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Atypical RNAs in the coelacanth transcriptome

Authors

  • Anne Nitsche,

    1. Department of Computer Science, Bioinformatics Group, University of Leipzig, Leipzig, Germany
    2. Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
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  • Gero Doose,

    1. Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    2. LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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  • Hakim Tafer,

    1. Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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  • Mark Robinson,

    1. Benaroya Research Institute at Virginia Mason, Seattle, Washington
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  • Nil Ratan Saha,

    1. Benaroya Research Institute at Virginia Mason, Seattle, Washington
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  • Marco Gerdol,

    1. Department of Life Sciences, University of Trieste, Trieste, Italy
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  • Adriana Canapa,

    1. Department of Life and Environmental Sciences Polytechnic, University of Marche, Ancona, Italy
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  • Steve Hoffmann,

    1. Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    2. LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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  • Chris T. Amemiya,

    1. Benaroya Research Institute at Virginia Mason, Seattle, Washington
    2. Department of Biology, University of Washington, Seattle, Washington
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  • Peter F. Stadler

    Corresponding author
    1. Department of Computer Science, Bioinformatics Group, University of Leipzig, Leipzig, Germany
    2. Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
    3. LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
    4. Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
    5. RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Leipzig, Germany
    6. Department of Theoretical Chemistry, University of Vienna, Wien, Austria
    7. Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
    8. Santa Fe Institute, Santa Fe, New Mexico
    • Correspondence to: Peter F. Stadler, Department of Computer Science, Bioinformatics Group, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany. E-mail: studla@bioinf.uni-leipzig.de

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  • Anne Nitsche and Gero Doose are joint first authors.
  • Conflicts of interest: None.

ABSTRACT

Circular and apparently trans-spliced RNAs have recently been reported as abundant types of transcripts in mammalian transcriptome data. Both types of non-colinear RNAs are also abundant in RNA-seq of different tissue from both the African and the Indonesian coelacanth. We observe more than 8,000 lincRNAs with normal gene structure and several thousands of circularized and trans-spliced products, showing that such atypical RNAs form a substantial contribution to the transcriptome. Surprisingly, the majority of the circularizing and trans-connecting splice junctions are unique to atypical forms, that is, are not used in normal isoforms. J. Exp. Zool. (Mol. Dev. Evol.) 322B: 342–351, 2014. © 2013 Wiley Periodicals, Inc.

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