Identification of a novel DR beta cDNA clone.

We have previously reported the sequence of a cDNA clone for a DR beta 1 chain obtained from mRNA of the DR4-Dwl4 homozygous typing cell LS40 (1). Here we report the sequence of a second clone obtained from the same library. Comparison of the sequence of this clone, LSI.1.1, with our previously published sequence and a DR beta 1 genomic sequence suggests that this clone is also a product of the DR beta 1 locus, but is differentially processed at its 3' end. Since the sequence is identical to the canonical sequence for the first 848 nucleotides of the 1165 base long insert, only the region from nucleotide 840 to the end of the insert is shown. No poly-A tail or polyadenylation signal was found. The insert could encode a DR beta chain 30 amino acids longer than the canonical sequence. The region at the 3' end of LSI.1.1 that lacks homology with the canonical cDNA sequence is more than 95% homolgous with the 5' end of the intron separating the fifth from the sixth exons of a DR beta 1 gene derived from a DR4-Dw4 cell (2). The disparities presumably reflect allelic differences. Although this clone was obtained from a cDNA library constructed from poly-A enriched cytoplasmic RNA, a 21 base long oligomer (Biotechnology Institute, University of Wisconsin) complementary to nucleotides 839-859 of clone LSI.1.1 failed to hybridize to LS40 RNA (not shown). SI protection experiments (not shown) also did not detect this novel pattern of splicing. Further study may determine a function for this alternative DR beta transcript.