splicesite

Splicesite is a term used to describe sequences at or near exon–intron boundaries that signal where pre-mRNA splicing occurs during gene expression. In eukaryotes, introns are removed and exons are joined to produce mature messenger RNA. Splice sites define the borders between exons and introns and are essential for correct exon connectivity.

The two primary splice sites are the donor site at the 5' end of an intron and the acceptor site at the 3' end. The majority of introns follow the GT–AG rule, with a GT dinucleotide at the 5' end and an AG dinucleotide at the 3' end of the intron in DNA. Rare noncanonical splice sites such as GC–AG or AT–AC occur in some introns. In addition to these dinucleotides, the branch point sequence (often containing an adenine) and a polypyrimidine tract near the 3' end help recruit the spliceosome.

Splice-site recognition is mediated by the spliceosome, a complex of small nuclear RNAs and proteins. U1 snRNP binds the 5' splice site, U2AF recognizes the 3' splice site and polypyrimidine tract, and U2 snRNP associates with the branch point to enable intron removal and exon joining.

Splice-site strength and regulatory elements influence site usage. Regulatory sequences such as exonic and intronic splicing enhancers or silencers modulate whether a given splice site is selected, enabling alternative splicing that expands protein diversity from a single gene.

Mutations at splice sites or nearby regulatory motifs can disrupt splicing and cause disease. Splice-site annotation is a core part of genome annotation and is commonly assessed with computational tools that predict splice-site strength and usage.