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. 2015 Feb;21(2):213–229. doi: 10.1261/rna.048009.114

FIGURE 9.

FIGURE 9.

A model for exon end-to-end contact in exon definition. (A) Communication between the two ends of the exon is mediated by protein–protein interaction (half-circles). The line represents the pre-mRNA, with the thick black section being the exon, the thin black sections being the intronic flanks, and the 5′SS indicated by the curly brace. A 55 nt exon is accommodated by protein factors binding to the ends of the exon (e.g., U2AF65 and U1 snRNP). SS Set 3 is being used. The distance between the emerging ends of the RNA molecule (arrows), designated the fitting distance (yi), was used to obtain an equation for the rate of formation of this complex. (B) A different splice site sequence (SS Set 2) could change the point and angle at which the pre-mRNA extends from a binding protein such that the fitting distance (yi) is increased compared with SS Set 3. The 55 nt exon can accommodate this difference. (C) Same as A but with a shorter 20 nt exon. The short fitting distance of SS Set 3 still allows coupling of the protein factors. (D) Same as B but showing that the long fitting distance of SS Set 2 precludes coupling of the two protein factors when the exon is only 20 nt long.