Niv-525 is a semi-dominant allele of the nivea locus, which encodes the enzyme chalcone synthase required for flower pigment biosynthesis in Antirrhinum majus. Plants heterozygous for niv-525 and wild-type (Niv+) allele, have flowers with a reduced intensity and novel spatial pattern of pigmentation compared with Niv+ homozygotes. In heterozygotes, niv-525 acts in trans to reduce the steady-state level of nivea transcript produced by its Niv+ homologue and hence the quantity of chalcone synthase protein. Niv-525 carries an inverted duplication of 207 bp in its promoter region which has arisen following excision of the transposable element Tam 3. This structure can be explained by a model of plant transposable element excision that involves resolution of two hairpin DNA molecules. Possible mechanisms for the trans-acting effect of niv-525 and its relationship to other examples of allelic interactions, such as transvection in Drosophila melanogaster, are discussed.