Recent characterization of the class III region of the human major histocompatibility complex (MHC), located in chromosome 6p21.3, has revealed that it is very gene dense and contains at least 47 transcriptional units. One of these is the gene G17, which lies 250 kb telomeric of the class II gene DRA. DNA sequence analysis of 5.5 kb of DNA corresponding to the G17 gene has revealed that it encodes PBX2, a homeodomain-containing protein with extensive similarity to PBX1 (which is involved in t(1;19) chromosomal translocations in acute pre-B-cell leukemias). Comparison of the genomic DNA sequence with the published PBX2 cDNA sequence, which are 99.7% identical, indicates that the G17 gene is split into 9 exons, with the intron/exon boundaries conforming to the normal pattern (AG/.../GT) for splice sites. Of the 9 differences observed between the PBX2 cDNA sequence and the G17 genomic sequence, only 1 is contained in the coding sequence and alters the derived amino acid sequence. This results in an Ile (PBX2)-Met (G17) substitution at amino acid 393 near the C-terminus. The PBX2 gene was originally localized only to human chromosome 3q22-q23. However, comparison of genomic and cosmid Southern blots clearly indicates that another copy(ies) of the PBX2 (G17) gene exist(s) in the genome. PCR amplification of exons III and IX of the G17 (PBX2) gene, corresponding to the coding and 3' untranslated regions, respectively, using as template genomic DNA from a panel of monochromosomal somatic human-rodent cell hybrids, gave specific products in hybrids that contain human chromosomes 6, 3, and 1. These results confirm that copies of the PBX2 gene are located on human chromosomes 6 and 3 and indicate that a gene homologous to PBX2 could exist on human chromosome 1. Further PCR analysis of the genes and reverse transcribed mRNA from the hybrid cell lines has revealed that the copies of the PBX2 gene on human chromosomes 6 and 1 are expressed, while the copy on human chromosome 3 may be a processed pseudogene.