rep:Gene: Difference between revisions
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|{{Sub}}[[#Sequence Features|Sequence Features]] | |{{Sub}}[[#Sequence Features|Sequence Features]] | ||
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]] | |{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]] | ||
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]] | |||
|{{Sub}}[[#Genetic Resources |Genetic Resources]] | |{{Sub}}[[#Genetic Resources |Genetic Resources]] | ||
|{{Sub}}[[#Accessions in Other Databases |Accessions]] | |{{Sub}}[[#Accessions in Other Databases |Accessions]] | ||
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****************************************************************************************** -->{{Gene_nomenclature_help}} | ****************************************************************************************** -->{{Gene_nomenclature_help}} | ||
{| | {| id="X46a9feac3337d" class=" tableEdit Gene_nomenclature_table" | ||
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!align=left {{table_heading_style}} |Synonyms | !align=left {{table_heading_style}} |Synonyms | ||
|| | || | ||
''ECK3770, b3778, JW5604, dasC, mbrA, mmrA, dasC?''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/> | ''ECK3770, b3778, JW5604, dasC, mbrA, mmrA, dasC?''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, mmrA?'' | ||
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****************************************************************************************** -->{{Gene_location_help}} | ****************************************************************************************** -->{{Gene_location_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N46a9feacb6204" class=" tableEdit Gene_location_table" | ||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links | !|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links | ||
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85.32 minutes | 85.32 minutes | ||
| | | | ||
MG1655: 3958700..3960721<br /> | MG1655: 3958700..3960721<br /><gbrowseImage> | ||
name=NC_000913:3958700..3960721 | |||
source=MG1655 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | | | ||
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10837 EcoCyc] | *[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10837 EcoCyc] | ||
{{GBrowseLink| | {{GBrowseLink|MG1655|NC_000913|3957700|3961721|GBrowse(MG1655)}} | ||
| | | | ||
{{GBrowseFastaLink| | {{GBrowseFastaLink|MG1655|NC_000913|3958700|3960721|FASTA Dump}} | ||
*[http://biocyc.org/ECOLI/sequence?object=EG10837 EcoCyc Sequence Dump] | *[http://biocyc.org/ECOLI/sequence?object=EG10837 EcoCyc Sequence Dump] | ||
|- | |- | ||
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NC_012967: 3922479..3924500<br /> | NC_012967: 3922479..3924500<br /><gbrowseImage> | ||
name=NC_012967:3922479..3924500 | |||
source=REL606 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | | | ||
{{GBrowseLink|REL606|NC_012967|3922479|3924500|GBrowse (REL606)}} | {{GBrowseLink|REL606|NC_012967|3922479|3924500|GBrowse (REL606)}} | ||
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NC_012759: 3848369..3850390<br /> | NC_012759: 3848369..3850390<br /><gbrowseImage> | ||
name=NC_012759:3848369..3850390 | |||
source=BW2952 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | | | ||
{{GBrowseLink|BW2952| | {{GBrowseLink|BW2952|NC_012759|3848369|3850390|GBrowse (BW2952)}} | ||
| | | | ||
{{GBrowseFastaLink|BW2952| | {{GBrowseFastaLink|BW2952|NC_012759|3848369|3850390|FASTA Dump}} | ||
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W3110: 3676004..3673983<br /> | W3110: 3676004..3673983<br /><gbrowseImage> | ||
name=NC_007779:3673983..3676004 | |||
source=W3110 | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | | | ||
{{GBrowseLink| | {{GBrowseLink|W3110|NC_007779|3672983|3677004|GBrowse(W3110)}} | ||
| | | | ||
{{GBrowseFastaLink| | {{GBrowseFastaLink|W3110|NC_007779|3673983|3676004|FASTA Dump}} | ||
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DH10B: 4057620..4059641<br /> | DH10B: 4057620..4059641<br /><gbrowseImage> | ||
name=NC_010473:4057620..4059641 | |||
source=DH10B | |||
preset=GeneLocation | |||
</gbrowseImage> | |||
| | | | ||
{{GBrowseLink| | {{GBrowseLink|DH10B|NC_010473|4053578|4063683|GBrowse(DH10B)}} | ||
| | | | ||
{{GBrowseFastaLink| | {{GBrowseFastaLink|DH10B|NC_010473|4053578|4063683|FASTA Dump}} | ||
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****************************************************************************************** -->{{Gene_sequence_features_help}} | ****************************************************************************************** -->{{Gene_sequence_features_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="I46a9fead7adba" class=" tableEdit Gene_sequence_features_table" | ||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes | !|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes | ||
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****************************************************************************************** -->{{Gene_alleles_help}} | ****************************************************************************************** -->{{Gene_alleles_help}} | ||
{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46a9feadc506b" class=" tableEdit Gene_allele_table dataTable" | ||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments | !|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments | ||
