A splice acceptor site is the splice site at the 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]
Splicing regulation at the second catalytic step by Sex-lethal involves 3′ splice site recognition by SPF45 by María José Lallena and others. Abstract, distinct U2AF/SPF45 interactions and regulation at the second catalytic step
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.
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