yaaI: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="D46a9a66b48d4f"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''yaaI''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''yaaI''
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
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||
''ECK0013, b0013, JW0012''<ref name='LIB:Riley_2006'/>, JW0012''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10603.D46a9a66b48d4f&page=10603&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0013, b0013, JW0012''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='125007'
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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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0.25 minutes&nbsp;
0.25 minutes&nbsp;
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MG1655: 11786..11382<br />{{GBrowseFigureByCoord|10382|12786|ecoli|MG1655}}
MG1655: 11786..11382<br /><gbrowseImage>
name=NC_000913:11382..11786
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8202 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8202 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:10382..12786 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|10382|12786|GBrowse(MG1655)}}
   
   
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:11382..11786&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|11382|11786|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G8202 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G8202 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 11784..11380<br /><gbrowseImage>
name=NC_012967:11380..11784
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|11380|11784|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|11380|11784|FASTA Dump}}
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[[BW2952]]
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NC_012759: 11382..11786<br /><gbrowseImage>
name=NC_012759:11382..11786
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|11382|11786|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|11382|11786|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 11786..11382<br />{{GBrowseFigureByCoord|10382|12786|ecoli_W3110|W3110}}  
W3110: 11786..11382<br /><gbrowseImage>
name=NC_007779:11382..11786
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|10382|12786|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|11382|11786|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 11786..11382<br /><gbrowseImage>
name=NC_010473:11382..11786
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:10382..12786 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|10574|12594|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:11382..11786&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|10574|12594|FASTA Dump}}
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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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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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0000043 yaaI::Tn5KAN-I-SceI] (FB20004)
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Insertion at nt 299 in Plus orientation
|
 
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PMID:15262929
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[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20004]
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does not contain [[pKD46]]
|-  
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&Delta;yaaI (Keio:JW0012)
''yaaI(del)'' (Keio:JW0012)
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deletion
deletion
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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]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106622 CGSC8341]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106622 CGSC8341]<ref name='LIB:cgsc'/>  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0000043 yaaI::Tn5KAN-I-SceI] (FB20003)
|
Insertion at nt 299 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20003]
|
contains [[pKD46]]
|-
|
''yaaI(del)::kan''
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
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''yaaI733(del)::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:103440|CGSC:103440]]
|
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0012
JW0012
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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:CCGTCGTCGCCGATAATTTTCAG  
Primer 2:CCGTCGTCGCCGATAATTTTCAG  
|-
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[[:Category:Kohara_Phage:9E4|9E4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=101 Genobase]
|
PMID:3038334
|-
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[[:Category:Kohara_Phage:6H3|6H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=102 Genobase]
|
PMID:3038334
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[[thrA:Gene|thrA34::Tn10]]
[[thrA:Gene|thrA34::Tn10]]
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CAG18442 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38985 CGSC7320]<ref name='LIB:cgsc'/>
CAG18442 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38985 CGSC7320]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 68% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 68% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:thr-34::Tn10  
Synonyms:thr-34::Tn10  
|-
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[[carB:Gene|carB96::Tn10]]
[[carB:Gene|carB96::Tn10]]
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CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 46% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 46% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:car-96::Tn10


Synonyms:car-96::Tn10
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G8202 EcoCyc:G8202] 
EcoCyc:G8202
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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]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1475 EchoBASE:EB1475] 
EcoGene:EG11513
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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]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0013 EcoliGenExpDB:b0013] 
RegulonDB:ECK120004453
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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]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0017 ECOL199310CYC:C0017]
[http://www.ncbi.nlm.nih.gov/gene?term=944751 GeneID:944751]
|
|
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=EG11513 EcoGene:EG11513] 
EchoBASE:EB1475
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YAAI ECOO157CYC:YAAI] 
ASAP:ABE-0000043
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yaa genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:36, 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

yaaI

Mnemonic

Systematic nomenclature

Synonyms

ECK0013, b0013, JW0012[1], JW0012

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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

0.25 minutes 

MG1655: 11786..11382
<gbrowseImage> name=NC_000913:11382..11786 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 11784..11380
<gbrowseImage> name=NC_012967:11380..11784 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 11382..11786
<gbrowseImage> name=NC_012759:11382..11786 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 11786..11382
<gbrowseImage> name=NC_007779:11382..11786 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 11786..11382
<gbrowseImage> name=NC_010473:11382..11786 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

yaaI::Tn5KAN-I-SceI (FB20004)

Insertion at nt 299 in Plus orientation

PMID:15262929[2]

E. coli Genome Project:FB20004

does not contain pKD46

yaaI(del) (Keio:JW0012)

deletion

deletion

PMID:16738554[3]

Shigen

CGSC8341[4]

yaaI::Tn5KAN-I-SceI (FB20003)

Insertion at nt 299 in Plus orientation

PMID:15262929[2]

E. coli Genome Project:FB20003

contains pKD46

yaaI(del)::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

yaaI733(del)::kan

PMID:16738554[3]

CGSC:103440


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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

JW0012

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAAATCCGTTTTTACGATTTC

Primer 2:CCGTCGTCGCCGATAATTTTCAG

9E4

Kohara Phage

Genobase

PMID:3038334[7]

6H3

Kohara Phage

Genobase

PMID:3038334[7]

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[4]

est. P1 cotransduction: 68% [8]
Synonyms:thr-34::Tn10

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[4]

est. P1 cotransduction: 46% [8]
Synonyms:car-96::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:G8202

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11513

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004453

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944751

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1475

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000043

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 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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. ↑ 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
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 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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