Primary cilia and motile cilia might play different roles in modulating cellular function. Markers that are differentially expressed in primary and motile cilia. How to differentiate between primary and motile cilia?
Most motile cilia also have signalling receptors on their surfaces, and so function just like non-motile primary cilia. Most mammalian motile cilia are only on multi-ciliated cells that express factors such as MCIDAS during their differentiation. An exception is the monociliated cells of the embryonic node, which assemble single motile cilia, and sperm with single motile flagella.
In general, primary cilia express receptors specific to the cell type, rather than specific to all primary cilia, and cells that have only primary cilia (with the exception of the nodal cilia discussed above) fail to express genes for the hundreds of proteins needed for motility (axonemal dynein subunits, radial spoke subunits, etc.).