Alternative splicing and one gene, many proteins

Many pre-mRNAs contain introns between exons. Exons are retained RNA regions and can include untranslated sequence as well as coding sequence. The spliceosome recognises a 5 prime splice site, a branch point adenosine and a 3 prime splice site. Two transesterification reactions remove an intron and join adjacent exons. Splicing can begin during transcription.

Alternative splicing changes exon inclusion or splice-site use. Patterns include exon skipping, intron retention and alternative 5 prime or 3 prime sites. Copies of the same pre-mRNA can yield different RNA isoforms. These need not encode different proteins: untranslated regions may differ, or an RNA may be degraded. An exon does not necessarily encode one whole protein domain.

Count only allowed arrangements and preserve exon order. Four independent optional exons, each kept or skipped with every combination allowed, give 2 times 2 times 2 times 2 = 16 arrangements. If exactly one of three alternatives must be retained, there are three arrangements instead. RNA counts do not by themselves give protein counts.

RNA-binding regulators influence splice-site use. Many SR proteins promote splicing and many hnRNP proteins repress particular sites, but effects depend on the protein and binding position. RNA structure and transcription speed also contribute. For a local prediction, use the stated effect and whether binding at that site increases or decreases.

Disrupting a splice site can cause exon skipping, intron retention or use of a cryptic site, an alternative site normally used little or not at all. An intronic variant can alter processing without directly changing coding DNA. The mature RNA can then change the reading frame or protein sequence. Other splice-site variants lie in coding exons, so splicing and coding effects can overlap.