Rat kidney band 3 Cl-/HCO3- exchanger mRNA is transcribed from an alternative promoter

We have previously shown that the rat kidney band 3 Cl-/HCO3- exchanger mRNA encodes an NH2-terminal truncated form of band 3 and that its 5' end differs from that of the erythrocyte band 3 mRNA (K. E. Kudrycki and G. E. Shull. J. Biol. Chem. 264: 8185-8192, 1989). To determine the genetic basis for the alternative kidney and erythroid mRNAs, we 1) isolated and characterized a rat erythroid band 3 cDNA, 2) isolated the rat band 3 gene and determined the exon/intron organization of sequences corresponding to the alternative 5' ends of the rat kidney and erythroid mRNAs, and 3) identified the transcription initiation sites of the two transcripts. The unique sequences at the 5' end of the rat erythroid mRNA are derived from exons 1-3 and are followed directly by sequences from exon 4 that are common to both mRNAs. In the kidney mRNA, sequences upstream of exon 4 are derived entirely from intron 3. Primer extension and S1 nuclease protection analyses demonstrate the presence of multiple transcription initiation sites for the rat erythroid band 3 mRNA at the beginning of exon 1, whereas the transcription initiation site for the kidney mRNA is located within intron 3. Thus two distinct promoters, separated by almost 5 kb of genomic sequence, are responsible for the highly tissue-specific transcription of the alternative rat erythroid and kidney band 3 mRNAs.