Many eukaryotic cell surface proteins are anchored to the membrane with glycosylphosphatidylinositol (GPI) that is covalently linked to the carboxyl-terminus. A Saccharomyces cerevisiae gaa1 mutant is defective in posttranslational attachment of GPI to proteins. A recent report demonstrated that the GPAA1 gene encodes a component of a transamidase that mediates GPI-anchor attachment. Here, we report structures and chromosome loci of human and mouse GPAA1 genes. Both genes consist of twelve exons that span about 4 kb. Human and mouse GPAA1s are located at 8q24.3 and 15E, respectively. There is a human pseudo GPAA1 gene (GPAA1P1) that is located at 2q12-->q14. Introns 8 of human and mouse GPAA1s were minor class introns bearing AT at the 5' splice sites and AC and AT at the 3' splice sites, respectively. The 3' splice sites of corresponding introns of African green monkey, Chinese hamster, dog and rat were AC, AT, AT and AA, respectively. The mouse GPAA1 gene (Gpaa1) bearing AG at the 3' splice site prepared by site-directed mutagenesis was functional, indicating that any nucleotide is allowed at the 3' end of a minor class intron.