Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.

There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first type is exon skipping where some exons, along with all the introns, are selectively removed. This is the most prominent type of alternative splicing observed in humans. The second type, intron retention, occurs when a specific intron is retained in the mature mRNA while the others are removed. This type of splicing is more prevalent in plants than humans. In the third and fourth types of alternative splicing, alternative 5' or 3’ splice sites are selected in specific exons, respectively. This change in 5' and 3' splicing sites shortens or lengthens the exon resulting in different types of mature mRNAs. This type of alternative splicing occurs both in humans and plants. The last and rarest type of alternative RNA splicing is mutually exclusive exons where out of two exons, only one is retained while another one was removed.

Alternative splicing is regulated by different cis-acting elements and trans-acting factors. Cis-acting elements are DNA sequences that are present near structural genes whereas trans-acting factors are other molecules that bind to the DNA. In alternative RNA splicing, the cis-acting elements mainly consist of exon and intron specific splicing enhancers and silencers. Trans-acting factors, like SR proteins (serine/arginine-rich splicing factors), can bind to the exon or intron splicing enhancers to help the splicing machinery to recognize weak splice sites. On the other hand, proteins like heterogeneous nuclear ribo­nucleoproteins bind to the exon or intron splicing silencers to prevent splicing by masking the splice sites from the spliceosome.

Alternative RNA splicing is common in higher eukaryotes. Almost 95% of human genes are alternatively spliced; therefore, defects in the machinery can significantly impair organ function and can result in cancer and other diseases including neurological and heart disorders. In humans, mutations that directly affect pre-mRNA splicing account for more than 15% of genetic diseases, such as Hutchinson-Gilford progeria and beta-thalassemia.