Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned PI clones

Shusei Sato, Hirokazu Kotani, Yasukazu Nakamura, Takakazu Kaneko, Erika Asamizu, Masanobu Fukami, Nobuyuki Miyajima, Satoshi Tabata

Research output: Contribution to journalArticlepeer-review

69 Citations (Scopus)

Abstract

A total of 20 PI clones with an average insert size of 80 kb and each containing a marker(s) specifically mapped on chromosome 5 were isolated from a PI library of the Arabidopsis thaliana genome, and their nucleotide sequences were determined according to a shotgun-based strategy and precisely located on the physical map of chromosome 5 separately constructed. The total length of the sequenced regions were summed up to 1,621,245 bp. By comparison with the sequences in protein and EST databases and analysis with computer programs for gene modeling, a total of 347 potential protein-coding genes and/or gene segments with known or predicted functions were identified. The positions of exons which do not exhibit any similarity to known genes were also predicted. An average density of the genes and/or gene segments assigned so far is 1 gene/4,672 bp. Introns were identified in approximately 78% of the potential genes, and the average number and length of the introns per gene were 3.7 and 161 bp. The transcription level of the predicted genes was roughly monitored by counting the numbers of identified Arabidopsis ESTs. The sequence data and gene information are available through the World Wide Web at http://www.kazusa.or.jp/arabi/.

Original languageEnglish
Pages (from-to)215-230
Number of pages16
JournalDNA Research
Volume4
Issue number3
DOIs
Publication statusPublished - 1997

Keywords

  • Arabidopsis thaliana chromosome 5
  • Gene prediction
  • Genomic sequence
  • P1 genomic library

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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