Figure 6

Bipartite model of intron retention. (A) "Two-step splice site recognition" (a mixed model of exon and intron recognition) for short introns in short "exon + intron + exon" units (< 400 nt, close to the size limit for exon recognition). In step 1, all the exons are defined, including the "exon + intron + exon" unit in black and gray. Step 2 is alternative, if intron definition occurs in the "exon + intron + exon" unit, the intron will be removed. Skipping of this step will lead to intron retention. (B) Model for long introns, typically with high scoring splice sites in long "exon + intron + exon" units. Step 1: exons are defined, including those flanking the intron to be retained (gray exons). In step 2, flanking introns are removed, joining the retained intron flanking exons to the outer exons. Step 3 is alternative, if the flanking exons are joined, the intron is removed; otherwise, abrogation of this step by hypothetical failure in E to A or A to B complex transition would lead to intron retention.