DoriC: an updated database of bacterial and archaeal replication origins

Bacteria Archaea
1. Comparisons between the predicted oriC regions and those identified experimentally for some completely sequenced prokaryotic chromosomes.
2. The prediction results and performance evaluation of Ori-Finder 2 is avialable at Ori-Finder 2 Document.
Bacteria Prediction Location Experiment Location Year PubMed DoriC AC Reference
Escherichia coli K12 3923657..3924034 3923767..3924011 1980 6991883 ORI10020002 Replication origin of the Escherichia coli K-12 chromosome: the size and structure of the minimum DNA segment carrying the information for autonomous replication
Pseudomonas putida KT2440 8947..9541 8947..9541 1990 2106132 ORI10010029 Pseudomonas chromosomal replication origins: a bacterial class distinct from Escherichia coli-type origins
Bacillus subtilis 168 4214414..409 + 1751..1938 4214414..409 (oriCI) + 1748..1938 (oriCII) 1992 9701812 ORI10010005, ORI10010006 A Bacillus subtilis gene-encoding protein homologous to eukaryotic SMC motor protein is necessary for chromosome partition
Mycoplasma capricolum 1009729..1010023 1009729..1010023 1992 1544573 ORI10010178 Structure of the dnaA and DnaA-box region in the Mycoplasma capricolum chromosome: conservation and variations in the course of evolution
Streptomyces coelicolor 4269844..4270777 4269844..4270780 1992 1577691 ORI10010061 Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome.
Coxiella burnetii RSA 493 1835517..1836065 1835664..1836065 1994 8071197 ORI10040015 Cloning and characterization of an autonomous replication sequence from Coxiella burnetii
Mycobacterium tuberculosis 1525..2051 1349..3162 1996 8733228 ORI10040003 Organization of the origins of replication of the chromosomes of Mycobacterium smegmatis, Mycobacterium leprae and Mycobacterium tuberculosis and isolation of a functional origin from M. smegmatis
Thermus thermophilus HB8 1849496..54 1849496..54 2000 10835275 ORI10010133 Identification of the chromosomal replication origin from Thermus thermophilus and its interaction with the replication initiator DnaA
Helicobacter pylori J99 1559163..1559314 1559163..1559314 2001 11376143 ORI10010004 Identification of a putative chromosomal replication origin from Helicobacter pylori and its interaction with the initiator protein DnaA
Caulobacter crescentus CB15 4016703..234 4016703..234 2002 - ORI10040008 Control of Chromosome Replication in Caulobacter Crescentus
Sinorhizobium meliloti 1021 1..477 1..477 2006 16436432 ORI10030017 The Sinorhizobium meliloti chromosomal origin of replication
Thermoanaerobacter tengcongensis MB4 2689326..364 2689326..364 2007 17452366 ORI10010060 Mechanism for the TtDnaA–Tt-oriC cooperative interaction at high temperature and duplex opening at an unusual AT-rich region in Thermoanaerobacter tengcongensis
Nostoc sp. PCC 7120 2404398..2404811 2404398..2404811~ 2011 21493684 ORI10010051 Identification of the oriC region and its influence on heterocyst development in the filamentous cyanobacterium Anabaena sp. strain PCC 7120
Caulobacter crescentus NA1000 4034858..4034961 4034858..4034961 2011 21843309 ORI92740179 The Caulobacter crescentus chromosome replication origin evolved two classes of weak DnaA binding sites
Helicobacter pylori 26695 1608998..1609149 1607395..1607624, 1608998..1609149 2012 22904070 ORI96010512 Helicobacter pylori oriC—the first bipartite origin of chromosome replication in Gram-negative bacteria
Cytophaga hutchinsonii ATCC 33406 4057683..4058133 4057683..4058133~ 2012 21935590 ORI30030113 Development of replicative oriC plasmids and their versatile use in genetic manipulation of Cytophaga hutchinsonii
Synechococcus elongatus PCC 7942 2695796..64 2695796..64~ 2012 22403820 ORI10030082 Light-dependent and asynchronous replication of cyanobacterial multi-copy chromosomes
Halomonas campaniensis strain LS21 1385994..1386513 1385994..1386513 2014 28348508 - A seawater-based open and continuous process for polyhydroxyalkanoates production by recombinant Halomonas campaniensis LS21 grown in mixed substrates
Cyanothece ATCC 51142 1886587..1887114 1886996..1887035 2015 26696980 ORI92330201;  ORI92330202 Identification of the Replication Origins from Cyanothece ATCC 51142 and Their Interactions with the DnaA Protein From In Silico to In Vitro Studies
