title: A survey of nematode SmY RNAs.
abstract: SmY RNAs are a family of approximately 70-90 nt small nuclear RNAs found in nematodes. In C. elegans, SmY RNAs copurify in a small ribonucleoprotein (snRNP) complex related to the SL1 and SL2 snRNPs that are involved in nematode mRNA trans-splicing. Here we describe a comprehensive computational analysis of SmY RNA homologs found in the currently available genome sequences. We identify homologs in all sequenced nematode genomes in class Chromadorea. We are unable to identify homologs in a more distantly related nematode species, Trichinella spiralis (class: Dorylaimia), and in representatives of non-nematode phyla that use trans-splicing. Using comparative RNA sequence analysis, we infer a conserved consensus SmY RNA secondary structure consisting of two stems flanking a consensus Sm protein binding site. A representative seed alignment of the SmY RNA family, annotated with the inferred consensus secondary structure, has been deposited with the Rfam RNA families database.
authors.affiliation: HHMI Janelia Farm Research Campus, Ashburn, Virginia, USA.
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Jones
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Otto
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.forename: Sean R
authors.initials: SR
authors.lastname: Eddy
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017173:Caenorhabditis elegans; D016678:Genome; D008969:Molecular Sequence Data; D009348:Nematoda / Q000235:genetics*; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012313:RNA / Q000378:metabolism*; D012342:RNA, Small Nuclear / Q000378:metabolism; D017160:Trichinella spiralis; D055517:snRNP Core Proteins / Q000737:chemistry
chemical_list: D012342:RNA, Small Nuclear; D055517:snRNP Core Proteins; D012313:RNA