recJ:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2887, b2892, JW2860''<ref name='LIB:Riley_2006'/>
''ECK2887, b2892, JW2860''<ref name='LIB:Riley_2006'/>, JW2860''


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{|   id="Q46a9e8b550bcc"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9e8b550bcc"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10830 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10830 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3033395|3037128|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3033395|3037128|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3034395|3036128|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3034395|3036128|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10830 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10830 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|2921543|NC_2923276|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|2921543|2923276|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|2921543|NC_2923276|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|2921543|2923276|FASTA Dump}}  
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W3110: 3036762..3035029<br /><gbrowseImage>
W3110: 3036762..3035029<br /><gbrowseImage>
name=AC_000091:3035029..3036762
name=NC_007779:3035029..3036762
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|ecoli_W3110|AC_000091|3034029|3037762|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3034029|3037762|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3035029|3036762|FASTA Dump}}  
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{{GBrowseLink|ecoli_DH10B|NC_010473|3124799|3133464|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3124799|3133464|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3124799|3133464|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3124799|3133464|FASTA Dump}}  


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{|   id="O46a9e8b60cf78"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9e8b60cf78"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="U46a9e8b65428d"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="U46a9e8b65428d"  class=" tableEdit Gene_allele_table dataTable"   
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!|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
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''recJ284::Tn10''
''recJ284''::Tn''10'' (KD2238)
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Resistant to
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Mutation increases resistance to Thymineless Death (TLD). Figure 1.
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PMID:2848620
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[[cgscmutation:72003|CGSC:72003]]
[[cgscmutation:72003|CGSC:72003]]
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Parent Strain: KD2197
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{|   id="N4e04c22cf39a1"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N4e04c22cf39a1"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="T46a9e8b710fcc"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9e8b710fcc"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCAATTGGCCAGATATTGTCGAT  
Primer 2:CCAATTGGCCAGATATTGTCGAT  
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[[:Category:Kohara_Phage:5B4|5B4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=467 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:22H4|22H4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=468 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:5E11|5E11]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=469 Genobase]
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PMID:3038334
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{|   id="B46a9e8b7aa66f"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9e8b7aa66f"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10830 EcoCyc:EG10830]
EcoCyc:EG10830
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0823 EchoBASE:EB0823]
EcoGene:EG10830
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2892 EcoliGenExpDB:b2892]
RegulonDB:ECK120000821
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C3472 ECOL199310CYC:C3472]
[http://www.ncbi.nlm.nih.gov/gene?term=947367 GeneID:947367]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10830 EcoGene:EG10830]
EchoBASE:EB0823
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=RECJ ECOO157CYC:RECJ]
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ASAP:ABE-0009492
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/17965 CGSC:17965]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009492&formSubmitReturn=1 ASAP:ABE-0009492]
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!|Name!!URL!!Comments
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Latest revision as of 20:44, 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

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

recJ

Mnemonic

Recombination

Synonyms

ECK2887, b2892, JW2860[1], JW2860

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Notes

Location(s) and DNA Sequence

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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

65.4 minutes 

MG1655: 3036128..3034395
<gbrowseImage> name=NC_000913:3034395..3036128 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2923859..2922126
<gbrowseImage> name=NC_012967:2922126..2923859 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2921543..2923276
<gbrowseImage> name=NC_012759:2921543..2923276 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3036762..3035029
<gbrowseImage> name=NC_007779:3035029..3036762 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3129998..3128265
<gbrowseImage> name=NC_010473:3128265..3129998 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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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

ΔrecJ (Keio:JW2860)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10217[3]

recJ::Tn5KAN-I-SceI (FB20963)

Insertion at nt 1026 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20963

contains pKD46

recJ::Tn5KAN-I-SceI (FB20964)

Insertion at nt 1026 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20964

does not contain pKD46

recJ284::Tn10

Insertion of Tn10 (Tetracycline-resistance) at nucleotide 434 relative to GTG start codon

truncation

null phenotype, recombination deficient and UV-sensitive in recBC sbcA and recBC sbcBC backgrounds. Highly synergistic for UV-sensitivity, recombination deficiency and partial inviability with recBC.

[5]

CGSC

recJ77

G to A nucleotide 281

G to D amino acid 78

similar to recJ284, null

[5] [6]

recJ153 recJ154

GTG to GTA at start codon

None

Reduces expression of recJ gene, can be suppressed by mutations in initiation factor IF3 for translation

[7] [5] [8]

recJ153

CGSC:7801

recJ284::Tn10 (KD2238)

Resistant to

Mutation increases resistance to Thymineless Death (TLD). Figure 1.

PMID:2848620[9]

CGSC:72003

Parent Strain: KD2197

ΔrecJ743::kan

PMID:16738554[2]

CGSC:102628


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW2860

Plasmid clone

Shigen

PMID:16769691[10]

Status:Clone OK

Primer 1:GCCAAACAACAGATACAACTTCG

Primer 2:CCAATTGGCCAGATATTGTCGAT

5B4

Kohara Phage

Genobase

PMID:3038334[11]

22H4

Kohara Phage

Genobase

PMID:3038334[11]

5E11

Kohara Phage

Genobase

PMID:3038334[11]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: % [12]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: 9% [12]
Synonyms:zgd-210::Tn10, zgf-210::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10830

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10830

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000821

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947367

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0823

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009492

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 5.0 5.1 5.2 Lovett, ST & Clark, AJ (1984) Genetic analysis of the recJ gene of Escherichia coli K-12. J. Bacteriol. 157 190-6 PubMed
  6. ↑ Gillen, JR et al. (1981) Genetic analysis of the RecE pathway of genetic recombination in Escherichia coli K-12. J. Bacteriol. 145 521-32 PubMed
  7. ↑ Horii, Z & Clark, AJ (1973) Genetic analysis of the recF pathway to genetic recombination in Escherichia coli K12: isolation and characterization of mutants. J. Mol. Biol. 80 327-44 PubMed
  8. ↑ Haggerty, TJ & Lovett, ST (1997) IF3-mediated suppression of a GUA initiation codon mutation in the recJ gene of Escherichia coli. J. Bacteriol. 179 6705-13 PubMed
  9. ↑ Nakayama, K et al. (1988) Thymineless death in Escherichia coli mutants deficient in the RecF recombination pathway. Can. J. Microbiol. 34 905-7 PubMed
  10. ↑ 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
  11. ↑ 11.0 11.1 11.2 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
  12. ↑ 12.0 12.1 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).

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