The rat posesses two cholecalciferol-induced calcium-binding proteins, the cholecalcins (CaBP). The 9-kDa CaBP is mainly concentrated in the duodenum while 28-kDa CaBP is located in the kidney and cerebellum. The mRNA encoding 9-kDa CaBP has been characterised using the cloned cDNA, pC109, synthesised from rat duodenal 9-kDa CaBP mRNA J. Biol. Chem. 258, 13502-135051. Nucleotide sequence analysis of this cDNA shows the presence of two stop codons, TGA and TAG, at positions 207 and 271, respectively, of the 3' untranslated region. The cDNA-hybridised mRNA, isolated from rat duodenum, directs the cell-free synthesis of two proteins precipitable by antisera to 9-kDa intestinal CaBP. A major protein comigrates with 9-kDa CaBP whereas a minor product corresponds to a protein which is larger by 2000 Da. The minor protein appears to result from read-through of the 'leaky' UGA stop signal. No protein band which was immunoprecipitable with 28-kDa CaBP antiserum was detected when cDNA-hybridised mRNA from rat kidney and cerebellum was translated in a cell-free system. Northern blots show that the cDNA pC109 sequence hybridises to a homogeneous mRNA species 500-600 nucleotides long from rat duodenum. Larger mRNA species encoding 28-kDa CaBP are undetectable in rat kidney and cerebellum even under low stringency conditions. All these findings demonstrate that there is no cross-hybridisation between 9-kDa and 28-kDa CaBP mRNAs. Southern blot analysis of rat genomic DNA, that shows only one homologous 9-kDa gene, is consistent with these findings. Thus, all our data indicate that there are distinct genes coding for each rat cholecalcin.Cholecalcin, which is also known as calcium-binding protein (CaBP), is one of a group of intracellular proteins which bind calcium with high affinity ( K , = lo6 M-I) [l, 21 and its concentration is dependent upon 1,25-dihydroxycholeca1-ciferol (calcitriol) [3,4], the hormonal form ofvitamin D. Two forms have been identified in the rat [4]. A 28 000-M, molecule (28-kDa cholecalcin), found in kidney and cerebellum, has four calcium-binding sites, whereas a 9000-Mr protein (9-kDa cholecalcin) is mainly located in the duodenum and possesses two calcium-binding domains [l, 2, 41. The presence of two distinct mRNAs encoding either 9-kDa or 28-kDa cholecalcin was deduced from cell-free translation assays, since rat duodenal poly(A)-rich RNA directs the synthesis of 9-kDa cholecalcin whereas mRNAs isolated from kidney and cerebellum code for the 28-kDa cholecalcin [5]. We recently reported the molecular cloning of a cDNA fragment synthesised from rat duodenal mRNA encoding 9-kDa cholecalcin [6]. Nucleotide sequence analysis of a resulting 375-base-pair cDNA clone, pC109, allowed the assignment of 207 nucleotides in the coding region before the TGA stop codon [7] (Fig. 1). The deduced amino acid sequence for 9-kDa cholecdlcin contains the two 'EF hand' domains described by Moews and Kretsinger [8] corresponding to the calcium-binding sites I and I1 [7]. The homology observed between site I structure ...