AP-1-binding elements from promoter proximal DNA (the small HpaII-digested fraction of mouse genomic DNA) were affinity-selected with recombinant AP-1 complexes. One of the selected AP-1-binding elements originated from 1 kb 3' of the transcription start site of SEZ-6. We show that the mouse SEZ-6 gene extends over 49 kbp and contains 17 exons. SEZ-6 has been reported as a mouse brain-specific transcript encoding an integral membrane protein with a short cytoplasmic tail which we note may have a signalling function. We show that SEZ-6 mRNA expression in rat brain is specific to neurons but shows sharp regional differences, unconnected with the localization of major neurotransmitters. Full-length and a 3' truncated transcript are also abundant in testis. We define the origins of all reported sequence variants. The hypothetical domain structure of the protein is in excellent agreement with the exonic structure of the gene. The SEZ-6 promoter is a CpG island. In transient transfections, even the smallest promoter fragment tested (157 bp) was extremely selective towards a mouse neuronal cell line, Neuro 2a, compared with NIH-3T3, a non-expressing line.