Figure 10.

ISEs compensate for a weakened PY tract. The four factors present in the early (E) complex (U1 snRNP, SF1, U2AF65 and U2AF35) recognize the four canonical intronic splicing elements (the 5' splice site, the branchpoint (BPS), the PY tract and the 3' splice site). During A complex formation, which follows E complex, the U2 snRNP is recruited by U2AF65 and replaces SF1 at the branchpoint. There are presumably multiple redundant pathways that compensate for weak U2AF65-PY tract interactions, including bridging interactions between SF1, U2AF65 and U2AF35, alternative PY tract binding proteins (shown here as factor 'P'), and pathways involving additional non-canonical motifs such as ESEs or ISEs. We propose that ISEs in the region upstream of a weak PY tract (nucleotides -30 to -80) are important for recognizing introns with weak PY tracts. Specifically, we have shown that G-rich and C-rich motifs are ISEs that compensate for weakened U2AF65-PY tract interactions. Factors X and Y represent proteins binding the compensating ISEs. We propose that ISE-factor X/Y interactions can compensate for weak PY tract-U2AF65 interactions and help recruit the U2 snRNP to the branchpoint. The dash (//) indicates the variable length between the 5' splice site and 3' end of the intron.