Pan-vertebrate developmental cis-regulatory elements are discernible as highly 
conserved noncoding elements (HCNEs) and are often dispersed over large areas 
around the pleiotropic genes whose expression they control. On the loci of two 
developmental transcription factor genes, SOX3 and PAX6, we demonstrate that 
HCNEs conserved between human and zebrafish can be systematically and reliably 
tested for their regulatory function in multiple stable transgenes in zebrafish, 
and their genomic reach estimated with confidence using synteny conservation and 
HCNE density along these loci. HCNEs of both human and zebrafish function as 
specific developmental enhancers in zebrafish. We show that human HCNEs result 
in expression patterns in zebrafish equivalent to those in mouse, establishing 
zebrafish as a suitable model for large-scale testing of human developmental 
enhancers. Orthologous human and zebrafish enhancers underwent functional 
evolution within their sequence and often directed related but non-identical 
expression patterns. Despite an evolutionary distance of 450 million years, one 
pax6 HCNE drove expression in identical areas when comparing zebrafish vs. human 
HCNEs. HCNEs from the same area often drive overlapping patterns, suggesting 
that multiple regulatory inputs are required to achieve robust and precise 
complex expression patterns exhibited by developmental genes.