Co-option of cis-regulatory modules has been suggested as a mechanism for the 
evolution of expression sites during development. However, the extent and 
mechanisms involved in mobilization of cis-regulatory modules remains elusive. 
To trace the history of non-coding elements, which may represent candidate 
ancestral cis-regulatory modules affirmed during chordate evolution, we have 
searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. 
We identified, for the first time, 183 non-coding sequences that are highly 
conserved between the two groups. Our results show that all but one element are 
conserved in non-syntenic regions between vertebrate and tunicate genomes, while 
being syntenic among vertebrates. Nevertheless, in all the groups, they are 
significantly associated with transcription factors showing specific functions 
fundamental to animal development, such as multicellular organism development 
and sequence-specific DNA binding. The majority of these regions map onto 
ultraconserved elements and we demonstrate that they can act as functional 
enhancers within the organism of origin, as well as in cross-transgenesis 
experiments, and that they are transcribed in extant species of Olfactores. We 
refer to the elements as 'Olfactores conserved non-coding elements'.