A single eukaryotic pre-mRNA does not always have only one possible mature form. In alternative splicing, different valid combinations of splice sites are selected so that different sets of exons are retained in mature RNA molecules.

The resulting mature transcripts are called transcript isoforms.

For example, suppose a pre-mRNA contains

exon 1 — exon 2 — exon 3 — exon 4

One cell state might produce

exon 1 — exon 2 — exon 4

while another produces

exon 1 — exon 3 — exon 4.

The underlying DNA sequence has not changed. What changes is how the RNA transcript is processed.

Alternative splicing can change downstream products

If the alternatively retained sequence lies within a region later used in protein synthesis, different mRNA isoforms can produce different polypeptides, meaning different amino-acid chains. Those products may consequently differ in localization, binding or function.

Alternative splicing can also alter untranslated regions of an RNA, changing RNA stability, localization or how efficiently it is used without changing an encoded amino-acid sequence.

Splicing is regulated

Splice-site choice depends on RNA sequence signals and proteins that promote or inhibit use of particular splice sites. Different cell types or physiological states can therefore produce different isoform mixtures from the same gene.

This provides a crucial distinction:

• genetic sequence variation changes the DNA;
• alternative splicing changes which portions of a transcript are retained.

Alternative splicing is therefore one way a fixed genome can generate context-dependent RNA and, for protein-coding genes, protein diversity.