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A study was made of the expression of the ceruloplasmin (Cp) gene, whose product, blue multicopper ferroxidase, acts as a neuron survival factor. Computer analysis predicted an alternative promoter in the 3′-terminal region of intron 2 of the rat Cp gene and showed that transcription from this promoter potentially yields an mRNA coding for a 109-kDa polypeptide. The alternative Cp form starts with a region of 25 amino acid residues encoded by a part of intron 2. From Gly113, its sequence is identical to that of the major Cp form. The in silico data were confirmed experimentally by RT-PCR. The predicted mRNA was found predominantly in the liver and brain of adult rats. Direct sequencing of the PCR product demonstrated the complete identity of the predicted and real mRNA sequences. It was shown in vitro that a Cp-like protein of about 110 kDa is synthesized in the cytosol and accumulates in the absence of mitochondria. The protein was transferred into isolated mitochondria in a reconstructed system. Transport was energy-dependent, was associated with no change in Cp polypeptide length, and required cytosolic factors. Mitochondrial import of the Cp form was probably determined by an internal mitochondrial localization signal, KVVYREFTDSTFRE, corresponding to region 756–769 of mature Cp. The possible role of Cp in mitochondrial iron metabolism is discussed. [ABSTRACT FROM AUTHOR]