The role of branchpoint‐3′ splice site spacing and interaction between intron terminal nucleotides in 3′ splice site selection in Saccharomyces cerevisiae

A conserved 3′ splice site YAG is essential for the second step of pre‐mRNA splicing but no trans ‐acting factor recognizing this sequence has been found. A direct, non‐Watson–Crick interaction between the intron terminal nucleotides was suggested to affect YAG selection. The mechanism of YAG recognition was proposed to involve 5′ to 3′ scanning originating from the branchpoint or the polypyrimidine tract. We have constructed a yeast intron harbouring two closely spaced 3′ splice sites. Preferential selection of a wild‐ type site over mutant ones indicated that the two sites are competing. For two identical sequences, the proximal site is selected. As previously observed, an A at the first intron nucleotide spliced most efficiently with a 3′ splice site UAC. In this context, UAA or UAU were also more efficient 3′ splice sites than UAG and competed more efficiently than the wild‐type sequence with a 3′ splice site UAC. We observed that a U at the first intron nucleotide is used for splicing in combination with 3′ splice sites UAG, UAA or UAU. Our data indicate that the 3′ splice site is not primarily selected through an interaction with the first intron nucleotide. Selection of the 3′ splice site depends critically on its distance from the branchpoint but does not occur by a simple leaky scanning mechanism.