3SpliceSites

3SpliceSites is a term used to describe the 3' splice sites involved in pre-mRNA splicing in eukaryotes. During RNA processing, introns are removed and exons are joined to generate mature mRNA. The 3' splice site, also known as the acceptor site, marks the end of an intron and the boundary to the downstream exon.

The 3' splice site is defined by several sequence features. The intron terminates with an AG dinucleotide at the exon–intron junction, and the region upstream commonly contains a polypyrimidine tract. A branch point sequence, usually located further upstream, is involved in lariat formation during splicing. These elements are recognized by components of the U2-type spliceosome, with additional regulation by splicing factors that modulate site choice and efficiency. The exact consensus sequences can vary among organisms and genes, and noncanonical 3' splice sites can be used in some contexts.

Biological significance includes the essential role of 3' splice sites in accurate exon ligation and transcript formation. The strength or usage of a 3' splice site can influence exon inclusion or skipping, contributing to alternative splicing and proteome diversity. Mutations that disrupt the 3' splice site can lead to aberrant splicing and are associated with various diseases and developmental disorders.

Detection and annotation of 3' splice sites rely on sequence motifs, evolutionary conservation, and experimental data. Computational tools use models such as position weight matrices or machine learning approaches to predict splice site strength and usage, while RNA sequencing provides empirical evidence of actual site utilization. In datasets and discussions, 3SpliceSites may be used as a shorthand label for the set of 3' splice sites within a gene or genome.