We have previously shown that the expression of the gene encoding murine beta 1,4-galactosyltransferase (beta 1,4-GT, UDP-galactose:N-acetyl-D-glucosaminyl-glycopeptide 4-beta-D galactosyltransferase, EC 2.4.1.38) is fundamentally different between somatic and male germ cells (Shaper et al., 1990b). In somatic cells, two transcripts of 3.9 kb and 4.1 kb are produced. In contrast, in spermatogonia only the 4.1 kb transcript is expressed. Maturation of spermatogonia to pachytene spermatocytes is accompanied by reduced expression of the 4.1 kb transcript to barely detectable levels. Continued differentiation to haploid round spermatids is coincident with renewed expression in which the 4.1 kb transcript is replaced by two truncated transcripts of 2.9 and 3.1 kb. In this study, we report the characterization of a full-length beta 1,4-GT cDNA clone from a murine round spermatid library that corresponds to the 2.9 kb transcript. This transcript encodes the same open reading frame as the 4.1 kb transcript, but utilizes alternative poly(A) signals embedded within the long 3'-untranslated region of the somatic transcript. Based on sequence analysis, together with primer extension and S1 nuclease protection experiments, both the 2.9 and the 3.1 kb round spermatid beta 1,4-GT transcripts are distinguished by the presence of an additional 5'-untranslated sequence of approximately 560 bp that is absent in premeiotic germ cells and somatic cells.(ABSTRACT TRUNCATED AT 250 WORDS)