title: Multiple forms of U2 snRNA coexist in the silk moth Bombyx mori.
abstract: Eight U2 snRNA variants were isolated from several Bombyx mori U2-specific RT-PCR libraries. U2 sequences and secondary structures were generated and examined in terms of potential RNA and protein interactions. Analysis indicated that nucleotide changes occurred in both stem/loop and single-stranded areas. Changes in the double stranded areas were either compensatory, single substitutions (e.g. C <--> U) or prevented the double-stranded formation of one or two base pairs. The polymorphisms were clustered in moderately conserved regions. Some of the changes observed generated stronger base pairing. Inter-species conserved protein or RNA-binding sites were relatively unaffected. No polymorphic sites were found in known functional sequences. Bombyx mori and Drosophila melanogaster U2 sequences are 95% and 70% similar at the 5'- and the 3'-ends of the molecule, respectively. Phylogenetic analysis of the U2 sequences demonstrates remarkable conservation across species.
authors.affiliation: Department of Biological Sciences, Florida International University, Miami, FL 33199, USA.
authors.forename: J M
authors.initials: JM
authors.lastname: Sierra-Montes
authors.forename: A V
authors.initials: AV
authors.lastname: Freund
authors.forename: L M
authors.initials: LM
authors.lastname: Ruiz
authors.forename: M N
authors.initials: MN
authors.lastname: Szmulewicz
authors.forename: D J
authors.initials: DJ
authors.lastname: Rowold
authors.forename: R J
authors.initials: RJ
authors.lastname: Herrera
mesh_terms: D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics*; D004735:Energy Transfer; D015723:Gene Library; D014644:Genetic Variation; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012342:RNA, Small Nuclear / Q000032:analysis* / Q000145:classification; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012342:RNA, Small Nuclear; C405484:U2 small nuclear RNA