Fer3 transcripts are restricted to the developing central nervous system. Transcripts are first detected in stage 11 embryos in single clusters of cells per hemisegment in the neurogenic ectoderm. Late in stage 11 a second small cluster of cells expressing Fer3 appears anteriorly to the initial cluster in each hemisegment. From 4-8 cells are detected in the large cluster and 1-2 cells in the small cluster. The staining and number of cells remains constant through stage 13. At stage 13 additional clusters of Fer3 expressing cells can be detected, including one group anterior to the large cluster in the first hemisegment and another posterior to the cluster in the 13th hemisegment. Three additional clusters of cells are detected in the procephalic region. By stage 14 expression of Fer3 transcripts are observed in approximately 20 cells in each brain lobe. Through stage 16 Fer3 transcript can still be detected in procephalic and ventral nerve cord regions although at reduced levels and in a more limited number of cells.

Fer3 is first detectable at 6 hours AEL. Expression is most pronounced between 9 and 15 hours AEL, then sharply decreases until almost undetectable in pupae. By in situ, Fer3 expression is first observed at embryonic stage 11, in the neurogenic region of the germband. Fer3 transcript is localized to small groups of cells on both sides of the neural midline in each segment: a posterior cluster of 2-4 cells, and a single anterior cell. The number of Fer3-expressing cells increases, peaking at stages 13-14, when the posterior clusters contain 5-7 cells, and the anterior clusters contain 1-2 cells. This pattern is detected in the subesophageal, thoracic, and abdominal ganglia. Fer3 is also expressed in a subset of neurons in the brain. This expression persists to the end of embryogenesis.