Four distinct compartments in photoreceptor primary cilia, indicating known proteins that define their respective extent. The four compartments are: (1) distal cilium or axoneme (Axo; green); (2) connecting cilium/transition zone (CC/TZ; orange); (3) basal body (BB; purple); and (4) periciliary complex or ciliary pocket (PCC/CP; red). These compartments serve discrete functions in the cilium. (A) Schematic of a photoreceptor, showing specialized domains of the cell. The primary cilium elaborates into stacks of outer segment disks packed with rhodopsin, which serves as the primary light sensors of the cell. (B) Enlargement of the photoreceptor transition zone in two dimensions showing the four structural and functional domains in which most ciliary proteins are expressed. These domains are identified by known protein markers, such as acetylated α-tubulin (Axo + CC/TZ) and γ-tubulin (BB). Note: illustration of outer segment is based on a traditional model of disc morphogenesis in which nascent discs are open to the extracellular milieu, but a newer model posits that new discs form within the enclosure of outer segment plasma membrane . (C) Cross-section through the CC/TZ of the photoreceptor showing the relationship between the microtubules of the cilium and the inner segment, via the PCC/CP. (D) Three-dimensional representation of the transition zone and adjacent domains shown in (B). Note the manner in which the PCC surrounds the TZ. Note also that the TZ is the one compartment that contacts all other compartments. (E) Electron micrographs showing longitudinal (top) and cross-section (bottom) views of mouse photoreceptors. Functional domains are highlighted with the corresponding colors shown in the other panels.