The different sets of transcriptional repression and activation which characterize a and α cells are caused by the presence of one of two alleles of a mating-type locus called MAT: MATa or MATα located on chromosome III. The MAT locus is usually divided into five regions (W, X, Y, Z1, and Z2) based on the sequences shared among the two mating types. The difference lies in the Y region (Ya and Yα), which contains most of the genes and promoters.
The MATa allele of MAT encodes a gene called a1, which in haploids direct the transcription of the a-specific transcriptional program (such as expressing STE2 and repressing STE3) that defines an a cell. The MATα allele of MAT encodes the α1 and α2 genes, which in haploids direct the transcription of the α-specific transcriptional program (such as expressing STE3, repressing STE2, producing prepro-α-factor) which causes the cell to be an α cell. S. cerevisiae has an a2 gene with no apparent function that shares much of its sequence with α2; however, other yeasts like Candida albicans do have a functional and distinct MATa2 gene.