Mouse kidney beta-1,6-GlcNAc-transferase (GNT) is the key enzyme for the synthesis of a glycosphingolipid (Galbeta1-4(Fucalpha1-3)GlcNAcbeta1-6(Galbeta1 -3)GalNAcbeta1-3Galalph a1-4Galbeta1-4Glcbeta1-ceramide) that contains the LeX trisaccharide epitope at its nonreducing terminus. The expression of this glycolipid in the kidney is polymorphic; it is expressed in BALB/c but not DBA/2 mice; and a single autosomal gene (Gsl5) is responsible for this polymorphism. We report here the cDNA sequence that encodes the kidney GNT of BALB/c mice, which possess a wild-type Gsl5 gene. The deduced amino acid sequence exhibits 84% identity to that of human core 2 beta-1,6-GlcNAc-transferase, which suggests that kidney GNT is a mouse homologue of human core 2 beta-1, 6-GlcNAc-transferase. The GNT mRNA is expressed abundantly in the kidney, but was not detected in other BALB/c organs or in the kidneys of DBA/2 mice by Northern blot analysis. In addition, we were able to clone and sequence another homologous cDNA from the submandibular gland. The two sequences differ only in their 5'-untranslated region. The submandibular gland type of cDNA was detected in various organs of DBA/2 mice by reverse transcription-polymerase chain reaction, which indicates that the submandibular gland type is ubiquitous and that its expression is not regulated by the Gsl5 gene. Results obtained using the long accurate polymerase chain reaction method indicate that the GNT gene is approximately 45 kilobases long, and the order of the exons from the 5'-end is exon 1 of the kidney type, exon 1 of the ubiquitous type, exon 2, and exon 3. Exons 2 and 3 are present in both transcripts, and the translated region is in exon 3. These data suggest that the expression of GNT is regulated by an alternative splicing mechanism and also probably by tissue-specific enhancers and that Gsl5 regulates the expression of GNT only in the kidney.