Alignment of octapeptide regions, homeodomains and OAR domains from representative hbn , otp and rx genes of cnidarians, protostomes and deuterostomes. Homeodomain sequences are aligned against the Drosophila antennapedia homeodomain. Nematostella, human and fruit fly representatives were taken from Ryan et al. . Homeodomains from additional taxa were identified by similarity searches (tBLASTn and BLASTp) conducted through the BLAST interface at National Center for Biotechnology Information (see Methods) and at respective genome assemblies available through the Joint Genome Institute. Abbreviations for taxa are as follows: (cnidarians: Acropora millepora (Acm), Hydra magnipapillata (Hym), Nematostella vectensis (Nev); placozoan: Trichoplax adhaerens (Tra); protostome bilaterians: Aedes aegypti (Aea), Anopheles gambiae (Ang), Apis mellifera (Apm), Caenorhabditis elegans (Cae), Capitella teleta (Cap), Lottia gigantea (Log), Tribolium castaneum (Trc); deuterostome bilaterians: Branchiostoma floridae (Brf), Ciona intestinalis (Cii), Danio rerio (Dar), Gallus gallus (Gag), Homo sapiens (Hos), Mus musculus (Mum), Saccoglossus kowalevskii (Sak), Strongylocentrotus purpuratus (Stp), Xenopus laevis (Xel)). The octapeptide [72, 73] and/or the OAR domain [51, 75] are indicated when identified. Two different versions of the Rx homeodomain of Nematostella are shown, and the polymorphic residues are highlighted.