Structural analysis of the human ret proto-oncogene using exon trapping

Abstract

A genomic contig of the human ret protooncogene was created with four overlapping cosmid clones isolated from two libraries. After southern analysis with portions of the ret cDNA, eight cosmid fragments were analysed in detail for the presence of ret exons using exon trapping. PCR products corresponding to spliced exons were isolated and subcloned. Exon boundaries were delineated by comparison of the PCR product sequence and the published ret cDNA sequence. The exons were initially positioned on a genomic map defined by BamHI, EcoRI and HindIII restriction sites. The positions of the exons were then refined by amplifying genomic DNA using primer pairs derived from one or more exons along the ret gene, the length of the PCR product indicating the approximate genomic distance between the exon sequences. The ret proto-oncogene is composed of at least 20 exons, ranging in size from 60 bp to 287 bp, distributed along 30 kb of genomic DNA. The extracellular domain is encoded by 10 exons and the cytoplasmic domain by 9 exons. The transmembrane domain is encoded by a single exon.