The C1 locus of Zea mays (maize) controls the expression of genes involved in anthocyanin biosynthesis in aleurone and scutellar tissue and encodes a protein with the features of a transcriptional activator. C1-I is a dominant negative mutant which inhibits pigment formation. The structure of the C1-I allele was determined by cloning and sequencing of this allele and of two distinct C1-I derived cDNAs. C1-I has two major and several minor sequence differences with respect to the wild-type C1 allele. Transcription initiation occurs at the same position as in wild-type but transcription yields two different products, one major RNA of 1.3 kb and one minor RNA of 1.45 kb in length, encoding two proteins of 252 and 108 amino acids respectively. The longer 252 amino acid C1-I protein differs from the 273 amino acid wild-type C1 protein at several positions but most prominently at its carboxy terminus, resulting in reduced acidity of the C1-I protein. A similar change in acidity of the Gal4 protein of yeast converted this transcriptional activator into a repressor protein. We discuss the dominant phenotype of C1-I with respect to its possible repressor function in contrast to the activator function of the C1 gene product.