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Background/Objectives: Tumors are induced by overactivation of oncogenes and loss of tumor suppressor genes. Recently, a family of proteins containing CID (C-terminal domain (CTD)-interacting domain) domains, named CREPT/RPRD1B and p15RS/RPRD1A, has been identified to be involved in tumorigenesis through the regulation of the cell cycle. Interestingly, while p15RS was shown to inhibit cell proliferation, CREPT was demonstrated to promote tumorigenesis by accelerating tumor cell cycle progression. Methods: To decipher why these two proteins function oppositely, we aimed to reveal the disparities in their clinical outcomes and protein properties. Results: We observed that CREPT and p15RS are both highly expressed in tumors, but with opposite prognostic implications. We confirmed that CREPT promotes, but p15RS inhibits cell proliferation via regulation of Wnt/β-catenin signaling activation. The CID domain of CREPT differs from that of p15RS in conformation and charge distribution. CREPT exhibits a significantly stronger oligomerization capacity than p15RS, which is mediated by the CCT (coiled-coil terminus) domain. We demonstrated that the differences in both CID and CCT domains between CREPT and p15RS contribute to their opposite physiological functions. Conclusions: In conclusion, our results demonstrate that despite high primary sequence similarity, CREPT and p15RS exhibit distinctive biochemical properties. These differences ultimately explain their functional divergence in tumorigenesis and offer novel insights into CREPT-targeted drug design. Full article