Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence features of the regions of 4,504,864 bp covered by sixty P1 and TAC clones

Based on the physical map of Arabidopsis thaliana chromosome 3 previously constructed with CIC YAC, TAC, P1 and BAC clones (Sato, S. et al., DNA Res., 5, 163-168, 1998), a total of 60 P1 and TAC clones were sequenced, and the sequence features of the resulting 4,504,864 bp regions were analyzed by applying various computer programs for similarity search and gene modeling. As a result, a total of 1054 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4066 bp. Introns were observed in 77% of the genes, and the average number per gene and the average length of the introns were 3.9 and 156 bp, respectively. These sequence features are essentially identical to those of chromosome 5 in our previous reports, but the gene density was slightly higher than that observed for chromosomes 2 and 4. The regions also contained 10 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/.