Human calcium-binding tyrosine-phosphorylation regulated protein (CABYR) is a polymorphic, testis-specific, calcium binding protein that undergoes tyrosine phosphorylation during in vitro capacitation. A protein kinase A (PKA) regulatory subunit type II alpha (RII-alpha) homologous domain in the N-terminus, phosphorylation dependent Ca(++) binding isoforms, and localization to the principal piece of the human sperm tail suggest that CABYR may be involved in sperm motility. In this paper, four mouse orthologous cDNAs and the genomic DNA of CABYR were cloned, nucleotide and protein sequences of mouse and humans were compared, and the genomic organization of the mCABYR gene was analyzed. Human and mouse CABYR conserve potential functional motifs including a domain homologous to the dimerization interface of cyclic adenosine monophosphate dependent PKA RII-alpha, 14 PXXP motifs, and regions of homology with extensins and src homology-3-binding protein 1. mCABYR is arranged into six exons spanning about 14 kb of DNA. Mouse CABYR showed several similarities with human CABYR: (1) the protein was localized to the principal piece of mouse epididymal spermatozoa; (2) mouse CABYR has two coding regions (CR-A and CR-B), with 66 and 82% identity, respectively to human; and (3) mCABYR showed the presence of two testis-specific transcripts of approximately 1.4 and approximately 2.4 kb. Three murine splice variants were identified, two of which spliced into CR-B. Exon 4, present in all human and mouse variants and comprising 85% of CR-A appears suitable for targeted deletion. The overall 81% nucleotide identity between mouse and human CABYR, the common genomic organization, presence of similar testis-specific transcripts, localization in the principal piece of tail and occurrence of homologous splice variants indicate an authentic murine orthologue of CABYR has been identified.