Full-length genomic clones for the alpha-chain of mouse Fc epsilon RI were isolated and the exon/intron structure of the gene determined. The gene consisted of 5 exons, of which the first and second comprised the 5' untranslated region and the leader sequence; the third and fourth, the extracellular domain; and the fifth, the transmembrane and cytosolic domains, plus the 3' untranslated region. The upstream region was highly homologous to that of the rat counterpart. Primer extension and RNase protection analyses revealed multiple transcription initiation sites, between 30 and 120 nucleotides 3' of the putative TATA box. Comparison with other Fc receptor genes (rat Fc epsilon RI, mouse Fc gamma RIII alpha, human Fc gamma RIIIB and human Fc gamma RIIIA alpha) revealed a high degree of gene organization conservation.