|- | |- | ||
| | | | ||
''rep(del)'' (Keio:JW5604) | |||
| | | | ||
deletion | deletion | ||
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0012344 rep::Tn5KAN] | [http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0012344 rep::Tn5KAN-I-SceI] (FB21451) | ||
| | | | ||
Insertion at nt 508 in Minus orientation | |||
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PMID: | PMID:15262929 | ||
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[ | [http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21451] | ||
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contains [[pKD46]] | |||
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'' | ''rep-729(del)::kan'' | ||
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|- | |||
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rep in [[MDS42]] | |||
| | |||
deletion | |||
| | |||
| | |||
Sensitivity to | |||
| | |||
increased sensitivity to [[Bicyclomycin]] | |||
| | |||
PMID:21183718 | |||
| | |||
| | |||
Fig. 2 | |||
|- | |||
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mbrA4 | |||
| | |||
| | |||
| | |||
Growth Phenotype | |||
| | |||
no growth in the first few hours at non-permissive conditions but eventually resumed growth, after exposed to LB cells began to elongate | |||
LB-Mac- | |||
| | |||
PMID:2176633 | |||
| | |||
| | |||
|- | |||
| | |||
mbrA15 | |||
| | |||
| | |||
| | |||
Growth Phenotype | |||
| | |||
temperature sensitive, forms two distinct populations, one more dense and one less dense than wild type | |||
| | |||
PMID:2176633 | |||
| | |||
| | |||
|- | |||
| | |||
''mbrA4'' | |||
| | |||
| | |||
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Resistant to | |||
| | |||
camphor resistance | |||
| | |||
PMID:2176633 | |||
PMID:1925019 | |||
| | |||
| | |||
Table 2 and table 1 | |||
|- | |||
| | |||
''mrbA15'' | |||
| | |||
| | |||
| | |||
Resistant to | |||
| | |||
Resistant to camphor | |||
| | |||
PMID:2176633 | |||
PMID:1925019 | |||
| | |||
| | |||
table 2 and table 1 | |||
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===Notes=== | ===Notes=== | ||
==Genetic Interactions== | |||
{{BacktoTop}} | |||
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="G4e04c23ae6338" class=" tableEdit Genetic_interaction_table dataTable" | |||
|- {{table_heading_style}} | |||
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes | |||
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===Notes=== | |||
==Genetic Resources== | ==Genetic Resources== | ||
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Primer 2:CCTTTCCCTCGTTTTGCCGCCAT | Primer 2:CCTTTCCCTCGTTTTGCCGCCAT | ||
|- | |||
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[[:Category:Kohara_Phage:2A8|2A8]] | |||
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Kohara Phage | |||
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=556 Genobase] | |||
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PMID:3038334 | |||
|- | |||
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[[:Category:Kohara_Phage:2E6|2E6]] | |||
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Kohara Phage | |||
| | |||
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=557 Genobase] | |||
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PMID:3038334 | |||
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{| | {| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J46a9feaf34a80" class=" tableEdit Gene_accessions_table" | ||
|- {{table_heading_style}} | |- {{table_heading_style}} | ||
!|Database!!Accession!!Notes | !|Database!!Accession!!Notes | ||
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[[EcoCyc]] | |||
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EcoCyc:EG10837 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[EcoGene]] | |||
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EcoGene:EG10837 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[RegulonDB]] | |||
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RegulonDB:ECK120000828 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[http:// | [http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]]) | ||
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[http:// | [http://www.ncbi.nlm.nih.gov/gene?term=948292 GeneID:948292] | ||
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Escherichia coli str. K-12 substr. MG1655 | |||
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[[EchoBASE]] | |||
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EchoBASE:EB0830 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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[[ASAP]] | |||
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ASAP:ABE-0012344 | |||
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]] | |||
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Latest revision as of 20:49, 19 September 2013
{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>
| Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
| Nomenclature | Location(s) and DNA Sequence | Sequence Features | Alleles and Phenotypes | Genetic Interactions | Genetic Resources | Accessions | Links | References | Suggestions |
Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
rep |
|---|---|
| Mnemonic |
Replicase |
| Synonyms |
ECK3770, b3778, JW5604, dasC, mbrA, mmrA, dasC?[1][2], mmrA? |
| edit table |
Notes
Location(s) and DNA Sequence
See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.
