A novel transcript containing homology to exons 5, 9, 10, and 11 of the beta-glucuronidase gene has been shown to be derived from Chromosome (Chr) 5. In situ hybridization analysis has shown that this transcript is homologous to four loci on Chr 5 (5p13.3, 5p15.1, 5q13.1, and 5q15), two loci on Chr 6 (6p11.2 and 6p21.3), and one on Chr 22 at 22q11.2. Analysis of cosmid clones from Chr 5 has defined three distinct contigs in which there are tandem genomic repeats of a unit containing sequences homologous to exons 5, 9, and 10 but not 11. Pulsed-field gel electrophoresis (PFGE) analysis has shown that the length of these repeats is highly variable between unrelated individuals, indicating that these regions of Chr 5 are prone to rearrangement. These sequences may be important with respect to stability around the Chr 5 centromere.