||The mab-21 gene was first identified in Caenorhabditis elegans as a critical component required for sensory organ identity determination. Mab21 homologs are highly conserved from invertebrates to vertebrates. In vertebrates, two Mab21 homologs, Mab21l1 and Mab21l2, have been identified. Mab21l2 knockout mice display defects in eye and ventral body wall formation. It appears that the role of Mab21s in sensory organ and neural development is conserved throughout evolution. Transcriptional regulation is an important part of development. Transcription factors and cis-regulatory elements are key components of this process. Comparative genomics enables us to identify conserved cis-regulatory elements with potential function. Orthologous Mab21l2 genomic regions of six vertebrate species, including human, were analyzed for enhancer identification. By linking these elements to a ß-galactosidase reporter gene under the control of a minimal promoter, four regulatory regions were identified to confer tissue-specific activity in transgenic mice at embryonic day 11.5. An element, MC9 enhancer, conferring neural tube enhancer activity was subjected to detailed molecular characterization. The expression pattern of the LacZ reporter with the neural tube enhancer from embryonic days 8.5 to 13.5 have been examined, especially in sections of transgenic mice at embryonic days 11.5. By using deletion studies, a highly conserved region was found to be required for the enhancer element to function in neural tube. Multiple predicted binding sites which are related to neural development were found in this highly conserved region. This study provides an entry point to uncover conserved components acting in the regulation of Mab21l2 during neural development.