Background: Sca1, also known as Ly6A/E, is a member of the Ly6 multigene family of type V glycophosphatidylinositol anchored cell surface proteins. It is expressed on multipotent hematopoietic stem cells in bone marrow of mice with both the Ly6.1 and Ly6.2 allotypes. In the periphery, Sca1 exhibits a pattern of expression which is based on differences between the two allotypes. Ly6.1 strains (e.g., A, BALB/c, CBA, C3H/He, DBA/1, NZB) have few Sca1+ resting peripheral lymphocytes, whereas Ly6.2 strains (e.g., AKR, C57BL, C57BR, C57L, DBA/2, PL, SJL, SWR, 129) have relatively high numbers of Sca1+ lymphocytes. The expression of Sca1 is dramatically upregulated in all strains upon cellular activation.