title: U7 snRNAs: a computational survey.
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.
authors.affiliation: Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig D-04107, Germany.
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.forename: Axel
authors.initials: A
authors.lastname: Mosig
authors.forename: Bärbel M R
authors.initials: BM
authors.lastname: Stadler
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D023281:Genomics / Q000706:statistics & numerical data; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D013045:Species Specificity; D014714:Vertebrates / Q000235:genetics
chemical_list: D012342:RNA, Small Nuclear; C405487:U7 small nuclear RNA