Comparisons of DNA sequences among evolutionarily distantly related genomes 
permit identification of conserved functional regions in noncoding DNA. Hox 
genes are highly conserved in vertebrates, occur in clusters, and are 
uninterrupted by other genes. We aligned (PipMaker) the nucleotide sequences of 
the HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, 
human, and mouse, which are separated by approximately 500 million years of 
evolution. In support of our approach, several identified putative regulatory 
elements known to regulate the expression of Hox genes were recovered. The 
majority of the newly identified putative regulatory elements contain short 
fragments that are almost completely conserved and are identical to known 
binding sites for regulatory proteins (Transfac database). The regulatory 
intergenic regions located between the genes that are expressed most anteriorly 
in the embryo are longer and apparently more evolutionarily conserved than those 
at the other end of Hox clusters. Different presumed regulatory sequences are 
retained in either the Aalpha or Abeta duplicated Hox clusters in the fish 
lineages. This suggests that the conserved elements are involved in different 
gene regulatory networks and supports the duplication-deletion-complementation 
model of functional divergence of duplicated genes.