Allellic loss of chromosome 12p is a frequent event in childhood acute lymphoblastic leukemia. This region is also deleted in several other hematological malignancies and in a variety of solid tumors, suggesting the presence of a tumor suppressor gene. The chromosomal region containing this suppressor locus was narrowed down to an interval of approximately 750 kilobases delimited by D12S98 and D12S358. Since no known candidate gene was found, we initiated the construction of a detailed transcription map, focusing on a contig of four overlapping BACs. We applied a strategy integrating several complementary approaches: (1) application of computer-based data-mining tools to the existing genomic sequence (750 kb) derived form the BAC contig; (2) deployment of exon amplification and expressed sequence tag resources to identify putative complementary DNAs; (3) determination of the general expression pattern by polymerase chain reaction with reverse transcription and northern blotting and (4) comparative genomic analysis with distant vertebrate species such as Fugu rubripes and Tetraodon nigroviridis. This transcript-mapping strategy has identified 32 potential transcription units, including 2 known genes, 5 new genes, 9 Unigene entries and 16 other expressed sequence tag clusters. The region also contains five pseudogenes. The map should facilitate subsequent efforts to characterize the candidate genes. This study illustrates how the integration of genome-based approaches facilitates the identification of genes in a large interval.