Analysis of pufferfish homologues of the AT-rich human APP gene

L. Villard, Flora Tassone, T. Crnogorac-Jurčević, K. Clancy, K. Gardiner

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

Mutations in the beta-amyloid precursor protein (APP) gene are associated with some forms of Familial Alzheimer's Disease. The human APP gene is large, the 19 exons span approximately 300 kb, and AT-rich, at 40% GC. We have examined the genomic structure and cDNA sequence of the APP) gene in the pufferfish Fugu rubripes and Tetraodon fluviatilis, respectively. In contrast to human, the Fugu APP gene spans less than 10 kb of DNA, with the introns compacted 48-fold on average. Two exons, alternatively processed in humans, are absent in both pufferfish. APP is the largest, most AT-rich gene examined in Fugu and is also the most highly compressed. The genomic sequences spanning the human and the Fugu APP genes were analysed with a set of exon and gene prediction programs. Results show that these are highly reliable for the Fugu gene with lower false positive and false negative rates than are seen in the analysis of the human gene. Comparative analysis of Fugu sequences homologous to very AT-rich regions in the human genome may, therefore, be advantageous in gene-finding efforts, both for their highly reduced sizes and their reliable gene predictions.

Original languageEnglish (US)
Pages (from-to)17-24
Number of pages8
JournalGene
Volume210
Issue number1
DOIs
StatePublished - Mar 27 1998
Externally publishedYes

Keywords

  • Base composition
  • Beta-amyloid gene
  • Exon prediction
  • Fugu rubripes
  • Intron size

ASJC Scopus subject areas

  • Genetics

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    Villard, L., Tassone, F., Crnogorac-Jurčević, T., Clancy, K., & Gardiner, K. (1998). Analysis of pufferfish homologues of the AT-rich human APP gene. Gene, 210(1), 17-24. https://doi.org/10.1016/S0378-1119(98)00032-8