Lymphocyte adhesion to high endothelial venule cells in lymphoid organs of mice is mediated by several cell-surface glycoproteins, one of which, gp90MEL-14, is detected by the MEL-14 monoclonal antibody (mAb). The MEL-14 mAb was used to select two variants of the EL4 cell line, EL4MEL-14-hi and EL4-MEL-14-lo, that have disparate cell surface expression of this adhesion receptor. A cDNA library constructed from EL4MEL-14-hi mRNA was enriched for sequences present at higher levels in EL4MEL-14-hi cells than EL4MEL-14-lo cells. Quantitative analysis of candidate differential clones by RNA probe protection methods identified five clones whose steady-state mRNA levels were increased in the EL4MEL-14-hi cells. One of these clones, DIFF6, is derived from an RNA whose expression level is higher in several cell lines producing high amounts of MEL-14-reactive gp90, and absent or present at lower levels in several cell lines expressing low levels of this glycoprotein. However, DIFF6 does not encode gp90MEL-14. The nucleotide sequence of this clone predicts a relatively hydrophilic protein characteristic of a cytoplasmic or nuclear protein. Present experiments indicate that expression of gp90MEL-14, a cell-surface-adhesion receptor molecule, may be coregulated with additional cytoplasmic or nuclear factors.