Abstract： Objective To examine the expression of molar root patterning gene 1 (Mrp1) and predict the Mrp1 structure by bioinformatics analysis. Methods A pair of Mrp1-specific PCR primers were designed, and RT-PCR method was used to study the mRNA's expression pattern in rat molar root and other organs. Gene positioning and other protein sequence prediction were carried out by chromosome analysis and other bioinformaties analysis. Results Mrp1 was expressed not only in the molar but also in the developing pancreas, liver, lung and kidney tissues. Mrp1 was located in the 18q12.3 chromosome of the rats and the Mrpl amino acids sequence had about 37% homology with a known protein Uroplakin Ⅲb (p35) which was an urothelial differentiation membrane molecular marker. A trans-membrane structure, 5 PKC phosphorylation sites and 4 CK Ⅱ phosphorylation sites in Mrpl were found. Conclusions Mrpl has a broad expression in different developing organs, and it may have a important function in the rat tooth root development.