We cloned a novel mouse gene that encodes a protein with homology to the mitochondria solute carrier proteins (Mscp). The major full-length Mscp transcript contains 4112 bp of cDNA and a deduced protein of 338 amino acids. The Mscp protein shares 50%, 40%, and 39% sequence identity with the C. elegans hypothetical protein T26089 and the yeast mitochondria carrier proteins MRS3 and MRS4, respectively. It also showed homology with the uncoupling proteins (UCP1, UCP2, and UCP3; 22%, 24%, and 29% identity, respectively). The protein has six transmembrane domains and three mitochondria energy-transfer protein signature motifs, which are conserved among all the members of mitochondria carrier protein family. Northern analysis indicated that the Mscp gene is highly expressed in the spleen. Using cDNA microarray and Northern analysis, we have shown a significant decrease of the splenic Mscp mRNA levels around 4-5 weeks of age in several mouse strains including C57BL/6J, nonobese diabetic (NOD), and several NOD-congenic mice. These results suggest that the Mscp gene is decreased during splenic lymphocyte maturation in these mice.