argK:Gene: Difference between revisions

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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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|{{Prettytable}}
{|   id="F46a9e95d6e798"  class=" tableEdit Gene_nomenclature_table" 
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!{{table_heading_style}} |Standard name
|
''argK''
|-
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Standard name
|
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Arginine<ref name='LIB:EcoGene'/>
''argK''
|-
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Mnemonic
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''ECK2914, b2918, JW2885, ygfD''<ref name='LIB:Riley_2006'/>
Arginine
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!align=left {{table_heading_style}} |Synonyms
||
''ECK2914, b2918, JW2885, ygfD''<ref name='LIB:Riley_2006'/>, meaB, scpK?, ygfD''
 
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===Notes===
===Notes===
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<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="O46a9e95dee31a"  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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MG1655
MG1655
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65.97 minutes&nbsp;
65.97 minutes&nbsp;
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MG1655: 3061009..3062004<br />{{GBrowseFigureByCoord|3060009|3063004|ecoli|MG1655}}
MG1655: 3061009..3062004<br /><gbrowseImage>
name=NC_000913:3061009..3062004
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11445 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11445 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3060009..3063004 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3060009|3063004|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3061009..3062004&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3061009|3062004|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11445 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11445 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2948738..2949733<br /><gbrowseImage>
name=NC_012967:2948738..2949733
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2948738|2949733|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2948738|2949733|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2948157..2949152<br /><gbrowseImage>
name=NC_012759:2948157..2949152
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2948157|2949152|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2948157|2949152|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3061643..3062638<br />{{GBrowseFigureByCoord|3060643|3063638|ecoli_W3110|W3110}}
W3110: 3061643..3062638<br /><gbrowseImage>
name=NC_007779:3061643..3062638
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3060643..3063638 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3060643|3063638|GBrowse(W3110)}}
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3061643..3062638&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3061643|3062638|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 3154879..3155874<br /><gbrowseImage>
name=NC_010473:3154879..3155874
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3152889|3157864|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3152889|3157864|FASTA Dump}}
 
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9e95eaac42"  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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9e95ef1ccb"  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!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-
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argKS68R
|
 
|
S68R
|
Auxotrophies
|
(in strain: RC101)
|
 
|
 
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P27254 UniProt:P27254]
|-
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argKT154A
|
 
|
T154A
|
Auxotrophies
|
(in strain: RC101)
|
 
|
 
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P27254 UniProt:P27254]
|-  
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&Delta;argK (Keio:JW2885)
ΔargK (Keio:JW2885)
|
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deletion
deletion
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deletion
deletion
|
|
 
Auxotrophies
|
|


|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
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<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="C4e04b78b3fbab"  class=" tableEdit Genetic_interaction_table dataTable" 
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW2885
JW2885
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCATCAAAATATTGCGTCTGGAT  
Primer 2:CCATCAAAATATTGCGTCTGGAT  
|-
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[[:Category:Kohara_Phage:1A2|1A2]]
|
Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=471 Genobase]
|
PMID:3038334
|-  
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[[recD:Gene|recD1901::Tn10]]
[[recD:Gene|recD1901::Tn10]]
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|
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
|-
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|
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[[speA:Gene|speA210::Tn10]]
[[speA:Gene|speA210::Tn10]]
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CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 40% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 40% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgd-210::Tn10, zgf-210::Tn10


Synonyms:zgd-210::Tn10, zgf-210::Tn10
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
|
EcoCyc:EG11445
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
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|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11445 EcoCyc:EG11445] 
EcoGene:EG11445
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1415 EchoBASE:EB1415] 
RegulonDB:ECK120001409
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2918 EcoliGenExpDB:b2918]
[http://www.ncbi.nlm.nih.gov/gene?term=947412 GeneID:947412]
|
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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=EG11445 EcoGene:EG11445] 
EchoBASE:EB1415
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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]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YGFD ECOO157CYC:YGFD] 
ASAP:ABE-0009579
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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:arg genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:45, 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

argK

Mnemonic

Arginine

Synonyms

ECK2914, b2918, JW2885, ygfD[1], meaB, scpK?, ygfD

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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

65.97 minutes 

MG1655: 3061009..3062004
<gbrowseImage> name=NC_000913:3061009..3062004 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2948738..2949733
<gbrowseImage> name=NC_012967:2948738..2949733 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2948157..2949152
<gbrowseImage> name=NC_012759:2948157..2949152 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3061643..3062638
<gbrowseImage> name=NC_007779:3061643..3062638 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3154879..3155874
<gbrowseImage> name=NC_010473:3154879..3155874 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

argKS68R

S68R

Auxotrophies

(in strain: RC101)

Strain variation; seeded from UniProt:P27254

argKT154A

T154A

Auxotrophies

(in strain: RC101)

Strain variation; seeded from UniProt:P27254

ΔargK (Keio:JW2885)

deletion

deletion

Auxotrophies

PMID:16738554[2]

Shigen


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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

JW2885

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCATTAATGAAGCCACGCTGGC

Primer 2:CCATCAAAATATTGCGTCTGGAT

1A2

Kohara Phage

Genobase

PMID:3038334[4]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[5]

est. P1 cotransduction: % [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[5]

est. P1 cotransduction: 40% [6]
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:EG11445

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11445

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001409

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947412

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1415

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009579

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. ↑ 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. ↑ 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
  4. ↑ 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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