alaC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|yfdZ}}{{Tab On|Gene|yfdZ}}{{Tab|Gene Product(s)|yfdZ}}{{Tab|Expression|yfdZ}}{{Tab|Evolution|yfdZ}}{{Tab|On One Page|yfdZ}}{{TabsBottom}}
{{Tab|Quickview|alaC}}{{Tab On|Gene|alaC}}{{Tab|Gene Product(s)|alaC}}{{Tab|Expression|alaC}}{{Tab|Evolution|alaC}}{{Tab|On One Page|alaC}}{{TabsBottom}}
{|
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|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
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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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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yfdZ''  
''alaC''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''yfdZ, ECK2375, b2379, JW2376''<ref name='LIB:Riley_2006'/>, JW2376''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15325.G46a9dcace5e9e&page=15325&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2375, b2379, JW2376''<ref name='LIB:Riley_2006'/>
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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="P46a9dcad6eee1"  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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53.78 minutes&nbsp;
53.78 minutes&nbsp;
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|
MG1655: 2496317..2495079<br />{{GBrowseFigureByCoord|2494079|2497317|ecoli|MG1655}}
MG1655: 2496317..2495079<br /><gbrowseImage>
name=NC_000913:2495079..2496317
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7242 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7242 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2494079..2497317 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2494079|2497317|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2495079..2496317&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2495079|2496317|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7242 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7242 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2432519..2431281<br /><gbrowseImage>
name=NC_012967:2431281..2432519
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2431281|2432519|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|2431281|2432519|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2380884..2382122<br /><gbrowseImage>
name=NC_012759:2380884..2382122
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2380884|2382122|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2380884|2382122|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 2503741..2502503<br />{{GBrowseFigureByCoord|2501503|2504741|ecoli_W3110|W3110}}
W3110: 2503741..2502503<br /><gbrowseImage>
name=NC_007779:2502503..2503741
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2501503..2504741 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2501503|2504741|GBrowse(W3110)}}
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2502503..2503741&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2502503|2503741|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 2588082..2586844<br /><gbrowseImage>
name=NC_010473:2586844..2588082
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2584368|2590558|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2584368|2590558|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="S46a9dcae267f8"  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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<protect><!--Sequence_notes--></protect>
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====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="S46a9dcae6bd62"  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;yfdZ (Keio:JW2376)
&Delta;yfdZ (Keio:JW2376)
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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=108179 CGSC9898]<ref name='LIB:cgsc'/>
|
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''&#916;yfdZ788::kan''
|
 
|
 
|
 
|
 
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PMID:16738554
|
[[cgscmutation:104728|CGSC:104728]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9dcaf2326e"  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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JW2376
JW2376
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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:CCTTCCGCGTTTTCGTGAATATG  
Primer 2:CCTTCCGCGTTTTCGTGAATATG  
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zfd-1::Tn10
zfd-1::Tn10
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CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 89% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 89% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zfb-1::Tn10  
Synonyms:zfb-1::Tn10  
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|-  
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[[nupC:Gene|nupC510::Tn10]]
[[nupC:Gene|nupC510::Tn10]]
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est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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|- {{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]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7242 EcoCyc:G7242] 
EcoCyc:G7242
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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=EB3950 EchoBASE:EB3950] 
EcoGene:EG14198
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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=b2379 EcoliGenExpDB:b2379] 
RegulonDB:ECK120003817
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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=C2916 ECOL199310CYC:C2916]
[http://www.ncbi.nlm.nih.gov/gene?term=946850 GeneID:946850]
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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=EG14198 EcoGene:EG14198] 
EchoBASE:EB3950
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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=Z3644 ECOO157CYC:Z3644] 
ASAP:ABE-0007850
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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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:yfd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:42, 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

alaC

Mnemonic

Systematic nomenclature

Synonyms

yfdZ, ECK2375, b2379, JW2376[1], JW2376

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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

53.78 minutes 

MG1655: 2496317..2495079
<gbrowseImage> name=NC_000913:2495079..2496317 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2432519..2431281
<gbrowseImage> name=NC_012967:2431281..2432519 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2380884..2382122
<gbrowseImage> name=NC_012759:2380884..2382122 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2503741..2502503
<gbrowseImage> name=NC_007779:2502503..2503741 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2588082..2586844
<gbrowseImage> name=NC_010473:2586844..2588082 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

ΔyfdZ (Keio:JW2376)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9898[3]

ΔyfdZ788::kan

PMID:16738554[2]

CGSC:104728


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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

JW2376

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGCTGACACTCGCCCTGAACG

Primer 2:CCTTCCGCGTTTTCGTGAATATG

zfd-1::Tn10

Linked marker

CAG18467 = CGSC7408[3]

est. P1 cotransduction: 89% [5]
Synonyms:zfb-1::Tn10

nupC510::Tn10

Linked marker

CAG18468 = CGSC7410[3]

est. P1 cotransduction: 59% [5]

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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:G7242

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14198

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003817

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946850

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3950

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007850

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. ↑ 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
  5. ↑ 5.0 5.1 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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