class, the enhancer sequencers were more prevalent and the silencer elements less prevalent in all exons compared with introns. A survey of 58 reported exonic splicing mutations showed good agreement between the splicing phenotype and the effect of the mutation on the motifs defined here. The large number of effective sequences implied by these results suggests that sequences that influence splicing may be very abundant in pre-mRNA.
DOI: 10.1101/gad.1195304
PubMed: 15145827
Affiliations:
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This type of comparison avoids the isolation of sequences that are distinguished by their protein-coding information. We classified sequence families comprising 2069 putative exonic enhancers and 974 putative exonic silencers. Representatives of each class functioned as enhancers or silencers when inserted into a test exon and assayed in transfected mammalian cells. As a class, the enhancer sequencers were more prevalent and the silencer elements less prevalent in all exons compared with introns. A survey of 58 reported exonic splicing mutations showed good agreement between the splicing phenotype and the effect of the mutation on the motifs defined here. The large number of effective sequences implied by these results suggests that sequences that influence splicing may be very abundant in pre-mRNA.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15145827</PMID><DateCompleted><Year>2004</Year><Month>07</Month><Day>09</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0890-9369</ISSN><JournalIssue CitedMedium="Print"><Volume>18</Volume><Issue>11</Issue><PubDate><Year>2004</Year><Month>Jun</Month><Day>01</Day></PubDate></JournalIssue><Title>Genes & development</Title><ISOAbbreviation>Genes Dev.</ISOAbbreviation></Journal><ArticleTitle>Computational definition of sequence motifs governing constitutive exon splicing.</ArticleTitle><Pagination><MedlinePgn>1241-50</MedlinePgn></Pagination><Abstract><AbstractText>We have searched for sequence motifs that contribute to the recognition of human pre-mRNA splice sites by comparing the frequency of 8-mers in internal noncoding exons versus unspliced pseudo exons and 5' untranslated regions (5' untranslated regions [UTRs]) of transcripts of intronless genes. This type of comparison avoids the isolation of sequences that are distinguished by their protein-coding information. We classified sequence families comprising 2069 putative exonic enhancers and 974 putative exonic silencers. Representatives of each class functioned as enhancers or silencers when inserted into a test exon and assayed in transfected mammalian cells. As a class, the enhancer sequencers were more prevalent and the silencer elements less prevalent in all exons compared with introns. A survey of 58 reported exonic splicing mutations showed good agreement between the splicing phenotype and the effect of the mutation on the motifs defined here. 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Chasin</name></noCountry><country name="États-Unis"><region name="État de New York"><name sortKey="Zhang, Xiang H F" sort="Zhang, Xiang H F" uniqKey="Zhang X" first="Xiang H-F" last="Zhang">Xiang H-F Zhang</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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