BACKGROUND: All vertebrates share a remarkable degree of similarity in their 
development as well as in the basic functions of their cells. Despite this, 
attempts at unearthing genome-wide regulatory elements conserved throughout the 
vertebrate lineage using BLAST-like approaches have thus far detected noncoding 
conservation in only a few hundred genes, mostly associated with regulation of 
transcription and development.
RESULTS: We used a unique combination of tools to obtain regional global-local 
alignments of orthologous loci. This approach takes into account shuffling of 
regulatory regions that are likely to occur over evolutionary distances greater 
than those separating mammalian genomes. This approach revealed one order of 
magnitude more vertebrate conserved elements than was previously reported in 
over 2,000 genes, including a high number of genes found in the membrane and 
extracellular regions. Our analysis revealed that 72% of the elements identified 
have undergone shuffling. We tested the ability of the elements identified to 
enhance transcription in zebrafish embryos and compared their activity with a 
set of control fragments. We found that more than 80% of the elements tested 
were able to enhance transcription significantly, prevalently in a 
tissue-restricted manner corresponding to the expression domain of the 
neighboring gene.
CONCLUSION: Our work elucidates the importance of shuffling in the detection of 
cis-regulatory elements. It also elucidates how similarities across the 
vertebrate lineage, which go well beyond development, can be explained not only 
within the realm of coding genes but also in that of the sequences that 
ultimately govern their expression.