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U7 snRNAs: a computational survey |
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| Authors: | Marz Manja Mosig Axel Stadler Bärbel M R Stadler Peter F |
| Institution: | aBioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig D-04107, Germany bDepartment of Combinatorics and Geometry, CAS/MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China cMax Planck Institute for Mathematics in the Sciences, Leipzig D-04103, Germany dInterdisciplinary Center for Bioin- formatics, University of Leipzig, Leipzig D-04107, Germany eFraunhofer Institute for Cell Therapy and Immunology, Leipzig D-04103, Germany fDepartment of Theoretical Chemistry, University of Vienna, Vienna A-1090, Austria gSanta Fe Institute, Santa Fe, NM 87501, USA |
| 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 functional 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 sequence 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 sequence 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. |
| Keywords: | U7 snRNA non-coding RNA RNA secondary structure evolution |
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