Alternative splicing of the agrin mRNA controls the ability of agrin p
rotein to induce the clustering of acetylcholine receptors at the neur
omuscular junction. Using a transfectable reporter gene, we show that
one agrin alternative exon, the Y exon, is controlled by a regulatory
sequence in the downstream intron. Portions of this intronic sequence
have the properties of a splicing enhancer that can activate splicing
of a heterologous exon when placed in the intron downstream. The regul
atory region is complex in structure, containing several different ele
ments capable of activating splicing. Individual enhancing elements di
ffer in their cell-type specificity, and are not apparently synergisti
c, as two elements together induce lower splicing than either does sep
arately. Essential nucleotides within these regulatory elements were i
dentified by scanning mutagenesis across the active region. Interestin
gly, the elements do not appear similar to known intronic splicing enh
ancer elements. This Y exon enhancer and its components take part in a
n apparent combinatorial system of control where multiple regulatory e
lements of varying activity combine to produce a precisely cell-specif
ic exon inclusion. As a major contributor to the regulation of the Y e
xon, the enhancer ultimately controls the properties of the agrin prot
ein.