Human systemic carnitine deficiency (SCD) is a hereditary disease caused by the mutation of OCTN2 and has the characteristics of cardiac hypertrophy. Previous studies based on JVS mouse, an animal model of this disease, showed that Cdv-1 was highly expressed in ventricles of normal mouse, but was remarkably down-regulated in JVS mouse and can be up-regulated to normal level by breeding carnitine, which suggested Cdv-1 was possibly involved in cardiac hypertrophy caused by carnitine deficiency. In this study, the expression of human CDV-1, a homolog of mouse Cdv-1, was undetectable in heart by northern hybridization. The inconsistent expression levels of human CDV-1 and mouse Cdv-1 in heart implied that cardiac hypertrophy in human SCD might not be associated with the abnormal expression of CDV-1. Interestingly, another long transcripts of the gene, Cdv-1R/CDV-1R, were cloned in the present study, in mouse and human, respectively. This long transcript predominantly expressed in both human and mouse testis and its expression level was increased with testis development. Furthermore, we proved that the open reading frame of Cdv-1R/CDV-1R spans the exons 2 approximately 19 instead of exons 9 approximately 19; and the peptide encoded by CDV-1R was composed of 676 amino acids containing a putative signal peptide instead of 414 amino acids described previously. In addition, it was proved that the expression level of Cdv-1R in JVS mouse testis was as high as that in normal mouse testis, and both were not regulated by carnitine.