Splice donor site

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.