DoriC database

DoriC accession number ORI10010047
Organism Listeria monocytogenes EGD-e
RefSeq NC_003210.1
Topology Circular
Lineage Bacteria, Firmicutes, Bacillales, Listeriaceae, Listeria.
Chromosome size 2944528 nt
Chromosome GC content 0.3798
OriC length 193 nt
OriC AT content 0.6736
The number of DnaA box 5
The location of oriC region 1674..1866 nt
The location of dnaA gene 318..1673 nt
The extremes of GC disparity 2944494 nt (minimum), 1443681 nt (maximum)
Note Dif-like sequence acttcctataatatatattatgtaaact (1 chain) was found between 1442174 and 1442201 nt, matches 27 sites compared with the 28-bp dif sequence acttcctagaatatatattatgtaaact of B. subtilis.
DnaA-trio The oriC contains the DnaA-trio element (3'-TTTAGGTGTCGCGGATAATGATAATGAT-5') retrieved by BLAST. Please refer to Richardson T.T. et al 2016 (Nature 534.7607: 412) fro more details.
OriC Sequence

tagacctgtgtacaaTGTGGATAActgaaacatacTTACCCACAagTTATCAACATGTGGAAAActttatgcagcatggcttgtaacctacTTATCCACAaatccacagcgcctattactattactacgattttttattaattaattaaaggtttttgaggttttacaaaatataaaaaaatgggggatactc

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.

12 136 R 12 136 0 6.24e-04 attaattaatta
12 137 P 12 137 0 6.24e-04 ttaattaattaa
14 132 P 14 136 -1 1.64e-03 ttt[ta]attaattaat
11 136 C 11 138 0 2.50e-03 attaattaatt
11 167 R 11 167 0 2.50e-03 aaaatataaaa
13 32 F 13 88 -1 6.09e-03 tactta[ct]ccacaa
10 139 R 10 139 0 9.99e-03 aattaattaa
12 14 F 12 54 -1 2.25e-02 atgtgga[ta]aact
12 14 P 12 44 -1 2.25e-02 atgt[gt]gataact
12 133 F 12 137 -1 2.25e-02 tt[ta]attaattaa
9 15 P 9 91 0 4.00e-02 tgtggataa
9 112 F 9 118 0 4.00e-02 ctattacta
9 173 R 9 173 0 4.00e-02 taaaaaaat
11 133 R 11 136 -1 8.24e-02 tt[ta]attaatta
8 7 R 8 51 0 1.60e-01 gtgtacaa
8 129 R 8 129 0 1.60e-01 atttttta
8 130 P 8 172 0 1.60e-01 ttttttat
8 141 P 8 141 0 1.60e-01 ttaattaa
10 28 F 10 84 -1 3.00e-01 aac[ac]tactta
10 133 C 10 139 -1 3.00e-01 tt[ta]attaatt
7 15 P 7 101 0 6.39e-01 tgtggat
7 19 P 7 44 0 6.39e-01 gataact
7 93 F 7 101 0 6.39e-01 atccaca
7 129 C 7 173 0 6.39e-01 atttttt
7 129 P 7 175 0 6.39e-01 atttttt
7 130 C 7 175 0 6.39e-01 tttttta
7 149 F 7 158 0 6.39e-01 aggtttt
7 151 R 7 151 0 6.39e-01 gtttttg
9 7 C 9 40 -1 1.08e+00 gtgt[at]caat
9 15 P 9 35 -1 1.08e+00 tgtgg[ag]taa
9 39 P 9 51 -1 1.08e+00 ccaca[at]gtt
9 46 F 9 91 -1 1.08e+00 ttatc[ac]aca
9 49 P 9 52 -1 1.08e+00 tc[ac]acatgt
9 55 P 9 91 -1 1.08e+00 tgtgga[at]aa
9 60 P 9 146 -1 1.08e+00 aaa[ac]cttta
9 68 P 9 68 -1 1.08e+00 atgc[at]gcat
9 129 C 9 164 -1 1.08e+00 at[tg]ttttat
9 130 C 9 167 -1 1.08e+00 tttt[ta]tatt
9 130 P 9 169 -1 1.08e+00 tttt[ta]tatt
9 133 P 9 136 -1 1.08e+00 tt[ta]attaat
9 147 C 9 162 -1 1.08e+00 aaa[gt]gtttt
9 170 F 9 172 -1 1.08e+00 ata[ta]aaaaa
6 8 C 6 52 0 2.56e+00 tgtaca
6 8 P 6 8 0 2.56e+00 tgtaca
6 12 R 6 81 0 2.56e+00 caatgt
6 18 C 6 111 0 2.56e+00 ggataa
6 27 R 6 164 0 2.56e+00 aaacat
6 35 C 6 179 0 2.56e+00 ttaccc
6 39 F 6 95 0 2.56e+00 ccacaa
6 46 R 6 117 0 2.56e+00 ttatca

Refseq NC_003210.1
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

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