Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes

Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3124-9. doi: 10.1073/pnas.97.7.3124.


Recent studies revealed a striking difference in the genomic organization of classic cadherin genes and one family of "nonclassic cadherin" genes designated protocadherins. Specifically, the DNA sequences encoding the ectodomain repeats of classic cadherins are interrupted by multiple introns. By contrast, all of the encoded ectodomains of each member of the protocadherin gene clusters are present in one large exon. To determine whether large ectodomain exons are a general feature of protocadherin genes we have investigated the genomic organization of several additional human protocadherin genes by using DNA sequence information in GenBank. These genes include protocadherin 12 (Pcdh12), an ortholog of the mouse vascular endothelial cadherin-2 gene; hFmi1 and hFmi2, homologs of the Drosophila planar cell polarity gene, flamingo; hFat2, a homolog of the Drosophila tumor suppressor gene fat; and the Drosophila DN-cadherin and DE-cadherin genes. Each of these genes was found to be a member of the protocadherin subfamily, based on amino acid sequence comparisons of their ectodomains. Remarkably, all of these protocadherin genes share a common feature: most of the genomic DNA sequences encoding their ectodomains are not interrupted by an intron. We conclude that the presence of unusually large exons is a characteristic feature of protocadherin genes.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cadherins / chemistry
  • Cadherins / genetics*
  • Evolution, Molecular
  • Exons*
  • Humans
  • Introns
  • Membrane Proteins / genetics
  • Molecular Sequence Data
  • Phylogeny
  • Sequence Homology, Amino Acid


  • Cadherins
  • FAT1 protein, human
  • FAT2 protein, human
  • Membrane Proteins
  • fat1 protein, mouse

Associated data

  • GENBANK/AF231022
  • GENBANK/AF231023
  • GENBANK/AF231024
  • GENBANK/AF231025