DoriC database

DoriC accession number ORI10010004
Organism Helicobacter pylori J99
RefSeq NC_000921.1
Topology Circular
Lineage Bacteria, Proteobacteria, Epsilonproteobacteria, Campylobacterales, Helicobacteraceae, Helicobacter.
Chromosome size 1643831 nt
Chromosome GC content 0.3919
OriC length 152 nt
OriC AT content 0.6776
The number of DnaA box 3
The location of oriC region 1559163..1559314 nt
The location of dnaA gene 1557789..1559162 nt
The extremes of GC disparity 1556599 nt (minimum), 686803 nt (maximum)
Note Here, the oriC region has been confirmed using in silico and in vitro studies. Please refer to Zawilak A. et al. 2001 (Nucleic Acids Res. 29(11):2251-2259) for more details. Note that the DnaA box motif (tcattcaca) was looked for with no more than one mismatch instead of E. coli perfect DnaA box (ttatccaca).
OriC Sequence

ggcgttattatagcgtgaataagtGGTGAATGAaaaaggaatagcaTGTGAATGAaaTGTGAATGAagccttaaaattaaggtgtttcttttaagggtttgtctataatgcttgctttataataagctaatggatgcgaaaaaaggattttc

The information of repeat
The following lines contain repeats found, one line each.
[1] - repeat length of the first part
[2] - starting position of the first part
[4] - repeat length of the second part
[5] - starting position of the second part
[6] - distance of this repeat
[7] - calculated evalue of this repeat
[8] - repeat sequence

For more details, please refer to The Manual of REPuter.

12 19 R 12 19 0 3.87e-04 taagtggtgaat
11 14 R 11 14 0 1.55e-03 gtgaataagtg
11 45 F 11 56 0 1.55e-03 atgtgaatgaa
10 25 F 10 47 0 6.20e-03 gtgaatgaaa
9 25 F 9 58 0 2.48e-02 gtgaatgaa
11 65 P 11 88 -1 5.11e-02 aa[gc]ccttaaaa
8 4 P 8 117 0 9.92e-02 ttattata
8 32 F 8 139 0 9.92e-02 aaaaagga
8 70 R 8 70 0 9.92e-02 ttaaaatt
8 137 R 8 137 0 9.92e-02 gaaaaaag
10 1 R 10 5 -1 1.86e-01 gcg[ta]tattat
10 28 R 10 31 -1 1.86e-01 aa[tg]gaaaaag
7 6 P 7 102 0 3.97e-01 attatag
7 84 R 7 84 0 3.97e-01 tttcttt
9 27 R 9 72 -1 6.69e-01 gaat[gt]aaaa
9 49 C 9 110 -1 6.69e-01 gaa[tc]gaaat
9 116 P 9 116 -1 6.69e-01 ttat[at]ataa
6 5 C 6 118 0 1.59e+00 tattat
6 14 F 6 25 0 1.59e+00 gtgaat
6 14 F 6 47 0 1.59e+00 gtgaat
6 14 F 6 58 0 1.59e+00 gtgaat
6 16 R 6 120 0 1.59e+00 gaataa
6 17 F 6 120 0 1.59e+00 aataag
6 19 R 6 58 0 1.59e+00 taagtg
6 19 R 6 47 0 1.59e+00 taagtg
6 31 F 6 137 0 1.59e+00 gaaaaa
6 31 R 6 139 0 1.59e+00 gaaaaa
6 32 R 6 137 0 1.59e+00 aaaaag
6 35 R 6 35 0 1.59e+00 aaggaa
6 68 P 6 76 0 1.59e+00 ccttaa
6 72 C 6 88 0 1.59e+00 aaaatt
6 74 R 6 74 0 1.59e+00 aattaa
6 76 F 6 90 0 1.59e+00 ttaagg
6 87 R 6 146 0 1.59e+00 ctttta
6 103 F 6 117 0 1.59e+00 tataat
6 116 P 6 116 0 1.59e+00 ttataa
6 118 R 6 118 0 1.59e+00 ataata
8 4 F 8 116 -1 2.38e+00 ttat[ta]ata
8 9 F 8 40 -1 2.38e+00 atagc[ga]tg
8 15 F 8 30 -1 2.38e+00 tgaa[ta]aag
8 16 R 8 30 -1 2.38e+00 gaa[ta]aagt
8 27 C 8 110 -1 2.38e+00 gaa[tc]gaaa
8 28 C 8 84 -1 2.38e+00 aa[ta]gaaaa
8 33 P 8 84 -1 2.38e+00 aaaag[ga]aa
8 49 R 8 73 -1 2.38e+00 gaat[gt]aaa
8 65 P 8 105 -1 2.38e+00 aagc[ca]tta
8 92 F 8 142 -1 2.38e+00 aagg[ga]ttt
8 103 P 8 113 -1 2.38e+00 tataa[ta]gc
7 1 P 7 104 -1 8.33e+00 gc[ga]ttat
7 3 C 7 102 -1 8.33e+00 g[ta]tatta

Refseq NC_000921.1
Legend Figure1 shows the Z-curves for the original sequence. Figure2 shows the Z-curves for the rotated sequence beginning and ending in dif site or the maximum of the GC disparity curve. Short vertical red line indicates the indicator gene (such as dnaA, dnaN, gidA, hemE etc) location, and short up vertical dark blue arrow indicates the identified oriC location, short down vertical brown arrow indicates dif site location. Purple peaks with the diamonds indicates the DnaA box clusters.
Figure 1
zcurve
Figure 2
zcurve

About
People
Publication
History
TUBIC
School of Science
Tianjin University, 300072
No. 92 Weijin Road
Nankai District, Tianjin
China
Tel: +86-22-27402697

Copyright © TUBIC, Tianjin University, Tianjin, China