The Ran-binding protein 2 (RanBP2) is a giant scaffold and mosaic cyclophilin-related nucleoporin implicated in the Ran-GTPase cycle. There are no orthologs of the RanBP2 gene in yeast and Drosophila genomes. In humans, this bona fide gene is partially duplicated in a RanBP2 gene cluster and lies in a hot spot for recombination on Chromosome (Chr) 2q. This genetic heterogeneity renders further significance of this genomic region in human disease due to its possible involvement in genetically linked disorders such as juvenile nephronophthisis, congenital hepatic fibrosis, and chorioretinal dysplasia. Structure-function studies on bovine RanBP2 indicate that this protein is involved in integrating nucleocytoplasmic transport pathways with protein biogenesis such as production of functional opsin. To gain further insight into the complex functions of RanBP2 in the development and function of the neuroretina and other tissues, and proceed towards the functional analysis of RanBP2 and its molecular partners in vivo, we have determined the complete genomic organization of the murine RanBP2 gene. The gene consists of 29 exons spread over 50 kb and contains a mega-exon of 4663 bp that encompasses the variable Zn-finger-rich domain of RanBP2. This may account, in part, for a predisposition of recombination of this locus and variability of the number of Zn-fingers across mammalian species. The RanBP2 promoter contains tissue-specific elements. A CpG island encompasses this region up to the first intron, making RanBP2 gene expression susceptible of epigenetic regulation. This murine RanBP2 transcript has a tissue-restricted expression profile, and the conceptual protein is 82% identical to human RanBP2. The gene maps to mouse Chr 10, 30 cM proximal of the centromere.