Transgenic animal models are a widely used and powerful tool to investigate human disease and develop therapeutic interventions. Making a transgenic mouse involves random integration of exogenous DNA into the host genome that can have the effect of disrupting endogenous gene expression. The J20 mouse model of Alzheimer's disease (AD) is a transgenic overexpresser of human APP with familial AD mutations and has been extensively utilised in preclinical studies and our aim was to determine the genomic location of the J20 transgene insertion. We used a combination of breeding strategy and Targeted Locus Amplification with deep sequencing to identify the insertion site of the J20 transgene array. To assess RNA and protein expression of we used qRT-PCR and Western Blotting. We demonstrate that the J20 transgene construct has inserted within the genetic locus of endogenous mouse gene on chromosome 16 in an array disrupting expression of mRNA from this gene in adult hippocampal tissue. Preliminary data suggests that ZBTB20 protein levels remain unchanged in this tissue, however further study is necessary. We note that the endogenous mouse gene also lies on chromosome 16, although 42 Mb from the locus. These data will be useful for future studies utilising this popular model of AD, particularly those investigating gene interactions between the J20 transgene and other genes present on Mmu16 in the mouse.