The triple-helical region of human type XIX collagen consists of multiple collagenous subdomains and exhibits limited sequence homology to alpha 1(XVI).

We previously isolated a clone from a human rhabdomyosarcoma (RH) cDNA library coding for a collagen chain different from those constituting the 18 reported types (Myers, J. C., Sun, M. J., D'Ippolito, J. A., Jabs, E. W., Neilson, E. G., and Dion, A. S. (1993) Gene (Amst.) 123, 211-217). The sequence translated to a 186-amino acid noncollagenous region, a 524-residue three-subdomain collagenous region, and a presumed 8-amino acid COOH-terminal peptide. To further elucidate the primary structure of this collagen, we have now determined the sequence of additional cDNA clones. Overlapping 3' clones, found to diverge exactly where the noncollagenous 8-residue COOH sequence began, encode two additional collagenous subdomains of 168 and 70 residues and a 19-residue COOH-terminal peptide. Analysis of genomic DNA spanning the region in question revealed several 45- and 51-base pair exons linked by 4 introns totaling over 5 kilobases (kb). A 2-kb intron, absent from the clones coding for the extended collagenous region, was used in Northern blot hybridization to detect an apparently prevalent splicing intermediate 2 kb larger than the major 12.4-kb RH transcript. Therefore, the triple-helical region of this collagen chain is likely to be composed of 832 amino acids divided into five collagenous subdomains separated by 20-44 residue interruptions. Two interruptions are similar in sequence and position to those located in the type XVI chain. Furthermore, the arrangement of 2 cysteines near the COOH terminus and two imperfections in collagenous subdomain 1 are conserved in the related subclass composed of type IX, XII, XIV, and XVI collagens. However, in contrast to the COOH-terminal interchain bridging in this latter collagen group, molecular modeling strongly predicts that the cysteines in RH collagen participate in intrachain disulfide bonds. Taken together, the data clearly show that RH collagen does not represent another chain of one of the known collagen types. We propose that it be designated the alpha 1 chain of type XIX collagen.