Structural analysis of Arabidopsis thaliana chromosome 5. IX. Sequence features of the regions of 1,011,550 bp covered by seventeen P1 and TAG clones

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

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

Abstract

In this series of projects sequencing the entire genome of Arabidopsis thaliana chromosome 5, non-redundant PI and TAC clones have been sequenced according to the fine physical map, and as of May 7, 1999, the sequences of 16.2 Mb representing approximately 60% of chromosome 5 have been accumulated and released at our web site. In parallel, structural features of the sequenced regions have been analyzed by applying a variety of computer programs, and to date we have predicted a total of 2380 potential proteincoding genes in the 10,154,580 bp regions, which are covered by 142 PI and TAC clones. In this paper, we newly analyzed the structural features of the 1,011,550 bp regions covered by additional 17 PI and TAG clones, and predicted 298 protein-coding genes. The average density of the genes identified was 1 gene per 3394 bp. Introns were observed in 67% of the genes, and the average number per gene and the average length of the introns were 3.2 and 159 bp, respectively. The gene density became higher than the value estimated in the previously analyzed regions (1 gene per 4,267 bp), as the data in this paper were compiled based on a new standard of gene assignment including the computer-predicted hypothetical genes. The regions also contained 8 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 on the database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/arabi/.

Original languageEnglish
Pages (from-to)183-195
Number of pages13
JournalDNA Research
Volume6
Issue number3
DOIs
Publication statusPublished - 1999

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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