THE EXON STRUCTURE OF THE MOUSE ALPHA-2(IX) COLLAGEN GENE SHOWS UNEXPECTED DIVERGENCE FROM THE CHICK GENE

One cosmid and two overlapping phage clones covering the entire mouse alpha 2(IX) collagen gene including 12 kilobase pairs (kb) of 5'- and 8 kb of 3'-flanking sequences were isolated from two genomic libraries . The overall gene structure was determined by restriction mapping and nucleotide sequencing. The gene spans 16 kb from the start of transcr iption to the polyadenylation site and contains 32 exons. It codes for a mRNA of 3 kb that translates into a polypeptide of 688 amino acids. The intron-exon junctions and mRNA structure were confirmed by amplif ication of cDNA made for mouse cartilage RNA. The coding sequence of t he mouse alpha 2(IX) collagen gene shows marked similarities to those for other type IX collagen chains. Although the overall exon-intron or ganization of the mouse gene is very similar to the chick alpha 2(IX) gene, some unexpected differences were observed at the splice junction s. Split codons characteristic for the central triple helical domain o f the chick were not found in the mouse gene that thus exhibited a lon g stretch of exons with sizes that are multiples of 9 base pairs in th is domain. The promoter of the mouse alpha 2(IX) collagen gene contain s some G + C-rich elements including three Sp1 consensus recognition s ites and a far upstream CCAAT box but no TATAA box. Both primer extens ion and RNase protection assays revealed several transcription start s ites within 418 base pairs of the promoter. The present study reports the first complete nucleotide sequence of any type IX collagen gene an d forms the basis for comparative structural studies on this collagen type and for experiments involving transgenic mice.