title: Conserved putative signals in 3' intron junctions in rodents.
abstract: Several 3' splice signals are known todate. At the 3' splice site an AG doublet is frequently found. Just upstream of the splice site there is a string of 6-11 pyrimidines. More recently it has been found that one of the stages in the splicing process involves formation of a lariat, in which the 5' end of the intron forms a 2'-5' branch with an A residue located 18-37 nucleotides upstream of the 3' splice site. The branching-point consensus is weakly defined and consists of the sequence YNYTRAY, where Y is a pyrimidine, R a purine and N any base. The A in the sixth position is the one with which branching occurs. Here we present the results of extensive searches for additional putative signals around the branching-point consensus and the 3' splice site in rodent nuclear precursor mRNAs. The signals obtained for the over 370 rodent introns are compared with those found in a larger eukaryotic sample containing over 900 nuclear pre-mRNA introns. Of particular interest are GGGA and CCCA. In both analyses GGGA occurs about 60 nucleotides upstream and CCCA is found 3-40 nucleotides downstream from the 3' splice site. A model explaining some of the putative signals discussed here is also proposed. This model involves formation of alternate stem-loop structures around the branching point and 3' splice site. Such signals and structures can possibly aid in protein or nucleoprotein branching point and splice site recognition.
authors.affiliation: Sackler Institute of Molecular Medicine, Tel Aviv University, Ramat Aviv, Israel.
authors.forename: R
authors.initials: R
authors.lastname: Nussinov
mesh_terms: D000818:Animals; D005091:Exons; D007438:Introns; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012322:RNA Precursors / Q000235:genetics; D012326:RNA Splicing; D012045:Regulatory Sequences, Nucleic Acid; D012377:Rodentia / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D012984:Software
chemical_list: D012322:RNA Precursors