Doppia (Dop) transposable elements were first identified from element termini found in the upstream portions of certain alleles of the pl1 and r1 loci of maize. At the r1 locus, these Dop end sequences are present in a region called sigma, which functions as the promoter for the S genes of the R-r haplotype, and which is required for efficient epigenetic modification of the S genes during paramutation. In order to better understand the significance of the Dop element sequences at R-r, and to investigate the Dop-encoded products that might regulate r1 genes in this haplotype, we have cloned a more complete Dop element, Dop4. The Dop4 element can encode two proteins that have strong sequence similarity to the TnpA and TnpD proteins of the well characterized maize transposable element En/Spm. The DOPA protein, which is similar to TnpA of En/Spm, is shown to bind to short, subterminal repeat motifs located in the Dop element ends. Like TnpA, DOPA promotes intermolecular associations between DNA molecules. In contrast to the activity of TnpA, which is a transcriptional repressor of En/Spm, DOPA activates expression of reporter genes driven by either the Dop promoter or sigma in transient expression assays.