Conserved putative signals in 3’intron junctions in rodents

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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 Yis a pyrimidine, R a purine and N any base. The Ain the sixth position is the one with which branching occurs. Here we present the resultsof 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.

Original languageEnglish
Pages (from-to)1051-1064
Number of pages14
JournalJournal of Biomolecular Structure and Dynamics
Issue number6
StatePublished - Jun 1987


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