cDNA hox sequences 3' of the homeobox isolated from the sea urchin Holopneustes purpurescens are definitive for sea urchin Hox orthologues.

In an investigation into Hox genes in sea urchin development, cDNA nucleotide sequences were isolated from seven Hox genes of Holopneustes purpurescens by 3' RACE. Each sequence extended from the homeobox through the coding region 3' of the homeobox to the 3'untranslated region and, in the majority of sequences, to a poly(A) signal and a poly(A) tail. The cDNA sequences 3' of the homeoboxes were very different between the seven Hox genes. In contrast, the sequences within each Hox gene 3' of the homeobox were very similar, especially at the amino acid level, between the sea urchin species for which sequences are available. The coding regions 3' of the homeodomains are thus a means of unambiguously identifying homologies between sea urchin Hox genes. A phylogenetic analysis where amino acid motifs in these 3' coding regions were aligned with similar motifs in chordate species led us to classify two posterior sea urchin Hox genes, of uncertain affinity, as orthologues of Hox9 and Hox10 genes. Putative cytoplasmic polyadenylation elements were mapped in the 3' untranslated region of sea urchin Hox genes.