Multiple forms of U2 snRNA coexist in the silk moth Bombyx mori

Insect Mol Biol. 2002 Feb;11(1):105-14. doi: 10.1046/j.0962-1075.2001.00313.x.


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.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • Bombyx / genetics*
  • Energy Transfer
  • Gene Library
  • Genetic Variation
  • Humans
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA, Small Nuclear / analysis*
  • RNA, Small Nuclear / classification
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid


  • RNA, Small Nuclear
  • U2 small nuclear RNA