ralR:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|lar}}{{Tab On|Gene|lar}}{{Tab|Gene Product(s)|lar}}{{Tab|Expression|lar}}{{Tab|Evolution|lar}}{{Tab|On One Page|lar}}{{TabsBottom}}
{{Tab|Quickview|ralR}}{{Tab On|Gene|ralR}}{{Tab|Gene Product(s)|ralR}}{{Tab|Expression|ralR}}{{Tab|Evolution|ralR}}{{Tab|On One Page|ralR}}{{TabsBottom}}
{|
{|
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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{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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==Nomenclature==
==Nomenclature==
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|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''lar''  
''ralR''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1345, b1348, JW5208, ydaB''<ref name='LIB:Riley_2006'/>
''ECK1345, b1348, JW5208, ydaB'', lar<ref name='LIB:Riley_2006'/>, lar, ral, ydaB''
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9c539a02e7"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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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MG1655
MG1655
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30.43 minutes&nbsp;
30.43 minutes&nbsp;
|
|
MG1655: 1411951..1411757<br />{{GBrowseFigureByCoord|1410757|1412951|ecoli|MG1655}}
MG1655: 1411951..1411757<br /><gbrowseImage>
name=NC_000913:1411757..1411951
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11900 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11900 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1410757..1412951 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|1410757|1412951|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1411757..1411951&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|1411757|1411951|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11900 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11900 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 1303816..1304010<br /><gbrowseImage>
name=NC_012759:1303816..1304010
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|012759|1303816|NC_1304010|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|012759|1303816|NC_1304010|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 1415641..1415447<br />{{GBrowseFigureByCoord|1414447|1416641|ecoli_W3110|W3110}}  
W3110: 1415641..1415447<br /><gbrowseImage>
name=NC_007779:1415447..1415641
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|1414447|1416641|GBrowse(W3110)}}
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{{GBrowseFastaLink|ecoli_W3110|NC_007779|1415447|1415641|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1414447..1416641 GBrowse(W3110)]
DH10B: 1501347..1501153<br /><gbrowseImage>
name=NC_010473:1501153..1501347
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1415447..1415641&plugin_action=Go FASTA Dump]
{{GBrowseLink|ecoli_DH10B|NC_010473|1500765|1501735|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1500765|1501735|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{|  id="D46a9c53a4ea63"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| {{Prettytable}} id="H46a9c53a90c21"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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&Delta;lar (Keio:JW5208)
|
deletion
|
deletion
|
 
|
 
|
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=109521 CGSC11240]<ref name='LIB:cgsc'/>
|
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004524 lar::Tn5KAN-2] (FB20282)
|
Insertion at nt 80 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20299]
|
does not contain [[pKD46]]
|-
|
''&#916;lar-785::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:101638|CGSC:101638]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y4e04c20119a35"  class=" tableEdit Genetic_interaction_table dataTable" 
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|  id="G46a9c53b3f626"  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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JW5208
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAGATATGACAATGTTAAACC
 
Primer 2:CCTACATGAACACCTCCATTATT
|-
|
[[:Category:Kohara_Phage:4A6|4A6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=262 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:2C3|2C3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=263 Genobase]
|
PMID:3038334
|-
|
[[recT:Gene|recT3061::Tn10]]
|
Linked marker
|
CAG12081 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39818 CGSC7375]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 96% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zcj-3061::Tn10, zda-3061::Tn10
|-
|
[[ompN:Gene|zhj-3076::Tn10]]
|
Linked marker
|
CAG18640 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40323 CGSC7453]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 45% <ref name='LIB:Nichols_linked_Tn'/>
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11900 EcoCyc:EG11900] 
EcoCyc:EG11900
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1845 EchoBASE:EB1845] 
EchoBASE:EB1845
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1348 EcoliGenExpDB:b1348]
[http://chase.ou.edu/macro/searchlink.php?bnum=b1348 EcoliGenExpDB:b1348]
|
|
   
   
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11900 EcoGene:EG11900] 
EcoGene:EG11900
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://BioCyc.org/ECOO157/new-image?object=LAR ECOO157CYC:LAR]
[http://BioCyc.org/ECOO157/new-image?object=LAR ECOO157CYC:LAR]
|
|
   
   
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])  
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])  
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/37053 CGSC:37053]
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/37053 CGSC:37053]
|
|
   
   
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[[ASAP]]
|
ASAP:ABE-0004524
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11900 ECOCYC:EG11900]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=945914 GeneID:945914]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120001829
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 
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===Notes===
===Notes===
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==Links==
==Links==
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Gene List:Rac prophage]]
[[Category:lar genes]][[Category:Gene_List:DH10B]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:29, 19 September 2013

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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

ralR

Mnemonic
Synonyms

ECK1345, b1348, JW5208, ydaB, lar[1], lar, ral, ydaB

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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

30.43 minutes 

MG1655: 1411951..1411757
<gbrowseImage> name=NC_000913:1411757..1411951 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1303816..1304010
<gbrowseImage> name=NC_012759:1303816..1304010 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1415641..1415447
<gbrowseImage> name=NC_007779:1415447..1415641 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1501347..1501153
<gbrowseImage> name=NC_010473:1501153..1501347 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

Δlar (Keio:JW5208)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11240[3]

lar::Tn5KAN-2 (FB20282)

Insertion at nt 80 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20299

does not contain pKD46

Δlar-785::kan

PMID:16738554[2]

CGSC:101638


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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

JW5208

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGATATGACAATGTTAAACC

Primer 2:CCTACATGAACACCTCCATTATT

4A6

Kohara Phage

Genobase

PMID:3038334[6]

2C3

Kohara Phage

Genobase

PMID:3038334[6]

recT3061::Tn10

Linked marker

CAG12081 = CGSC7375[3]

est. P1 cotransduction: 96% [7]
Synonyms:zcj-3061::Tn10, zda-3061::Tn10

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[3]

est. P1 cotransduction: 45% [7]

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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:EG11900

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1845

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1348

EcoGene

EcoGene:EG11900

Escherichia coli str. K-12 substr. MG1655

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:LAR

CGSC (EcoliWiki Page)

CGSC:37053

ASAP

ASAP:ABE-0004524

Escherichia coli str. K-12 substr. MG1655

EcoCyc (EcoliWiki Page)

ECOCYC:EG11900

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945914

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001829

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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).

Categories

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