splicesites

Splice sites are nucleotide sequences at the boundaries between exons and introns in eukaryotic pre-mRNA. They mark where introns are removed and exons joined during RNA splicing, producing mature mRNA.

In most organisms, the major splice sites are the canonical 5' donor site at the beginning of an intron, usually characterized by the dinucleotide GU, and the 3' acceptor site at the end of an intron, typically containing AG. The splicing reaction also involves a branch point, usually containing an adenine, and a polypyrimidine tract upstream of the 3' site. The spliceosome, a large complex of small nuclear RNAs and proteins, recognizes these signals; the U1 snRNP binds the 5' site, and U2 snRNP binds the branch point, with additional factors driving catalysis.

Alternative splicing allows a single gene to produce multiple mRNA isoforms by selecting alternative splice sites, exons, or intron retention. Splice-site choice is regulated by cis-acting elements such as exonic and intronic splicing enhancers and silencers and by trans-acting factors including SR proteins and hnRNPs.

Mutations at splice sites or regulatory elements can disrupt normal splicing, potentially leading to disease. Cryptic splice sites may be used when canonical sites are mutated, generating aberrant transcripts.

Splice sites are annotated in genomes and studied with transcriptomic data; computational tools identify and predict splice junctions, while experimental methods such as RT-PCR and minigene assays validate them.