| U7 snRNAs： A Computational Survey |
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| 作者单位： | Mania Marz（Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig D-04107, Germany） ;
Axel Mosig（Departraent of Combinatorics and Geometry, CAS/MPG Partner Institute for Computational Biology, Shang-hai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China;Max Planck Institute for Mathematics in the Sciences, Leipzig D-04103, Germany） ;
B(a)rbel M.R. Stadler（Max Planck Institute for Mathematics in the Sciences, Leipzig D-04103, Germany） ;
Peter F. Stadler（Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig D-04107, Germany;Interdisciplinary Center for Bioin-formatics, University of Leipzig, Leipzig D-04107, Germany;Fraunhofer Institute for Cell Therapy and Im- munology, Leipzig D-04103, Germany;Department of Theoretical Chemistry, University of Vienna, ViennaA-1090, Austria;Santa Fe Institute, Santa Fe, NM 87501, USA） ; |
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| 摘 要： | U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for func- tional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase Ⅱ. Based on the results of this search, we discuss the high variability of U7 snRNAs in both se- quence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short se- quence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database.
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| 关 键 词： | U7 snRNA 非编码RNA RNA分子构造 进化过程 |
U7 snRNAs: A Computational Survey |
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| Authors: | Mania Marz Axel Mosig Brbel MR Stadler Peter F Stadler |
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| Institution: | [1]Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig D-04107, Germany [2]Department of Combinatorics and Geometry, CAS/MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China [3]Max Planck Institute for Mathematics in the Sciences, Leipzig D-04103, Germany [4]Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig D-04107, Germany [5]Fraunhofer Institute for Cell Therapy and Immunology, Leipzig D-04103, Germany [6]Department of Theoretical Chemistry, University of Vienna, Vienna A-1090, Austria [7]Santa Fe Institute, Santa Fe, NM 87501, USA |
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| Abstract: | U7 small nuclear RNA (snRNA) sequences have been described only for a handful of animal species in the past. Here we describe a computational search for func- tional U7 snRNA genes throughout vertebrates including the upstream sequence elements characteristic for snRNAs transcribed by polymerase Ⅱ. Based on the results of this search, we discuss the high variability of U7 snRNAs in both se- quence and structure, and report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-drosophilids insect genomes based on a combination of sequence, structure, and promoter features. Due to the extremely short se- quence and the high variability in both sequence and structure, no unambiguous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms that are reported in the most recent release of the Rfam database. |
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| Keywords: | U7 snRNA non-coding RNA RNA secondary structure evolution Survey cast recent release database candidates short promoter features report find insect genomes combination high variability structure Based results computational |
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