alternative exons

Alternative exons are targets of alternative splicing.

Typical features of alternative exons:
1. on average are less than half the size of constitutive exons,
2. include weak 5' and/or 3' splice sites.
3. auxiliary elements aid or prevent the recognition of these exons by binding trans-acting factors depending upon cell type, developmental stage, disease state, or in different environments, and
4. frequency of inclusion of an alternative exon in the mRNA transcript depends on a balance between positive and negative regulation. Enhancer (+) and silencer (-) elements can be found within the alternative exon or the flanking introns (ESE, ISE, ESS, ISS).

Splicing regulation is controlled by multiple elements – for a particular alternative exon these can be different elements, multiple copies of the same element located at different sites, or a combination of both. Different sets of auxiliary elements regulate alternative exons, but those alternative exons that are regulated by the same trans-acting factors share some common elements.

Intronic elements can be distal, but are more often located in the introns adjacent to the alternative exon (exon-intron junction). In some cases, intronic elements overlap with, or are included within, the consensus splice site sequences that are recognized by the basal spliceosomal machinery.

Exon isoforms include:
a. extension/truncation of an exon,
b. cassette exons in which an exon is present in one transcript but absent in an isoform of the transcript,
c. alternating exons that are used in alternative transcripts in a mutually exclusive manner, and d. intron retention in which a nucleotide region is used as an exon in a transcript while it is an intron in an alternative transcript.

Cassette exon, alternating exon, and intron retention can be further characterised as 'complex' or 'simple' depending on whether the 5' or/and 3' flanking exons also undergo modifications. For example, the flanking exon may be extended or truncated, or the exon that flanks a retained intron may be cassetted or alternated.