Schematic diagram of synonymous substitutions between human and murine HoxC6 and HoxB6 nucleotide sequences. This diagram shows that many more synonymous substitutions (blue bars) are present in HoxB6 than in HoxC6. The two conserved elements (CEs) identified in HoxC6 by Lin et al.  are indicated, as well as the position of the homeodomain (HD). The sliding-window strategy is visualized by the positioning of a 120-bp window within a CE as well as over the homeodomain, which is not a CE because it does not contain stretches of 120 consecutive bases devoid of synonymous substitutions. The sequence encoding the homeodomain, at the amino acid sequence level one of the most conserved features of Hox genes, still contains multiple synonymous substitutions in both HoxC6 and HoxB6, whereas the 5' region of HoxC6, which encodes a domain of the protein without any clearly defined function, is virtually 100% conserved. It should be noted that the HoxB6 protein is overall slightly less conserved than HoxC6, between mouse and human, and contains five nonsynonymous nucleotide substitutions (which are not indicated here), whereas HoxC6 is fully conserved at the amino acid level.
Woltering and Duboule Journal of Biology 2009 8:17 doi:10.1186/jbiol116