Although several splicing regulatory proteins have been identified in Drosophila through characterization of various genetic mutations, including sex-lethal, transformer, transformer-2, suppressor-of-white-apricot (su(wa)), and possibly suppressor-of-sable, none of these have been identified in vertebrates. We describe the cloning and characterization of human (HsSWAP) and mouse (MmSWAP) homologs of the su(wa) gene. Comparison of the Drosophila and mammalian proteins reveals five highly homologous regions, including an arginine/serine-rich domain and two repeated modules that are homologous to regions in the constitutive splicing factor, SPP91/PRP21. These modules thus define a new motif likely important in the regulatory and constitutive splicing functions of these proteins. The Drosophila su(wa) gene autoregulates its expression by control of splicing of its first two introns. Comparison of mammalian and Drosophila SWAP mRNAs revealed that the splice junctions of these regulated introns are precisely conserved, showing definitively that these genes are ancestrally related. Moreover, mammalian SWAP mRNAs are also alternatively spliced at the same splice sites, showing that mammalian SWAP expression is regulated (presumably autogenously) by control of splicing of these two introns. These several structural features therefore strongly suggest that the mammalian SWAP gene functions as a vertebrate alternative splicing regulator.