csgG: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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{| id="J46a9be229eec5"  class=" tableEdit Gene_nomenclature_table"   
{|   id="J46a9be229eec5"  class=" tableEdit Gene_nomenclature_table"   


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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1023, b1037, JW1020''<ref name='LIB:Riley_2006'/>
''ECK1023, b1037, JW1020''<ref name='LIB:Riley_2006'/>, agfG, JW1020''


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*  
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{|   id="H46a9be23238c5"  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="H46a9be23238c5"  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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23.71 minutes&nbsp;
23.71 minutes&nbsp;
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MG1655: 1100907..1100074<br />{{GBrowseFigureByCoord|1100074|1100907|ecoli|MG1655}}
MG1655: 1100907..1100074<br /><gbrowseImage>
name=NC_000913:1100074..1100907
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6543 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6543 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1099074|1101907|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1099074|1101907|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1100074|1100907|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1100074|1100907|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6543 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6543 EcoCyc Sequence Dump]  
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NC_012967: 1116253..1115420<br />{{GBrowseFigureByCoord|1115420|1116253|REL606|NC_012967}}
NC_012967: 1116253..1115420<br /><gbrowseImage>
name=NC_012967:1115420..1116253
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|1115420|1116253|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|1115420|1116253|GBrowse (REL606)}}
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NC_012759: 1003999..1004832<br />{{GBrowseFigureByCoord|1003999|1004832|BW2952|NC_012759}}
NC_012759: 1003999..1004832<br /><gbrowseImage>
name=NC_012759:1003999..1004832
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|1003999|NC_1004832|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|1003999|1004832|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|1003999|NC_1004832|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|1003999|1004832|FASTA Dump}}  
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&nbsp;
&nbsp;
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W3110: 1101925..1101092<br />{{GBrowseFigureByCoord|1101092|1101925|ecoli_W3110|W3110}}
W3110: 1101925..1101092<br /><gbrowseImage>
name=NC_007779:1101092..1101925
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_W3110|AC_000091|1100092|1102925|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1100092|1102925|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1101092|1101925|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1101092|1101925|FASTA Dump}}  
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DH10B: 1156352..1155519<br />{{GBrowseFigureByCoord|1155519|1156352|ecoli_DH10B|DH10B}}
DH10B: 1156352..1155519<br /><gbrowseImage>
name=NC_010473:1155519..1156352
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_DH10B|NC_010473|1153853|1158018|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1153853|1158018|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1153853|1158018|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1153853|1158018|FASTA Dump}}  


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{|   id="T46a9be23c3520"  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="T46a9be23c3520"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
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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="E46a9be24101f7"  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="E46a9be24101f7"  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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|-  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0003516 csgG]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0003516 csgG::Tn5KAN-2] (FB20087)
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Insertion at nt 685 in Minus orientation
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PMID:12519969
PMID:15262929
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[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20087]
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At position 685 in Minus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB20087
does not contain [[pKD46]]  
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csgG
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deletion
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Sensitivity to
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increases sensitivity to bicyclomycin
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PMID:21357484
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fig 2


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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12623.S4e04b919c10c0-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S4e04b919c10c0"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.12623.S4e04b919c10c0&page=12623&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12623.S4e04b919c10c0--></protect>
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="S46a9be24af60a"  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="S46a9be24af60a"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCGGATTCCGGTGGAACCGACAT  
Primer 2:CCGGATTCCGGTGGAACCGACAT  
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[[:Category:Kohara_Phage:9G7|9G7]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=230 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:1C7|1C7]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=231 Genobase]
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PMID:3038334
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{|   id="I46a9be2545d3c"  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="I46a9be2545d3c"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
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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=G6543 EcoCyc:G6543]
EcoCyc:G6543
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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=EB3189 EchoBASE:EB3189]
EcoGene:EG13413
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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=b1037 EcoliGenExpDB:b1037]
RegulonDB:ECK120003139
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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=C1299 ECOL199310CYC:C1299]
[http://www.ncbi.nlm.nih.gov/gene?term=945619 GeneID:945619]
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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=EG13413 EcoGene:EG13413]
EchoBASE:EB3189
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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=CSGG ECOO157CYC:CSGG]
ASAP:ABE-0003516
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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=0003516&formSubmitReturn=1 ASAP:ABE-0003516]
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Latest revision as of 20:31, 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

csgG

Mnemonic

Curlin sigma S-dependent growth

Synonyms

ECK1023, b1037, JW1020[1], agfG, JW1020

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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

23.71 minutes 

MG1655: 1100907..1100074
<gbrowseImage> name=NC_000913:1100074..1100907 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1116253..1115420
<gbrowseImage> name=NC_012967:1115420..1116253 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1003999..1004832
<gbrowseImage> name=NC_012759:1003999..1004832 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1101925..1101092
<gbrowseImage> name=NC_007779:1101092..1101925 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1156352..1155519
<gbrowseImage> name=NC_010473:1155519..1156352 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

ΔcsgG (Keio:JW1020)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8992[3]

csgG::Tn5KAN-2 (FB20087)

Insertion at nt 685 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20087

does not contain pKD46

ΔcsgG::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

ΔcsgG778::kan

PMID:16738554[2]

CGSC:100418

csgG

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[6]

fig 2

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Notes

Genetic Interactions

[back to top]



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


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

JW1020

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCCAGCGCTTATTTCTTTTGGT

Primer 2:CCGGATTCCGGTGGAACCGACAT

9G7

Kohara Phage

Genobase

PMID:3038334[8]

1C7

Kohara Phage

Genobase

PMID:3038334[8]

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[3]

est. P1 cotransduction: 21% [9]

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[3]

est. P1 cotransduction: 7% [9]

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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:G6543

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13413

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003139

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945619

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3189

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003516

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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 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
  6. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 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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