In the synsytial embryo Fkbp12 mRNA is expressed in the cytoplasm. At cellular blastoderm it is located in the inner limits of the blastoderm cells and is higher in the anterior region of the embryo than at the posterior region. Later expression is mainly in the developing gut and in muscle.

Expression pattern inferred from unspecified enhancer trap line.

In the syncytial blastoderm embryo, Fkbp12 protein localizes mainly to the aneterior and posterior poles. In the cellular blastoderm, staining is mainly in the cortex. It is concentrated in the basal-cell layer zone and aggregated in the basement membrane. At germ band extension, Fkbp12 is mainly expressed in neuroblasts, stomodeum, and the developing gut. At later stages, expression is in the brain, supraesophageal ganglion, ventral nervous system, midgut, and posterior midgut rudiment. At late gastrulation, expression is continuously detected in the digestive, muscular, and nervous systems including the mouth hook. head muscle, pharyngeal musculature, brain supraesophageal ganglion, subesophageal ganglion, ventral nervous system, proventriculus, midgut, and salivary gland.

FK506-bp2 protein is detected in stage 8 egg chambers in follicle cells and nurse cells and at lower levels in oocytes.