The human CD39-like-1 gene (CD39L1) was isolated from a selected cDNA library enriched for transcripts from regions of human Chromosome (Chr) 9q. Database searches with sequences of one group of clones from the selected cDNA library showed strong amino acid homology to the lymphoid cell activation antigen CD39, an ecto-apyrase gene from human and mouse. The full-length sequence for CD39L1 identified a putative 472 amino acid protein with greater than 60% identity with the chicken muscle ecto-ATPase protein, as well as homology to a number of other known ecto-ATPases and ecto-apyrases from rat, garden pea, yeast, and Toxoplasma gondii. A high level of amino acid identity suggests that CD39L1 is closely related to the chicken muscle ecto-ATPase. The presence of the human ABC2 gene on an overlapping cosmid and hybridizations to somatic cell mapping panels suggest that CD39L1 maps to human Chr 9q34. A mouse homolog was isolated (showing greater than 78% nucleotide sequence identity) and mapped by FISH to mouse Chr 2, the syntenic region of human 9q34. The genomic structure of CD39L1 reveals 9 exons covering less than 7 kb.