Expression analysis of new Ly49 genes: most transcripts of Ly49j lack the transmembrane domain

Five new Ly49 genes, named Ly49j-n, have recently been identified in C57BL/ 6 mice. This study examined the expression of three of these new genes, Ly4 9j, k, and n. To determine whether the Ly49j, k, and n genes were transcrib ed, gene-specific primers were used to amplify cDNA clones for each gene fr om C57BL/6 interleukin-2-activated natural killer (NK) cell cDNA. A full-le ngth cDNA for Ly49j was detected which encodes a 267 amino acid protein and shares approximately 96% nucleotide identity with Ly49c and i. COS cells t ransfected with the Ly49j cDNA were shown to react with the monoclonal anti body 8H7, suggesting that the gene likely encodes a functional protein. Man y different sized Ly49k and n transcripts were observed, although it is lik ely that they do not encode functional proteins due to missing exons or sev ere truncations in the open reading frames. Interestingly, the most abundan t Ly49j transcript detected was shown to lack exon 3, which encodes the tra nsmembrane domain. Similar studies performed on the same source of NK cell cDNA using Ly49c- and i-specific primers revealed the presence of transmemb rane-less Ly49i transcripts, although at a much lower frequency than observ ed for Ly49j. We also detected Ly49g and h transcripts lacking the transmem brane domain. Despite the absence of the transmembrane region, the resultin g Ly49 transcripts maintain their open reading frames, and therefore could potentially encode cytoplasmic proteins with a role in NK cell function.