Ttc39c has been identified as a novel gene in skeletal muscle that is upregulated in response to neurogenic atrophy in mice. Quantitative PCR and Western blot analysis confirmed that Ttc39c is expressed in both proliferating and differentiated muscle cells. Furthermore, comparison of Ttc39c expression in undifferentiated and differentiated C2C12 cells demonstrated that Ttc39c levels peak in early differentiation, but decreases as cells become fully differentiated myotubes. The transcriptional regulation of Ttc39c was examined by cloning promoter fragments of the gene and fusing it with the SEAP reporter gene. The Ttc39c reporter gene constructs were transfected into muscle cells and confirmed to have significant transcriptional activity in cultured muscle cells and were also found to be transcriptionally repressed in response to ectopic expression of myogenic regulatory factors (MRF). Furthermore, conserved E-box elements in the proximal promoter region were identified, mutated, and analyzed for their role in the transcriptional regulation of Ttc39c expression. Mutation of the conserved E-box sequences reduced the activity of the Ttc39c reporter gene, suggesting that these elements are potentially necessary for full Ttc39c expression. To determine the sub-cellular location of Ttc39c in muscle cells, the Ttc39c cDNA was fused with the green fluorescent protein (GFP), expressed in muscle cells, and visualized by confocal microscopy revealing that Tct39c is localized to the cytoplasm of proliferating myoblasts and differentiating myotubes. Furthermore, Ttc39c appears to localize to the microtubule network and differentiating muscle cells developed elongated primary cilia in response to Ttc39c ectopic expression. Additionally, Ttc39c overexpression resulted in impaired muscle cell differentiation, attenuated Hedgehog and MAP Kinase signaling, and increased expression of IFT144, a component of the intraflagellar transport complex A involved in retrograde movement in primary cilia. Interestingly, Ttc39c knockdown also resulted in abrogated muscle cell differentiation and impaired Hedgehog and MAP Kinase signaling, but did not affect IFT144 expression levels. These results suggest that muscle cell differentiation is sensitive to aberrant Ttc39c expression, that Ttc39c is necessary for proper muscle cell differentiation, and that Ttc39c may participate in retrograde transport of the primary cilia of developing muscle cells.