COMPLETE PRIMARY STRUCTURE OF 2 SPLICE VARIANTS OF COLLAGEN-XII, AND ASSIGNMENT OF ALPHA-1(XII) COLLAGEN (COL12A1), ALPHA-1(IX) COLLAGEN (COL9A1), AND ALPHA-1(XIX) COLLAGEN (COL19A1) TO HUMAN-CHROMOSOME 6Q12-Q13

Overlapping cDNA clones that encode the full-length human alpha 1(XII) collagen polypeptides were isolated. The long variant molecule cDNA o f 9750 nucleotides (nt) contains a 9189-nt open reading frame encoding 3063 amino acid residues. The short variant molecule cDNA of 6258 nt contains a 5697-nt open reading frame encoding 1899 amino acid residue s. At the amino terminus of each variant is a 24-residue signal peptid e that is followed by the mature polypeptides of 3039 amino acid resid ues with a calculated molecular mass of 330,759 Da for the long varian t and 1875 amino acid residues with a calculated molecular mass of 203 ,163 Da for the short variant polypeptide. The human collagen XII chai ns are predicted to have all the structural domains described for the molecules in chicken and mouse, including, fibronectin type III repeat s, von Willebrand factor A domains, and two triple-helical domains sim ilar to those of all the other collagen family members. The amino acid residue sequence of human alpha 1(XII) collagen showed 92% identity t o the mouse chain and 78% identity to the chicken chain. The sequence of three peptide fragments of collagen XII isolated from human placent a was identical to the sequence predicted from the deduced cDNA sequen ce and confirms that the cDNA encodes human alpha 1(XII) collagen. An isolated genomic clone was used to map the locus of the COL12A1 gene t o chromosome 6q12-q13, very close to the locus of the FACIT collagen g enes COL9A1 and COL19A1. RT-PCR on a variety of cDNAs demonstrates tha t both variant transcripts appear in human amnion, chorion, skeletal m uscle, small intestine, and in cell cultures of human dermal fibroblas ts, keratinocytes, and endothelial cells. Only the small. variant tran script is apparent in human lung, placenta, kidney, and a squamous cel l carcinoma cell line. These results confirm the previous observations showing that collagen XII is found in collagen I-containing tissues. (C) 1997 Academic Press.