The Hox-C6 gene, in common with its Xenopus and human homologues, is organised as 3 exons with 2 distinct promoters (PRI and PRII) producing 2 different transcripts. The PRII promoter produces a 'typical' Hox transcript by splicing 2 exons separated by a 700 bp intron. The PRI promoter initiates transcription from a 3rd exon, 9 kbp 5' of PRII. This exon is spliced into the 1st exon of the PRII transcript at a point 3' of the translation start codon. This means that the predicted protein product of the PRI protein contains the Hox-C6 homeodomain but is truncated by 82 amino acids compared with the PRII product. In situ hybridisation using probes specific for PRI or PRII showed them to have essentially the same distribution in the developing nervous system and prevertebrae of 12.5 d embryos. However, the distribution of transcripts in the CNS was distinctly different from that reported previously for a probe containing the Hox-C6 homeobox.