Arcobacter butzleri RM4018 2341023..2341251 2341023..2341251, 1318..1475 2016 27746772 ORI92240124 Unique and Universal Features of Epsilonproteobacterial Origins of Chromosome Replication and DnaA-DnaA Box Interactions
Thiomicrospira denitrificans ATCC 33889 2201475..14 2201475..14, 1323..1490 2016 27746772 ORI10010173 Unique and Universal Features of Epsilonproteobacterial Origins of Chromosome Replication and DnaA-DnaA Box Interactions
Wolinella succinogenes DSM 1740 2110228..2110355 2110228..2110355, 1315..1474 2016 27746772 ORI10010101 Unique and Universal Features of Epsilonproteobacterial Origins of Chromosome Replication and DnaA-DnaA Box Interactions
Bdellovibrio bacteriovorus HD100 1417..1648 1581..1626 2016 27965633 ORI10040030 Initiation of Chromosomal Replication in Predatory Bacterium Bdellovibrio bacteriovorus
Archaea Prediction Location Experiment Location Year PubMed DoriC AC Reference
Aeropyrum pernix K1 331264..331446 - - - - -
444838..445534 ~445000 2007 17392430 ORI10010002 Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes
Pyrococcus abyssi GE5 122701..123499 122701..123499 2000; 2003 12612604;- ORI10010003 Identification of short 'eukaryotic' Okazaki fragments synthesized from a prokaryotic replication origin; Bacterial Mode of Replication with Eukaryotic-Like Machinery in a Hyperthermophilic Archaeon
Methanothermobacter thermautotrophicus str. Delta H chromosome 1277375..1277679 1277180..1278180 2,008 17956224 - A conserved mechanism for replication origin recognition and binding in archaea
1277833..1278179 ORI10010005
Halobacterium sp. NRC-1 33916..34650 - - - - -
919978..920668 - - - - -
921863..922014 - - - - -
1806444..1807229 ~1800000 2003 19502403 ORI10010009 Multiple Replication Origins of Halobacterium sp. Strain NRC-1: Properties of the Conserved orc7-Dependent oriC1
Hyperthermus butylicus DSM 5456 5011..5539 ~5000 2007 17392430 ORI10010035 Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes
Haloferax volcanii DS2 11529..11896 - - - - -
570430..571176 ~570000 2013 24185008 ORI10010163 Accelerated growth in the absence of DNA replication origins
1593326..1594706 ~1594707 2007 17511521; 24185008 ORI10010164 Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii; Accelerated growth in the absence of DNA replication origins
1887008..1888353 - - - - -
1889584..1890203 - - - - -
2846902..257 ~258 2007 17511521; 24185008 ORI10010162 Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii; Accelerated growth in the absence of DNA replication origins
Haloarcula hispanica ATCC 33960 chromosome II 29015..29327 - - - - -
109422..110206 - - - - -
152106..152392 ~152106 2012 22978470 - Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea
191488..191811 - - - -
383109..383351 - - - - -
384540..385697 ~385697 2012 22978470 ORI10010179 Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea
488056..0 - - - - -
Haloarcula hispanica ATCC 33960 chromosome I 2994338..0 ~1 2012 22978470 ORI10010185 Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea
Nitrosopumilus maritimus SCM1 1644927..145 1644927..145 2013 23991938 ORI10010053 Mapping of active replication origins in vivo in thaum- and euryarchaeal replicons
Natrinema sp. J7 120674..121225 120345..123145 2017 28348508 ORI10010217 Construction of Expression Shuttle Vectors for the Haloarchaeon Natrinema sp. J7 Based on Its Chromosomal Origins of Replication
122480..122746 ORI10010218 Construction of Expression Shuttle Vectors for the Haloarchaeon Natrinema sp. J7 Based on Its Chromosomal Origins of Replication
435362..435598 - - - - -
437384..437454 - - - - -
1278254..1279363 - - - - -
1280840..1281049 - - - - -
2211357..2211903 2211560..2213764 2017 28348508 ORI10010222 Construction of Expression Shuttle Vectors for the Haloarchaeon Natrinema sp. J7 Based on Its Chromosomal Origins of Replication
2213131..2213289 ORI10010223 Construction of Expression Shuttle Vectors for the Haloarchaeon Natrinema sp. J7 Based on Its Chromosomal Origins of Replication
2573530..2574273 - - - - -
3151407..3151637 - - - - -
3153862..3154084 - - - - -