= Splice acceptor site
A \b[splice acceptor site] is the <splice site> at the $3'$ 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.<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]{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.
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