Computational definition of sequence motifs governing constitutive exon splicing.
Identifieur interne : 003074 ( Main/Exploration ); précédent : 003073; suivant : 003075Computational 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:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 002390
- to stream PubMed, to step Curation: 002390
- to stream PubMed, to step Checkpoint: 002279
- to stream Ncbi, to step Merge: 000279
- to stream Ncbi, to step Curation: 000279
- to stream Ncbi, to step Checkpoint: 000279
- to stream Main, to step Merge: 003106
- to stream Main, to step Curation: 003074
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Computational definition of sequence motifs governing constitutive exon splicing.</title><author><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><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, MC2433, Columbia University, New York, New York 10027, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, MC2433, Columbia University, New York, New York 10027</wicri:regionArea><orgName type="university">Université Columbia</orgName><placeName><settlement type="city">New York</settlement><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Chasin, Lawrence A" sort="Chasin, Lawrence A" uniqKey="Chasin L" first="Lawrence A" last="Chasin">Lawrence A. Chasin</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2004">2004</date><idno type="RBID">pubmed:15145827</idno><idno type="pmid">15145827</idno><idno type="doi">10.1101/gad.1195304</idno><idno type="wicri:Area/PubMed/Corpus">002390</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002390</idno><idno type="wicri:Area/PubMed/Curation">002390</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002390</idno><idno type="wicri:Area/PubMed/Checkpoint">002279</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002279</idno><idno type="wicri:Area/Ncbi/Merge">000279</idno><idno type="wicri:Area/Ncbi/Curation">000279</idno><idno type="wicri:Area/Ncbi/Checkpoint">000279</idno><idno type="wicri:doubleKey">0890-9369:2004:Zhang X:computational:definition:of</idno><idno type="wicri:Area/Main/Merge">003106</idno><idno type="wicri:Area/Main/Curation">003074</idno><idno type="wicri:Area/Main/Exploration">003074</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Computational definition of sequence motifs governing constitutive exon splicing.</title><author><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><affiliation wicri:level="4"><nlm:affiliation>Department of Biological Sciences, MC2433, Columbia University, New York, New York 10027, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, MC2433, Columbia University, New York, New York 10027</wicri:regionArea><orgName type="university">Université Columbia</orgName><placeName><settlement type="city">New York</settlement><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Chasin, Lawrence A" sort="Chasin, Lawrence A" uniqKey="Chasin L" first="Lawrence A" last="Chasin">Lawrence A. Chasin</name></author></analytic><series><title level="j">Genes & development</title><idno type="ISSN">0890-9369</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>5' Untranslated Regions</term><term>Animals</term><term>Base Sequence</term><term>Cells, Cultured</term><term>Computer Simulation</term><term>Enhancer Elements, Genetic</term><term>Exons</term><term>Genes</term><term>Humans</term><term>I-kappa B Kinase</term><term>Introns</term><term>Mammals</term><term>Models, Genetic</term><term>Molecular Sequence Data</term><term>Mutation</term><term>Protein-Serine-Threonine Kinases (genetics)</term><term>RNA Splicing</term><term>Regulatory Sequences, Ribonucleic Acid</term><term>Silencer Elements, Transcriptional</term><term>Transfection</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Cellules cultivées</term><term>Données de séquences moléculaires</term><term>Exons</term><term>Gènes</term><term>Humains</term><term>I-kappa B Kinase</term><term>Introns</term><term>Mammifères</term><term>Modèles génétiques</term><term>Mutation</term><term>Protein-Serine-Threonine Kinases (génétique)</term><term>Régions 5' non traduites</term><term>Simulation numérique</term><term>Séquence nucléotidique</term><term>Séquences régulatrices de l'acide ribonucléique</term><term>Transfection</term><term>Éléments activateurs (génétique)</term><term>Éléments silenceurs transcriptionnels</term><term>Épissage des ARN</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Protein-Serine-Threonine Kinases</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>5' Untranslated Regions</term><term>I-kappa B Kinase</term><term>Regulatory Sequences, Ribonucleic Acid</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protein-Serine-Threonine Kinases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Cells, Cultured</term><term>Computer Simulation</term><term>Enhancer Elements, Genetic</term><term>Exons</term><term>Genes</term><term>Humans</term><term>Introns</term><term>Mammals</term><term>Models, Genetic</term><term>Molecular Sequence Data</term><term>Mutation</term><term>RNA Splicing</term><term>Silencer Elements, Transcriptional</term><term>Transfection</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Cellules cultivées</term><term>Données de séquences moléculaires</term><term>Exons</term><term>Gènes</term><term>Humains</term><term>I-kappa B Kinase</term><term>Introns</term><term>Mammifères</term><term>Modèles génétiques</term><term>Mutation</term><term>Régions 5' non traduites</term><term>Simulation numérique</term><term>Séquence nucléotidique</term><term>Séquences régulatrices de l'acide ribonucléique</term><term>Transfection</term><term>Éléments activateurs (génétique)</term><term>Éléments silenceurs transcriptionnels</term><term>Épissage des ARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>État de New York</li></region><settlement><li>New York</li></settlement><orgName><li>Université Columbia</li></orgName></list><tree><noCountry><name sortKey="Chasin, Lawrence A" sort="Chasin, Lawrence A" uniqKey="Chasin L" first="Lawrence A" last="Chasin">Lawrence A. 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)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 003074 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 003074 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:15145827
|texte= Computational definition of sequence motifs governing constitutive exon splicing.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:15145827" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |