Structure of the rat ornithine carbamoyltransferase gene, a large, X chromosome-linked gene with an atypical promoter.

Rat mitochondrial ornithine carbamoyltransferase (EC 2.1.3.3) is encoded by a gene located on the X chromosome and expressed specifically in the liver and small intestine; we have cloned this gene and determined its structure. The gene is 75 kilobases long and is split into 10 exons. The introns range in length from 85 bases to 26 kilobases. The sum of the total exons is 1.5 kilobases and occupies only 2% of the gene; this value being one of the lowest among genes heretofore reported. The first exon encodes most of the NH2-terminal presequence that functions as a mitochondrial targeting signal. Putative binding sites for the two substrates of the enzyme, carbamoyl phosphate and ornithine, are encoded by exons 3 and 9, respectively. A set of "CAAT box"- and "ATA box"-like sequences is present about 200 bases upstream from the 5' end of the mRNA. About 35 bases downstream from this set of putative promoter elements, an 11-nucleotide sequence around the 5' end of the mRNA reappears, as a direct repeat. This pair of direct repeats may play a role in pulling the cap site and the promoter elements together. Upstream and downstream from the 5' end of the mRNA there are several sequences that resemble the transcription factor Sp1 binding site, the enhancer core sequence, the consensus sequence for the glucocorticoid receptor binding sites, and the putative enhancer element of the antithrombin III gene, another gene that is expressed specifically in the liver.