Does gene number correlate with complexity? As shown to the rightt, it obviously does not. Rather, alternative splicing correlates with complexity. 95% of Human genes are known to exhibit alternative splicing. Complex Transcription Units use alternative splicing to produce more than one type of mRNA. Patterns of RNA spliciing can combine to produce a dizzying array of alternatively spliced isoforms: the Slo or Bk channel has over 500 isoforms; the neurexin protein has 2,346 isoforms; the para-sodium channel has 1,536 isoforms; the Drosophila DSCAM Receptor can potentially be made in 38,016 different spliced isoforms. Somatic sexual development in Drosophila is controlled by a cascade of splicing factors each regulating the splicing of genes downstream in the pathway. And cochlear hair cells are tuned to respond to different frequencies via alternative RNA splicing.

There are many examples of regulation in mammals where important changes in gene activity are regulated by alternative splicing. These systems use pre-mRNA binding proteins to enhance or repress particular splicing choices. These proteins have different types, numbers, and arrangements of RNA binding domains, and other domains that can be involved in protein/protein interactions. The RNA binding domains target the proteins to specific short sequence elements adjacent to sites of regulation. Alternative splicing is especially common in the mammalian nervous system, where it is used to diversify many proteins important for neuronal development and function. Small cassette exons create short peptide inserts that determine precise changes in ligand binding, electrophysiology, or subcellular targeting.