title: A new U2 RNA secondary structure provided by phylogenetic analysis of trypanosomatid U2 RNAs.
abstract: A new model of U2 RNA secondary structure has been developed by comparing U2 RNA sequences from distantly related trypanosomatids, which process their RNAs by trans-splicing, and U2 RNAs from cis-splicing organisms. The trypanosomatid U2 RNA retains structural similarity in important functional domains of cis-splicing U2 RNAs yet differs from previous consensus models in that only two helices, rather than three, can form in the stem-loop II region. This alteration eliminates the capacity for pseudoknot formation and produces a single-stranded region 3' to stem-loop II, which may be accessible for snRNP protein binding. Trypanosomatid U2 RNAs differ in the putative branchpoint recognition sequences, which completely diverge from the conserved GUAGUA consensus of cis-splicing organisms.
authors: School of Pharmacy, University of California, San Francisco 94143-1204.
authors: T
authors: T
authors: Hartshorne
authors: N
authors: N
authors: Agabian
mesh_terms: D000818:Animals; D001483:Base Sequence; D015139:Blotting, Southern; D016384:Consensus Sequence; D005786:Gene Expression Regulation; D005796:Genes; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012326:RNA Splicing; D016053:RNA, Protozoan / Q000235:genetics; D012342:RNA, Small Nuclear / Q000235:genetics*; D015183:Restriction Mapping; D014346:Trypanosoma brucei brucei / Q000145:classification / Q000235:genetics*; D014349:Trypanosoma cruzi / Q000145:classification / Q000235:genetics*; D014351:Trypanosomatina / Q000145:classification / Q000235:genetics*
chemical_list: D016053:RNA, Protozoan; D012342:RNA, Small Nuclear