Mouse kidney -1,6-GlcNAc-transferase (GNT) is the key enzyme for the synthesis of a glycosphingolipid (Gal1-4(Fuc␣1-3)GlcNAc1-6(Gal1-3)GalNAc1-3Gal␣1-4Gal1-4Glc1-ceramide) that contains the Le X 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 -1,6-GlcNAc-transferase, which suggests that kidney GNT is a mouse homologue of human core 2 -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 ϳ45 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.Carbohydrate chains of cell-surface glycoconjugates play important roles in cell-cell and cell-matrix communication (1). The diversity of the carbohydrate structures provides a basis for cell-specific recognition. The expression of carbohydrate chains is highly regulated and changes during embryogenesis, differentiation, and oncogenic transformation (2). The regulatory process may be mediated by many different gene products, including glycosyltransferases (3, 4), transcription factors (5-10), nucleotide sugar transporters (11-14), kinases and phosphatases that act on transferases (15,16), and other genes. The objective of our studies is to understand the genetic basis and mechanisms that regulate the expression of carbohydrates.We have identified an autosomal mouse gene (Gsl5) that controls the expression of GlcNAc1-6(Gal1-3)GalNAc1-3Gb 3 Cer and its elongated glycolipids by regulating -1,6-GlcNAc-transferase (GNT) 1 activity in the kidney (17). DBA/2 mice are not able to express detectable levels of GNT activity or the glycolipids containing GlcNAc1-6(Gal1-3)GalNAc1-3Gb 3 Cer as a core structure because of a defect of the Gsl5 gene. To elucidate the role of Gsl5, the mouse k...