glnD: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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{| id="A46a9a9ea52151"  class=" tableEdit Gene_nomenclature_table"   
{|   id="A46a9a9ea52151"  class=" tableEdit Gene_nomenclature_table"   


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*  
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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="D46a9a9eacaca9"  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="D46a9a9eacaca9"  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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4.01 minutes 
4.01 minutes 
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MG1655: 188650..185978<br />{{GBrowseFigureByCoord|185978|188650|ecoli|MG1655}}
MG1655: 188650..185978<br /><gbrowseImage>
name=NC_000913:185978..188650
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11411 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11411 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|184978|189650|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|184978|189650|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|185978|188650|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|185978|188650|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11411 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11411 EcoCyc Sequence Dump]  
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NC_012967: 191492..188820<br />{{GBrowseFigureByCoord|188820|191492|REL606|NC_012967}}
NC_012967: 191492..188820<br /><gbrowseImage>
name=NC_012967:188820..191492
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|188820|191492|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|188820|191492|GBrowse (REL606)}}
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NC_012759: 185977..188649<br />{{GBrowseFigureByCoord|185977|188649|BW2952|NC_012759}}
NC_012759: 185977..188649<br /><gbrowseImage>
name=NC_012759:185977..188649
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|185977|NC_188649|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|185977|188649|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|185977|NC_188649|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|185977|188649|FASTA Dump}}  
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&nbsp;
&nbsp;
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W3110: 188650..185978<br />{{GBrowseFigureByCoord|185978|188650|ecoli_W3110|W3110}}
W3110: 188650..185978<br /><gbrowseImage>
name=NC_007779:185978..188650
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|184978|189650|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|184978|189650|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|185978|188650|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|185978|188650|FASTA Dump}}  
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DH10B: 162754..160082<br />{{GBrowseFigureByCoord|160082|162754|ecoli_DH10B|DH10B}}
DH10B: 162754..160082<br /><gbrowseImage>
name=NC_010473:160082..162754
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|154738|168098|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|154738|168098|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|154738|168098|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|154738|168098|FASTA Dump}}  


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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="H46a9a9eb73db4"  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="H46a9a9eb73db4"  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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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="H46a9a9ebb47ac"  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="H46a9a9ebb47ac"  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;glnD (Keio:JW0162)
''glnD(del) (Keio:JW0162)''
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deletion
deletion
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0000568 glnD]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0000568 glnD::Tn5KAN-2] (FB20031)
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Insertion at nt 2325 in Plus 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:FB20031]
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At position 2325 in Plus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB20031
does not contain [[pKD46]]  
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10907.A4e04bc25741ff-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04bc25741ff"  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.10907.A4e04bc25741ff&page=10907&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10907.A4e04bc25741ff--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="W46a9a9ec5d063"  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="W46a9a9ec5d063"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCCCCTTTATCGTTTGGATTGAG  
Primer 2:CCCCCTTTATCGTTTGGATTGAG  
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[[:Category:Kohara_Phage:21C8|21C8]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=119 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:12D5|12D5]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=120 Genobase]
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PMID:3038334
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{|   id="A46a9a9ece63ef"  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="A46a9a9ece63ef"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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=EG11411 EcoCyc:EG11411]
EcoCyc:EG11411
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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=EB1383 EchoBASE:EB1383]
EcoGene:EG11411
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0167 EcoliGenExpDB:b0167]
[http://www.ncbi.nlm.nih.gov/gene?term=944863 GeneID:944863]
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Escherichia coli str. K-12 substr. MG1655
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C0202 ECOL199310CYC:C0202]
RegulonDB:ECK120001377
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG11411 EcoGene:EG11411]
EchoBASE:EB1383
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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=GLND ECOO157CYC:GLND]
ASAP:ABE-0000568
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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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/704 CGSC:704]
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|-
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000568&formSubmitReturn=1 ASAP:ABE-0000568]
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{|   id="B46a677255873f"  class=" tableEdit Links_table"   
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|- {{table_heading_style}}
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:37, 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

glnD

Mnemonic

Glutamine

Synonyms

ECK0165, b0167, JW0162, glnD5[1]

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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

4.01 minutes 

MG1655: 188650..185978
<gbrowseImage> name=NC_000913:185978..188650 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 191492..188820
<gbrowseImage> name=NC_012967:188820..191492 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 185977..188649
<gbrowseImage> name=NC_012759:185977..188649 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 188650..185978
<gbrowseImage> name=NC_007779:185978..188650 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 162754..160082
<gbrowseImage> name=NC_010473:160082..162754 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

glnD(del) (Keio:JW0162)

deletion

deletion

PMID:16738554[2]

Shigen

glnD::Tn5KAN-2 (FB20031)

Insertion at nt 2325 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB20031

does not contain pKD46

GlnD G93

G93L or G93V

loss of UTase activity

PMID:20363937[4]

GlnD G94

G94D

loss of UTase activity

PMID:20363937[4]

GlnD D107

D107A or D107V or D107Y

loss of UTase activity

PMID:20363937[4]


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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

JW0162

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAATACCCTTCCAGAACAGTA

Primer 2:CCCCCTTTATCGTTTGGATTGAG

21C8

Kohara Phage

Genobase

PMID:3038334[6]

12D5

Kohara Phage

Genobase

PMID:3038334[6]

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[7]

est. P1 cotransduction: 21% [8]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[7]

est. P1 cotransduction: 13% [8]
Synonyms:zae-502::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:EG11411

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11411

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944863

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001377

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1383

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000568

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. ↑ 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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  4. ↑ 4.0 4.1 4.2 Zhang, Y et al. (2010) Mutagenesis and functional characterization of the four domains of GlnD, a bifunctional nitrogen sensor protein. J. Bacteriol. 192 2711-21 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 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
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  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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