A lambda gt11 cDNA clone isolated by use of a polyclonal antispicule matrix protein antiserum is shown in the accompanying paper [S. C. Benson, H. M. Sucov, L. Stephens, E. H. Davidson, and F. Wilt (1987) Dev. Biol. 120, 499-506] to encode a prominent 50-kDa spicule matrix protein (SM50). This clone was used to select homologous genomic recombinants, and the structure of the gene was determined. The SM50 gene occurs once per haploid genome. It contains a single intron located within the 35th codon. A unique transcription initiation site 110 nucleotide pairs prior to the translation start signal was mapped by primer extension. The mRNA is 1895 nucleotides in length, excluding the 3' poly(A) sequence, and contains a single open reading frame 450 codons in length. Though rare in whole embryo RNA the prevalence of the SM50 mRNA is calculated to be about 1% of the total mRNA in skeletogenic mesenchyme cells. The derived peptide sequence indicates a typical N-terminal signal peptide, and an N-linked glycosylation site near the C terminus. About 45% of the length of the protein is included in a domain composed of consecutive approximate repetitions of a 13-amino-acid element, the consensus sequence of which is Trp-Val-Gly-Asp-Asn-Gln-Ala-LeuTrp-Val-IleAsp-Asn-GlnPro+ ++-ValGlu. The protein also contains an internal domain unusually rich in proline residues and a very basic C-terminal region.