Figure 2.

Typical features of alternative exons. Alternative exons are on average less than half the size of constitutive exons and have weak 5' and/or 3' splice sites. Auxiliary elements aid or prevent the recognition of these exons by binding trans-acting factors in different cellular contexts, and how often an exon is included in the mRNA depends on a balance between positive and negative regulation. Enhancer (+) and silencer (-) elements can be found within the alternative exon (yellow box in the center) or the flanking introns (lines). Splicing decisions are controlled by multiple elements, and for a given exon these can be different elements, multiple copies of the same element located at different sites, or a combination of the two (as indicated by the non-yellow colored boxes). Different alternative exons are regulated by different sets of auxiliary elements, but alternative exons that are regulated by the same trans-acting factors have some common elements. Intronic elements can be distal, but are more often located in the introns adjacent to the alternative exon (near the exon-intron boundary), and in some cases can overlap with, or be contained within, the consensus splice site sequences that are recognized by the basal spliceosomal machinery.