queG:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|yjeS}}{{Tab On|Gene|yjeS}}{{Tab|Gene Product(s)|yjeS}}{{Tab|Expression|yjeS}}{{Tab|Evolution|yjeS}}{{Tab|On One Page|yjeS}}{{TabsBottom}}
{{Tab|Quickview|queG}}{{Tab On|Gene|queG}}{{Tab|Gene Product(s)|queG}}{{Tab|Expression|queG}}{{Tab|Evolution|queG}}{{Tab|On One Page|queG}}{{TabsBottom}}
{|
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|{{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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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''yjeS''  
''queG''
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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Systematic nomenclature<ref name='LIB:EcoGene'/>
Systematic nomenclature
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK4162, b4166, JW4124''<ref name='LIB:Riley_2006'/>
''ECK4162, b4166, JW4124''<ref name='LIB:Riley_2006'/>, yjeS, JW4124''
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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="D46aa08d4f0b4e"  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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94.64 minutes, 94.64 minutes&nbsp;
94.64 minutes, 94.64 minutes&nbsp;
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|
MG1655: 4392090..4390951<br />{{GBrowseFigureByCoord|4389951|4393090|ecoli|MG1655}}
MG1655: 4392090..4390951<br /><gbrowseImage>
name=NC_000913:4390951..4392090
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7843 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7843 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4389951..4393090 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4389951|4393090|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4390951..4392090&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4390951|4392090|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7843 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7843 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 4372222..4371083<br /><gbrowseImage>
name=NC_012967:4371083..4372222
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4371083|4372222|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4371083|4372222|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 4329686..4330825<br /><gbrowseImage>
name=NC_012759:4329686..4330825
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4329686|4330825|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|4329686|4330825|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 4398747..4397608<br />{{GBrowseFigureByCoord|4396608|4399747|ecoli_W3110|W3110}}  
W3110: 4398747..4397608<br /><gbrowseImage>
name=NC_007779:4397608..4398747
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4396608|4399747|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|4397608|4398747|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 4492452..4491313<br /><gbrowseImage>
name=NC_010473:4491313..4492452
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4396608..4399747 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|4489035|4494730|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4397608..4398747&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|4489035|4494730|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="A46aa08d5b8eb1"  class=" tableEdit Gene_sequence_features_table" 
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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="C46aa08d6103e2"  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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&Delta;yjeS (Keio:JW4124)
&Delta;yjeS (Keio:JW4124)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109250 CGSC10969]<ref name='LIB:cgsc'/>
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''&#916;yjeS788::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:105520|CGSC:105520]]
|
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Strain [[BW2952]]
|
G70A
 
G625A
|
 
|
 
|
 
|
PMID:19376874
|
 
|
Relative to MG1655.
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B4e04cb59af527"  class=" tableEdit Genetic_interaction_table dataTable" 
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46aa08d6cc7f2"  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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JW4124
JW4124
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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:CCGGCGTCACGCGGTAACCCTTT  
Primer 2:CCGGCGTCACGCGGTAACCCTTT  
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[[cadB:Gene|cadB2231::Tn10]]
[[cadB:Gene|cadB2231::Tn10]]
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CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 25% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 25% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zjd-2231::Tn10  
Synonyms:zjd-2231::Tn10  
|-
|-  
|
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[[cycA:Gene|cycA30::Tn10]]
[[cycA:Gene|cycA30::Tn10]]
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est. P1 cotransduction: 24% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 24% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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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=G7843 EcoCyc:G7843] 
EcoCyc:G7843
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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=EB2374 EchoBASE:EB2374] 
EcoGene:EG12481
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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=b4166 EcoliGenExpDB:b4166] 
RegulonDB:ECK120004339
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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=C5250 ECOL199310CYC:C5250]
[http://www.ncbi.nlm.nih.gov/gene?term=948686 GeneID:948686]
|
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12481 EcoGene:EG12481] 
EchoBASE:EB2374
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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=YJES ECOO157CYC:YJES] 
ASAP:ABE-0013641
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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:yje genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:51, 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

queG

Mnemonic

Systematic nomenclature

Synonyms

ECK4162, b4166, JW4124[1], yjeS, JW4124

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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

94.64 minutes, 94.64 minutes 

MG1655: 4392090..4390951
<gbrowseImage> name=NC_000913:4390951..4392090 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4372222..4371083
<gbrowseImage> name=NC_012967:4371083..4372222 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4329686..4330825
<gbrowseImage> name=NC_012759:4329686..4330825 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4398747..4397608
<gbrowseImage> name=NC_007779:4397608..4398747 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4492452..4491313
<gbrowseImage> name=NC_010473:4491313..4492452 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

ΔyjeS (Keio:JW4124)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10969[3]

ΔyjeS788::kan

PMID:16738554[2]

CGSC:105520

Strain BW2952

G70A

G625A

PMID:19376874[4]

Relative to MG1655.

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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

JW4124

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCAGAGCCCCTCGATCTCAA

Primer 2:CCGGCGTCACGCGGTAACCCTTT

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[3]

est. P1 cotransduction: 25% [6]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[3]

est. P1 cotransduction: 24% [6]

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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:G7843

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12481

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004339

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948686

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2374

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013641

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. ↑ Ferenci, T et al. (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J. Bacteriol. 191 4025-9 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 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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