Previously we isolated a cDNA clone which encoded the carboxyl-terminal portion of the rat link protein (Doege, K., Hassell, J.R., Caterson, B., and Yamada, Y. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3761-3765). Here we report the isolation of cDNA clones encoding the remainder of the protein. Sequence analysis revealed two classes of cDNA clones identical except for the occurrence of an additional internal nucleotide segment of 159 base pairs coding for 53 amino acids in one of the clones. Genomic clones were then isolated using the cDNA as a probe. Sequence analysis of genomic clones revealed that the internal 159-base pair cDNA segment was contained in a single exon. The protein sequence deduced from these two cDNAs were Mr = 44,779 (link 45) and Mr = 38,570 (link 39). Northern blotting of chondrosarcoma RNA revealed that both the alternate exon specific to link 45 and an exon common to both link 45 and 39 hybridized to the same size classes of link protein transcripts (1.5-5.5 kilobases), although link 45 transcripts are much less prevalent than link 39 transcripts. The link 39 sequence corresponds exactly with the predominant form of chondrosarcoma link protein. The similarity in size between link 45 and the larger form of link protein (LP1) observed in other species appears fortuitous.