Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 07-010

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U7 snRNAs: A Computational Survey

Manja Lindemeyer, Axel Mosig, Bärbel M. R. Stadler, Peter F. Stadler


U7 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 which included the upstream sequence elements characteristic for snRNAs transcribed by pol-II. Based on the results of this search, we discuss the high variability of U7 snRNAs in both sequence and structure and we report on an attempt to find U7 snRNA sequences in basal deuterostomes and non-Drosohilid 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 unambigous candidates were found. These results cast doubt on putative U7 homologs in even more distant organisms which are reported in the most recent release of the Rfam database.

Keywords: U7 snRNA, Noncoding RNA, RNA Secondary Structure, evolution

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