In the absence of maternal expression of the pecanex gene, the embryo develops severe hyperneuralization similar to that characteristic of Notch mutant embryos. We have extended a previous molecular analysis of the chromosomal interval that encompasses pecanex by using additional deficiencies to localize the locus on the molecular map. RNA blot analysis shows that the locus encodes a rare 9-kb transcript as well as minor transcripts of 3.7 and 2.3 kb. The temporal expression of these transcripts is appropriate for a neurogenic locus. Phenocopies of the mutant phenotype have been produced following microinjection of antisense RNA corresponding to a portion of the pecanex transcripts. Conceptual translation of a partial coding sequence compiled from cDNA and genomic clones indicates that the pecanex locus potentially encodes a large, membrane-spanning protein.