The derived protein sequence of the presumptive oncogene rhombotin is virtually identical between human and mouse (Boehm et al., 1990), rendering it difficult to identify functionally important regions or motifs. We have therefore sought to isolate and compare rhombotin sequences from disparate species. Here we show that a sequence which is highly homologous to that of human and mouse rhombotin exists in Drosophila DNA. Comparison of the sequences shows the main conserved feature to be a cysteine-rich region (CRR). The mammalian rhombotin gene has tandemly duplicated CRR's (CRR-1 and CRR-2) and comparison of CRR-1 and -2 with other known proteins shows close homology to the proposed LIM domains of the nematode cell lineage proteins lin-11 and mec-3 (Freyd et al., 1990), and of a vertebrate transcription factor (Isl-1) (Karlsson et al., 1990). The latter three proteins share a homeodomain, in addition to the LIM domains. These observations suggest that the LIM domain might facilitate protein-protein interactions in a manner analogous to the leucine zipper or the helix-loop-helix motifs. Thus, since rhombotin lacks a DNA-binding homeodomain, this protein might belong to a new class of transcriptional regulators which modulate transcription via intermolecular competitive binding to the LIM domains of certain DNA-binding transcription factors.