At embryonic stage 15, Pax transcript is expressed at a high level in ventral acute muscle 2, at a median level in A1-7 dorsal transverse muscle 1, and at low levels in the segment border muscle, dorsal acute muscle 1, and ventral transverse muscle 1.

Northern analysis using a probe specific to long (~2.4 kB) isoforms are expressed from early embryogenesis with expression peaks at embryonic stage 17--first larval instar and in pharate adults. A probe spefic to only Pax-RD (1.4 kB) is expressed faintly at 8-16 hr AEL and at the third larval instar, at a moderate level in male and female adults, very strongly from 16 hr AEL through the second larval instar and in pharate adults, and not expressed 0-8 hr AEL or in prepupae.

The Pax protein is enriched at the muscle-tendon junction in third instar larvae and is found primarily in muscle cell in the region near the membrane.

In cultured NIH-3T3 cells, fluorescently-tagged Pax-PD short isoform protein localizes along actin bundles, while the long isoform is localized to focal adhesions. In the embyronic/larval muscle system of late embryos, the Pax long isoform is localized to muscle tendon junctions, while the short isoform has particularly strong staining along segment boundaries in the somatic muscle system.