cspC:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1821, b1823, JW1812, msmB''<ref name='LIB:Riley_2006'/>
''ECK1821, b1823, JW1812, msmB''<ref name='LIB:Riley_2006'/>, msmB''


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{|   id="T46a9cfbcc8b5b"  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="T46a9cfbcc8b5b"  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=EG12204 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12204 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1904250|1906459|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1904250|1906459|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1905250|1905459|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1905250|1905459|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12204 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12204 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|1797309|NC_1797518|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|1797309|1797518|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|1797309|NC_1797518|FASTA Dump}}  
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W3110: 1909149..1908940<br /><gbrowseImage>
W3110: 1909149..1908940<br /><gbrowseImage>
name=AC_000091:1908940..1909149
name=NC_007779:1908940..1909149
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|1907940|1910149|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1907940|1910149|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1908940|1909149|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1908940|1909149|FASTA Dump}}  
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{{GBrowseLink|ecoli_DH10B|NC_010473|1995403|1996448|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1995403|1996448|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1995403|1996448|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1995403|1996448|FASTA Dump}}  


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{|   id="C46a9cfbd7c3e8"  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="C46a9cfbd7c3e8"  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="K46a9cfbdbffbe"  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="K46a9cfbdbffbe"  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
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&Delta;cspC (Keio:JW1812)
''cspC(del)'' (Keio:JW1812)
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deletion
deletion
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PMID:16738554
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107796 CGSC9515]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=107796 CGSC9515]<ref name='LIB:cgsc'/>  
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''&#916;cspC747::kan''
''cspC747(del)::kan''
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''cspC747(del)''::FRTKanFRT
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Mutagenesis rate
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Decreased stress-induced mutagenesis (SIM) phenotype.
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PMID:23224554
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Parental Strain: SMR4562
Experimental Strain: SMR12148
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Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
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SMR4562 yiaG-yfp FRTcatFRT ''cspC747(del)''::FRTKanFRT
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deletion
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Sigma <sup>S</sup> activity
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Decrease in Sigma<sup>S</sup> activity
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PMID:23224554
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Parental Strain: SMR10582
Experimental Strain: SMR14263
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See table S8 for full experimental data. 


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{|   id="M4e04b921af493"  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="M4e04b921af493"  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="W46a9cfbe72aeb"  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="W46a9cfbe72aeb"  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:CCGATAGCTGTTACGTTAACAGC  
Primer 2:CCGATAGCTGTTACGTTAACAGC  
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[[:Category:Kohara_Phage:15D5|15D5]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=335 Genobase]
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PMID:3038334
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{|   id="M46a9cfbf0f8fe"  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="M46a9cfbf0f8fe"  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=EG12204 EcoCyc:EG12204]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2120 EchoBASE:EB2120]
EcoCyc:EG12204
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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]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1823 EcoliGenExpDB:b1823]
EcoGene:EG12204
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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]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C2231 ECOL199310CYC:C2231]
RegulonDB:ECK120002092
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG12204 EcoGene:EG12204]
[http://www.ncbi.nlm.nih.gov/gene?term=946339 GeneID:946339]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=CSPC ECOO157CYC:CSPC]
EchoBASE:EB2120
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/35339 CGSC:35339]
ASAP:ABE-0006070
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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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=0006070&formSubmitReturn=1 ASAP:ABE-0006070]
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!|Name!!URL!!Comments
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Latest revision as of 20:39, 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

cspC

Mnemonic

Cold shock protein

Synonyms

ECK1821, b1823, JW1812, msmB[1], msmB

edit table


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

41.06 minutes, 41.06 minutes 

MG1655: 1905459..1905250
<gbrowseImage> name=NC_000913:1905250..1905459 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1886014..1885805
<gbrowseImage> name=NC_012967:1885805..1886014 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1797309..1797518
<gbrowseImage> name=NC_012759:1797309..1797518 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1909149..1908940
<gbrowseImage> name=NC_007779:1908940..1909149 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1996030..1995821
<gbrowseImage> name=NC_010473:1995821..1996030 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

Coding Start (SO:0000323)

MG1655

1905253

Edman degradation

PMID:8740179[2]
PMID:9298646[3]
PMID:9868784[4]


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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

cspC(del) (Keio:JW1812)

deletion

deletion

PMID:16738554[5]

Shigen

CGSC9515[6]

cspC747(del)::kan

PMID:16738554[5]

CGSC:100424

cspC747(del)::FRTKanFRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[7]

Parental Strain: SMR4562

Experimental Strain: SMR12148

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

SMR4562 yiaG-yfp FRTcatFRT cspC747(del)::FRTKanFRT

deletion

Sigma S activity

Decrease in SigmaS activity

PMID:23224554[7]

Parental Strain: SMR10582 Experimental Strain: SMR14263

See table S8 for full experimental data.

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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

JW1812

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCGCAAAGATTAAAGGTCAGGT

Primer 2:CCGATAGCTGTTACGTTAACAGC

15D5

Kohara Phage

Genobase

PMID:3038334[9]

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[6]

est. P1 cotransduction: 24% [10]
Synonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[6]

est. P1 cotransduction: 39% [10]

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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:EG12204

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12204

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002092

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946339

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2120

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006070

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. ↑ Pasquali, C et al. (1996) Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 17 547-55 PubMed
  3. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  4. ↑ Wasinger, VC & Humphery-Smith, I (1998) Small genes/gene-products in Escherichia coli K-12. FEMS Microbiol. Lett. 169 375-82 PubMed
  5. ↑ 5.0 5.1 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
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  8. ↑ 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
  9. ↑ 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
  10. ↑ 10.0 10.1 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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