Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones

Shusei Sato, Yasukazu Nakamura, Takakazu Kaneko, Tomohiko Katoh, Erika Asamizu, Hirokazu Kotani, Satoshi Tabata

Research output: Contribution to journalArticlepeer-review

29 Citations (Scopus)

Abstract

In our ongoing project to deduce the nucleotide sequence of Arabidopsis thaliana chromosome 5, non-redundant P1 and TAC clones have been sequenced on the basis of the fine physical map, and as of January, 2000, the sequences of 16.6 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. Along with the sequence determination, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and we already predicted a total of 2697 potential protein coding genes in the 11, 166, 130 bp regions, which are covered by 159 P1 and TAC clones. In this paper, we describe the structural features of the 3,076,755 bp regions covered by newly analyzed 60 P1 and TAC clones. A total of 715 potential protein coding genes were identified, giving an average density of the genes identified of 1 gene per 4001 bp. Introns were observed in 80% of the genes, and the average number per gene and the average length of the introns were 4.5 and 147 bp, respectively. These sequence features are nearly identical to those in our latest report in which the data were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 12 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/kaos/.

Original languageEnglish
Pages (from-to)31-63
Number of pages33
JournalDNA Research
Volume7
Issue number1
DOIs
Publication statusPublished - 2000
Externally publishedYes

Keywords

  • Arabidopsis thaliana chromosome 5
  • P1 genomic library
  • TAC genomic library
  • gene prediction
  • genomic sequence

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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