We have identified and characterized the approximately 12-kb cDNA of a novel human gene (designated HALR for "homologous to ALR" and given the symbol MLL3 by the HUGO Gene Nomenclature Committee) for which open reading frame (ORF) encodes a predicted large hydrophilic nuclear protein comprising 4,025 amino acids with a calculated molecular mass of approximately 443 kD. Within the amino acid sequence of HALR were identified a SUVAR3-9, enhancer of zeste, trithorax (SET) domain, three plant homeodomain (PHD)-type zinc fingers, a high motility group (HMG)-1 box, a leucine-zipper-like pattern, two potential transactivating domains, several nuclear localization signals, and multiple nuclear receptor interaction signature motifs. Especially within the SET domain, PHD fingers and several other regions, the HALR protein exhibits significant similarity to ALR (acute lymphoblastic leukemia [ALL]-1 related), ALL-1/myeloid/lymphoid or mixed-lineage leukemia (ALL-1/MLL), and trithorax, evolutionarily conserved proteins that influence differentiation and development. Northern blot analysis demonstrated transcripts of approximately 11-12 kb, while reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that HALR is expressed in a wide range of human tissues and cancer cell lines. The HALR gene contains 46 exons, is estimated to span >101 kb, and is located on chromosome region 7q36. Terminal 7q deletions are common chromosomal aberrations encountered in hematological neoplasia and in holoprosencephaly 3, a midline embryonic defect involving forebrain development. We have also isolated the partial cDNA of the murine homologue of HALR, which displays high homology to its human counterpart. Taking into consideration its notable protein motifs, ubiquitous expression, evolutionary conservation and chromosomal position, HALR is likely to play a housekeeping role in transcriptional regulation, and may be involved in leukemogenesis and developmental disorders.