Aligning and comparing genomic sequences enables the identification of conserved 
sequence signatures and can enrich for coding and noncoding functional regions. 
In vertebrates, the comparison of human and rodent genomes and the comparison of 
evolutionarily distant genomes, such as human and pufferfish, have identified 
specific sets of 'ultraconserved' sequence elements associated with the control 
of early development. However, is this just the tip of a 'conservation iceberg' 
or do these sequences represent a specific class of regulatory element? Studies 
on the zebrafish phox2b gene region and the ENCODE project suggest that many 
regulatory elements are not highly conserved, posing intriguing questions about 
the relationship between noncoding sequence conservation and function and the 
evolution of regulatory sequences.