asnA:Gene: Difference between revisions

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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3738, b3744, JW3722''<ref name='LIB:Riley_2006'/>
''ECK3738, b3744, JW3722''<ref name='LIB:Riley_2006'/>, JW3722''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="Z46a9fdd9e5eaf"  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="Z46a9fdd9e5eaf"  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: 3925178..3926170<br /><gbrowseImage>
MG1655: 3925178..3926170<br /><gbrowseImage>
name=NC_000913:3925178..3926170
name=NC_000913:3925178..3926170
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10091 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10091 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3924178|3927170|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3924178|3927170|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3925178|3926170|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3925178|3926170|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10091 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10091 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|3813511|NC_3814503|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3813511|3814503|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|3813511|NC_3814503|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|3813511|3814503|FASTA Dump}}  
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W3110: 3709526..3708534<br /><gbrowseImage>
W3110: 3709526..3708534<br /><gbrowseImage>
name=AC_000091:3708534..3709526
name=NC_007779:3708534..3709526
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|3707534|3710526|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3707534|3710526|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3708534|3709526|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3708534|3709526|FASTA Dump}}  
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DH10B: 4022762..4023754<br /><gbrowseImage>
DH10B: 4022762..4023754<br /><gbrowseImage>
name=NC_010473:4022762..4023754
name=NC_010473:4022762..4023754
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|4020778|4025738|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4020778|4025738|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4020778|4025738|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|4020778|4025738|FASTA Dump}}  


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*  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="K46a9fddaaa0a5"  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="K46a9fddaaa0a5"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="L46a9fddb000ac"  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="L46a9fddb000ac"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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;asnA (Keio:JW3722)
ΔasnA (Keio:JW3722)
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deletion
deletion
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deletion
deletion
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Auxotrophies
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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=109000 CGSC10719]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://cgsc2.biology.yale.edu/Strain.php?ID=109000 CGSC10719]<ref name='LIB:cgsc'/>  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0012242 asnA::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0012242 asnA::Tn5KAN-I-SceI] (FB21433)
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Insertion at nt 517 in Plus orientation
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Auxotrophies
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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:FB21433]
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At position 517 in Plus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB21433
contains [[pKD46]]  
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Auxotrophies
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leaky for the Asn- phenotype
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PMID:6102983
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[[cgscmutation:5119|CGSC:5119]]
[[cgscmutation:5119|CGSC:5119]]
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''&#916;asnA773::kan''
''ΔasnA773::kan''
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deletion
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deletion
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Auxotrophies
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18051.J4e04b7d3db0ed-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04b7d3db0ed"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.18051.J4e04b7d3db0ed&page=18051&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18051.J4e04b7d3db0ed--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="J46a9fddbb7e5f"  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="J46a9fddbb7e5f"  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:CCaAGCAGAGAAGGGACGCTCTC  
Primer 2:CCaAGCAGAGAAGGGACGCTCTC  
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[[:Category:Kohara_Phage:4F4|4F4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=559 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:2A1|2A1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=560 Genobase]
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PMID:3038334
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{|   id="O46a9fddc631ff"  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="O46a9fddc631ff"  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=EG10091 EcoCyc:EG10091]
EcoCyc:EG10091
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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=EB0089 EchoBASE:EB0089]
EcoGene:EG10091
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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=b3744 EcoliGenExpDB:b3744]
RegulonDB:ECK120000087
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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=C4672 ECOL199310CYC:C4672]
[http://www.ncbi.nlm.nih.gov/gene?term=948258 GeneID:948258]
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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=EG10091 EcoGene:EG10091]
EchoBASE:EB0089
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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]])
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[http://BioCyc.org/ECOO157/new-image?object=ASNA ECOO157CYC:ASNA]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/995 CGSC:995]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012242&formSubmitReturn=1 ASAP:ABE-0012242]
ASAP:ABE-0012242
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:49, 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

asnA

Mnemonic

Asparagine

Synonyms

ECK3738, b3744, JW3722[1], JW3722

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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

84.6 minutes 

MG1655: 3925178..3926170
<gbrowseImage> name=NC_000913:3925178..3926170 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3887516..3888508
<gbrowseImage> name=NC_012967:3887516..3888508 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3813511..3814503
<gbrowseImage> name=NC_012759:3813511..3814503 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3709526..3708534
<gbrowseImage> name=NC_007779:3708534..3709526 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4022762..4023754
<gbrowseImage> name=NC_010473:4022762..4023754 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

ΔasnA (Keio:JW3722)

deletion

deletion

Auxotrophies

PMID:16738554[2]

Shigen CGSC10719[3]

asnA::Tn5KAN-I-SceI (FB21433)

Insertion at nt 517 in Plus orientation

Auxotrophies

PMID:15262929[4]

E. coli Genome Project:FB21433

contains pKD46

asnA31

Auxotrophies

leaky for the Asn- phenotype

PMID:6102983[5]

CGSC:5119

ΔasnA773::kan

deletion

deletion

Auxotrophies

PMID:16738554[2]

CGSC:100104


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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

JW3722

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAAAACCGCTTACATTGCCAA

Primer 2:CCaAGCAGAGAAGGGACGCTCTC

4F4

Kohara Phage

Genobase

PMID:3038334[7]

2A1

Kohara Phage

Genobase

PMID:3038334[7]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[3]

est. P1 cotransduction: 9% [8]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[3]

est. P1 cotransduction: 86% [8]
Synonyms:zie-296::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:EG10091

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10091

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000087

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948258

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0089

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012242

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. ↑ Felton, J et al. (1980) Mutations in two unlinked genes are required to produce asparagine auxotrophy in Escherichia coli. J. Bacteriol. 142 221-8 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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