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Keywords {🔍}

introns, retained, pubmed, genes, intron, article, irfinder, samples, gene, data, cell, google, scholar, protein, sequencing, events, reads, found, file, splicing, levels, cas, additional, expression, mrna, nmd, fig, differentiation, rna, genome, retention, enriched, central, cycle, proteins, cells, analysis, output, transcripts, ratio, intronic, number, human, frequently, study, tissue, analyzed, binding, regulation, exons,

Topics {✒️}

r- ratio=\frac{intronic\ abundance}{\left article download pdf nonsense-mediated mrna decay escape nonsense-mediated decay ejc-sr protein nexus post-implantation embryonic development cfx96 real-time system rna-binding protein tia-1 coded direct plug-ins false discovery rate-adjusted splicing regulatory factors nuclear mrna half-life egf-binding arginine esterase nonsense-mediated decay medical research council alternative splicing complexity ribosome-protected mrna fragments post-transcriptionally spliced introns dadi gao ultra-deep sequencing technologies matched mrna-seq samples pre-aligned sequencing data sr proteins auto-regulate rna binding sites privacy choices/manage cookies mammalian nonsense codons discover dna motifs alternative splicing er related subjects reverse-complementary part commencing mammalian gene expression human stem cells alternative splicing program standard paired-end library human genetic research genetically matched hesc functionally related genes excluding multi-mapping reads rna binding proteins rna-binding proteins normal splicing abundance creative commons license gene expression omnibus unix based system rna binding motifs full access rna-seq data sh3 adapter cortactin measuring intron retention william ritchie

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         headline:IRFinder: assessing the impact of intron retention on mammalian gene expression
         description:Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.
         datePublished:2017-03-15T00:00:00Z
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            Intron retention
            Gene regulation
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:IRFinder: assessing the impact of intron retention on mammalian gene expression
      description:Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.
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      dateModified:2017-03-15T00:00:00Z
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         Intron retention
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         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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            type:Organization
            name:University of Sydney
            address:
               name:Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, Australia
               type:PostalAddress
            type:Organization
      name:Alexandra Bomane
      affiliation:
            name:Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS
            address:
               name:Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, Paris, France
               type:PostalAddress
            type:Organization
      name:Bertrand Cosson
      affiliation:
            name:Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS
            address:
               name:Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, Paris, France
               type:PostalAddress
            type:Organization
      name:Eduardo Eyras
      affiliation:
            name:Pompeu Fabra University, UPF
            address:
               name:Pompeu Fabra University, UPF, Barcelona, Spain
               type:PostalAddress
            type:Organization
            name:Catalan Institution for Research and Advanced Studies, ICREA
            address:
               name:Catalan Institution for Research and Advanced Studies, ICREA, Barcelona, Spain
               type:PostalAddress
            type:Organization
      name:John E. J. Rasko
      affiliation:
            name:Gene & Stem Cell Therapy Program, Centenary Institute
            address:
               name:Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, Australia
               type:PostalAddress
            type:Organization
            name:University of Sydney
            address:
               name:Sydney Medical School, University of Sydney, Sydney, Australia
               type:PostalAddress
            type:Organization
            name:Cell and Molecular Therapies, Royal Prince Alfred Hospital
            address:
               name:Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
               type:PostalAddress
            type:Organization
      name:William Ritchie
      url:http://orcid.org/0000-0001-8162-1439
      affiliation:
            name:Centenary Institute
            address:
               name:Bioinformatics Laboratory, Centenary Institute, Camperdown, Australia
               type:PostalAddress
            type:Organization
            name:CNRS, UPR 1142
            address:
               name:CNRS, UPR 1142, Montpellier, France
               type:PostalAddress
            type:Organization
            name:CNRS, UMR 5203
            address:
               name:CNRS, UMR 5203, Montpellier, France
               type:PostalAddress
            type:Organization
      email:[email protected]
PostalAddress:
      name:Bioinformatics Laboratory, Centenary Institute, Camperdown, Australia
      name:Bioinformatics Laboratory, Centenary Institute, Camperdown, Australia
      name:Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, USA
      name:Boston & Harvard Medical School, Boston, USA
      name:Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, Australia
      name:CNRS, UPR 1142, Montpellier, France
      name:Pompeu Fabra University, UPF, Barcelona, Spain
      name:Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, Australia
      name:Sydney Medical School, University of Sydney, Sydney, Australia
      name:Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, Australia
      name:Sydney Medical School, University of Sydney, Sydney, Australia
      name:Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, Australia
      name:Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, Paris, France
      name:Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, Paris, France
      name:Pompeu Fabra University, UPF, Barcelona, Spain
      name:Catalan Institution for Research and Advanced Studies, ICREA, Barcelona, Spain
      name:Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, Australia
      name:Sydney Medical School, University of Sydney, Sydney, Australia
      name:Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
      name:Bioinformatics Laboratory, Centenary Institute, Camperdown, Australia
      name:CNRS, UPR 1142, Montpellier, France
      name:CNRS, UMR 5203, Montpellier, France

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