Required for assembly of dynein regulatory complex (DRC) and inner dynein arm complexes, which are responsible for ciliary beat regulation, by acting as a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella (PubMed:25395538). Together with CCDC40/FAP172 forms a 96-nm-long complex in flagella. This complex does not act as a physical ruler, but rather act as a negative regulator for radial spokes: the complex lays along specific protofilaments, masking radial spoke binding sites and allowing recruitment of inner dynein arm (IDA) and nexin-dynein regulatory complexes (N-DRC) (PubMed:25395538). Interacts with CCDC40/FAP172. Phosphorylated in flagella. Short and immotile flagella. Inner dynein arm (IDA) and nexin-dynein regulatory complex (N-DRC) components are absent or severely reduced. Radial spokes are attached to doublet microtubules with an irregular periodicity of 32 nm instead of 96 nm. Belongs to the CCDC39 family.