Several modes of HCO3- transport occur in the kidney, including Na+-independent Cl/HCO3- exchange (mediated by the AE family of Cl-/HCO3- exchangers), sodium-dependent Cl-/HCO3- exchange, and Na+:HCO3- cotransport. The functional similarities between the Na+-coupled HCO3- transporters and the AE isoforms (i.e. transport of HCO3- and sensitivity to inhibition by 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid) suggested a strategy for cloning the other transporters based on structural similarity with the AE family. An expressed sequence tag encoding part of a protein that is related to the known anion exchangers was identified in the GenBankTM expressed sequence tag data base and used to design an oligonucleotide probe. This probe was used to screen a human kidney cDNA library. Several clones were identified, isolated, and sequenced. Two overlapping cDNA clones were spliced together to form a 7.6-kilobase cDNA that contained the entire coding region of a novel protein. Based on the deduced amino acid sequence, the cDNA encodes a protein with a Mr of 116,040. The protein has 29% identity with human brain AE3. Northern blot analysis reveals that the 7.6-kilobase mRNA is highly expressed in kidney and pancreas, with detectable levels in brain. Functional studies in transiently transfected HEK-293 cells demonstrate that the cloned transporter mediates Na+:HCO3- cotransport.