| Strain | Map location | Genome coordinates | Genome browsers | Sequence links |
|---|---|---|---|---|
|
MG1655 |
85.32 minutes |
MG1655: 3958700..3960721 |
||
|
NC_012967: 3922479..3924500 |
||||
|
NC_012759: 3848369..3850390 |
||||
|
W3110 |
|
W3110: 3676004..3673983 |
||
|
DH10B: 4057620..4059641 |
||||
| edit table |
Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
| Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
|---|---|---|---|---|---|
|
Coding Start (SO:0000323) |
3958700 |
Edman degradation |
| ||
| edit table |
Notes
Alleles and Phenotypes
See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.
| Allele | Nt change(s) | AA change(s) | Phenotype: Type | Phenotype: Description | Reference | Availability | Comments |
|---|---|---|---|---|---|---|---|
|
rep(del) (Keio:JW5604) |
deletion |
deletion |
|||||
|
rep::Tn5KAN-I-SceI (FB21451) |
Insertion at nt 508 in Minus orientation |
contains pKD46 | |||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire Acetate |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire a-Hydroxybutyrate |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire a-Ketobutyrate |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire a-Ketoglutarate |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire Succinate |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire Bromosuccinate |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire L-Alanine |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire L-Asparagine |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire L-Aspartate |
||||
|
Δrep::kan |
deletion |
Biolog:respiration |
unable to respire L-Serine |
||||
|
rep-5 |
|||||||
|
rep-3 |
|||||||
|
rep-142(ts) |
temperature sensitive |
||||||
|
[rep-71] |
null allele | ||||||
|
rep-729(del)::kan |
|||||||
|
rep in MDS42 |
deletion |
Sensitivity to |
increased sensitivity to Bicyclomycin |
Fig. 2 | |||
|
mbrA4 |
Growth Phenotype |
no growth in the first few hours at non-permissive conditions but eventually resumed growth, after exposed to LB cells began to elongate LB-Mac- |
|||||
|
mbrA15 |
Growth Phenotype |
temperature sensitive, forms two distinct populations, one more dense and one less dense than wild type |
|||||
|
mbrA4 |
Resistant to |
camphor resistance |
Table 2 and table 1 | ||||
|
mrbA15 |
Resistant to |
Resistant to camphor |
table 2 and table 1 | ||||
| edit table |
Notes
Genetic Interactions
| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
| edit table |
Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW5604 |
Plasmid clone |
Status:cloned as old JW Primer 1:GCCCGTCTAAACCCCGGCCAACA Primer 2:CCTTTCCCTCGTTTTGCCGCCAT | |
|
Kohara Phage |
|||
|
Kohara Phage |
|||
|
Linked marker |
est. P1 cotransduction: 83% [15] | ||
|
metEo-3079::Tn10 |
Linked marker |
est. P1 cotransduction: 10% [15] | |
| edit table |
Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
| edit table |
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
<protect>
References
See Help:References for how to manage references in EcoliWiki.
- ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ Bialkowska-Hobrzanska, H et al. (1985) Escherichia coli rep gene: identification of the promoter and N terminus of the rep protein. J. Bacteriol. 164 1004-10 PubMed
- ↑ 4.0 4.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
- ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
- ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
- ↑ Takahashi, S et al. (1979) The rep mutation. VI. Purification and properties of the Escherichia coli rep protein, DNA helicase III. Can. J. Biochem. 57 855-66 PubMed
- ↑ Tessman, I et al. (1982) Relative map location of the rep and rho genes of Escherichia coli. J. Bacteriol. 151 1637-40 PubMed
- ↑ Washburn, RS & Gottesman, ME (2011) Transcription termination maintains chromosome integrity. Proc. Natl. Acad. Sci. U.S.A. 108 792-7 PubMed
- ↑ 10.0 10.1 10.2 10.3 Trun, NJ & Gottesman, S (1990) On the bacterial cell cycle: Escherichia coli mutants with altered ploidy. Genes Dev. 4 2036-47 PubMed
- ↑ 11.0 11.1 Trun, NJ & Gottesman, S () Characterization of Escherichia coli mutants with altered ploidy. Res. Microbiol. 142 195-200 PubMed
- ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
- ↑ 13.0 13.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
- ↑ 14.0 14.1 CGSC: The Coli Genetics Stock Center
- ↑ 15.0 15.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).