We previously cloned a lyn cDNA-encoding 56-kd Src-like protein-tyrosine kinase, p56lyn. Anti-Lyn antibodies raised against a sequence of 95 amino acids (Arg-25 to Ala-119 of p56lyn) recognized two species of the protein, p56lyn and p53lyn. V8 proteinase analysis showed that p53lyn differs only slightly from p56lyn. Analysis of mRNA from B lymphocytes by the polymerase chain reaction indicated the presence of two forms of alternatively spliced lyn mRNA. Nucleotide sequencing of the corresponding cDNAs revealed that these two forms of lyn mRNA differ in the presence and absence of a 63 nucleotides sequence near the 5'-terminus of the coding region; 21 amino acid residues (Pro-23 to Arg-43 or Val-24 to Pro-44) of p56lyn were tentatively concluded to be missing in p53lyn. On cross-linking of the membrane-bound IgM (mIgM) on the surface of B lymphocytes, the kinetics of down-regulations of the two Lyn proteins demonstrated to be associated with the mIgM antigen receptor were found to be different. This observation suggests that the amino terminal proximal sequence of the Lyn protein is important for determining its mode of interaction with mIgM.