Cocultivation of cells from the gamma irradiated D2XRII murine bone marrow stromal cell line with Interlcukin-3/granulocyte-macrophage colony-stimulating factor(GM-CSF)-dependent hematopoietic progenitor cell line FDC-PlJL26 stimulates the emergence of factor independent hematopoietic cell sublines. Several lines of evidence suggested that M-CSF or a protein antigenetically related to M-CSF(LSF) expressed by D2XRII cells, may have played a role in the emergence of the factor independent sublines. In an effort to isolate a factor antigenetically related to M-CSF, molecular clones were isolated from a D2XRII cDNA library that hybridized to a mouse M-CSF, genetic probe. Two of these molecular clones, designated 60.8.2 and 6452. contained an 885 base-pari(bp) deletion in the M-CSF coding region. Such a cDNA clone has not been previously described in the mouse but a cDNA clone homologous to it has been isolated from a human pancreatic tumor cell line, MIA-PaCa-2. Three transcripts(4.8 Kb, 3.4 kb, and 1.8kb) were detected that hybridized to an oligonucleotide that was specific to RNA transcripts containing the 60.8.2 deletion. These deleted transcripts do not appear to be induced by ionizing irradiation; however, two other M-CSF transcripts of sizes to 4.4 kb and 2.3 kb show increased accumulation after gamma irradiation. Reverse transcription-polymerase chain reaction(RT-PCR) revealed that the deletion specific transcript(8) were detected not only in D2XRII cells but also in several mouse bone marrow stromal cell lines and in several mouse tissues.