Splice site

A precursor-RNA position used as a boundary in RNA splicing. Selecting different donor or acceptor sites changes which sequences remain in the mature product.

A splice acceptor site is the splice site at the $3^{\prime }$ end of an intron, at its boundary with the downstream exon, in a precursor RNA. Selecting it determines where the downstream exon begins in the joined product. It is distinct from both the upstream splice donor site and the RNA splicing branch point.

For a toy precursor A|intron|B, the acceptor is the boundary intron|B. If an alternative acceptor lies farther into B, the intervening part of B is removed along with the intron. Thus alternative splicing can change mature sequence without changing the underlying DNA. Coordinates must specify whether they refer to precursor RNA, mature RNA or a genomic reference.

Acceptor recognition can involve more than one stage. In an experimental splice substrate containing two AG sequences separated by a polypyrimidine tract, U2AF recognized the tract and downstream AG, whereas SPF45 recognized the upstream AG used for the second catalytic step. Regulation could therefore block the second step after earlier assembly events.^[ref]

This observation explains why simply spotting an AG sequence is insufficient to identify which acceptor is used. Sequence context, interacting RNA splicing factors and measurements of the resulting splice junctions distinguish a candidate boundary from an experimentally observed one.

A splice donor site is the splice site at the $5^{\prime }$ end of an intron in a precursor RNA. It marks the boundary between the upstream exon and the intron. Its name is oriented along the precursor RNA, not along whichever direction a DNA reference sequence happens to be displayed.

In the toy precursor A|intron|B, with letters representing whole exons, the first boundary is the splice donor site and the second is the splice acceptor site. Removing the intron and joining A to B gives the mature splice junction. A change in donor choice can change the end of A even when acceptor choice remains fixed; this is one route to alternative splicing.

Recognition involves sequence and molecular context. The RNA component of U1 snRNP can base-pair with the donor region. A particularly informative experiment changed a donor sequence and then changed U1 to restore complementarity. Rescue of one donor mutation supported direct pairing; weak rescue of another showed that complementarity alone did not guarantee productive RNA splicing.^[ref]

This is a useful causal test: perturbing either partner can disrupt an interaction, while a compensating change in the other partner can distinguish a specific pairing model from a generic loss of function. A candidate sequence bound by U1 snRNP still has to participate in the rest of the spliceosome's reaction.