The larval nervous system of the ascidian Ciona intestinalis exhibits an 
abstract form of the vertebrate nervous system. The Ci-Galphai1 gene, which 
encodes a G-protein alpha subunit, is specifically expressed in distinct sets of 
neurons in C. intestinalis larvae, including papillar neurons of the adhesive 
organ, ocellus photoreceptor cells, and cholinergic and GABAergic neurons in the 
central nervous system (CNS). A GFP reporter gene driven by the 4.2-kb 5' 
flanking region of Ci-Galphai1 recapitulated the endogenous gene expression 
patterns. Comparative genomic analysis of the Galphai1 gene between C. 
intestinalis and Ciona savignyi identified an 87-bp highly conserved non-coding 
sequence located between -3176 and -3090 bp upstream of the gene. Deletion of 
this conserved upstream sequence resulted in the complete loss of reporter 
expression in the central nervous system, while reporter expression in the 
adhesive organ and mesenchyme cells remained unaffected. The conserved upstream 
sequence can activate gene expression from basal promoters in the brain vesicle, 
although it requires additional cis-regulatory sequences to fully activate the 
CNS-specific gene expression. These results suggest that different types of 
central neurons share a common transcriptional activation mechanism that is 
different from that of papillar neurons.