Regulation and different patterns of alternative splicing. (a) Alternative pre-mRNA splicing involves a complex interplay of trans-acting splicing factors with numerous cis-acting regulatory elements within the precursor mRNA sequences of eukaryotic genes. Trans-acting factors recognise and interact with different cis-acting RNA motifs present within the pre-mRNA sequence of genes; these include 5' donor and 3' acceptor sites at exon-intron boundaries; exon and intron enhancer elements (ESE, ISE), which can promote the use of specific splice sites; and exon and intron silencer elements (ESS, ISS), which when bound by proteins can repress the use of specific splice sites (adapted from ). (b) Different patterns of alternative splicing include: (i) normal pattern of splicing – removing introns 1, 2 and 3; (ii) whole exon exclusion – introns 1, 2 and 3, and entire exon 2 are removed; (iii) mutually exclusive exons – either exon 2 or exon 3 is removed and both exons are never retained together; (iv) intron retention – intron 2 is retained in the mRNA; and (v) cryptic splice sites – exon 2 contains a 3' cryptic splice site and exon 3 contains a 5' cryptic splice site. These compete with the native splice site to generate mRNA lacking part of an exon.