argK: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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''ECK2914, b2918, JW2885, ygfD''<ref name='LIB:Riley_2006'/>
''ECK2914, b2918, JW2885, ygfD''<ref name='LIB:Riley_2006'/>, meaB, scpK?, ygfD''


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{|   id="O46a9e95dee31a"  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="O46a9e95dee31a"  class=" tableEdit Gene_location_table"   
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|- {{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: 3061009..3062004<br /><gbrowseImage>
MG1655: 3061009..3062004<br /><gbrowseImage>
name=NC_000913:3061009..3062004
name=NC_000913:3061009..3062004
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=EG11445 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11445 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3060009|3063004|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3060009|3063004|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3061009|3062004|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3061009|3062004|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11445 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11445 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|2948157|NC_2949152|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|2948157|2949152|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|2948157|NC_2949152|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|2948157|2949152|FASTA Dump}}  
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W3110: 3061643..3062638<br /><gbrowseImage>
W3110: 3061643..3062638<br /><gbrowseImage>
name=AC_000091:3061643..3062638
name=NC_007779:3061643..3062638
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|3060643|3063638|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3060643|3063638|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3061643|3062638|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3061643|3062638|FASTA Dump}}  
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DH10B: 3154879..3155874<br /><gbrowseImage>
DH10B: 3154879..3155874<br /><gbrowseImage>
name=NC_010473:3154879..3155874
name=NC_010473:3154879..3155874
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|3152889|3157864|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3152889|3157864|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3152889|3157864|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3152889|3157864|FASTA Dump}}  


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{|   id="Z46a9e95eaac42"  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="Z46a9e95eaac42"  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="R46a9e95ef1ccb"  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="R46a9e95ef1ccb"  class=" tableEdit Gene_allele_table dataTable"   
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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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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16403.C4e04b78b3fbab-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C4e04b78b3fbab"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.16403.C4e04b78b3fbab&page=16403&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="I46a9e95fae355"  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="I46a9e95fae355"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCATCAAAATATTGCGTCTGGAT  
Primer 2:CCATCAAAATATTGCGTCTGGAT  
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[[:Category:Kohara_Phage:1A2|1A2]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=471 Genobase]
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PMID:3038334
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{|   id="Z46a9e96052d17"  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="Z46a9e96052d17"  class=" tableEdit Gene_accessions_table"   
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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=EG11445 EcoCyc:EG11445]
EcoCyc:EG11445
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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=EB1415 EchoBASE:EB1415]
EcoGene:EG11445
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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=b2918 EcoliGenExpDB:b2918]
RegulonDB:ECK120001409
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11445 EcoGene:EG11445]
[http://www.ncbi.nlm.nih.gov/gene?term=947412 GeneID:947412]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=YGFD ECOO157CYC:YGFD]
EchoBASE:EB1415
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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=0009579&formSubmitReturn=1 ASAP:ABE-0009579]
ASAP:ABE-0009579
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:45, 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

argK

Mnemonic

Arginine

Synonyms

ECK2914, b2918, JW2885, ygfD[1], meaB, scpK?, ygfD

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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

65.97 minutes 

MG1655: 3061009..3062004
<gbrowseImage> name=NC_000913:3061009..3062004 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2948738..2949733
<gbrowseImage> name=NC_012967:2948738..2949733 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2948157..2949152
<gbrowseImage> name=NC_012759:2948157..2949152 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3061643..3062638
<gbrowseImage> name=NC_007779:3061643..3062638 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3154879..3155874
<gbrowseImage> name=NC_010473:3154879..3155874 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

argKS68R

S68R

Auxotrophies

(in strain: RC101)

Strain variation; seeded from UniProt:P27254

argKT154A

T154A

Auxotrophies

(in strain: RC101)

Strain variation; seeded from UniProt:P27254

ΔargK (Keio:JW2885)

deletion

deletion

Auxotrophies

PMID:16738554[2]

Shigen


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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

JW2885

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCATTAATGAAGCCACGCTGGC

Primer 2:CCATCAAAATATTGCGTCTGGAT

1A2

Kohara Phage

Genobase

PMID:3038334[4]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[5]

est. P1 cotransduction: % [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[5]

est. P1 cotransduction: 40% [6]
Synonyms:zgd-210::Tn10, zgf-210::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:EG11445

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11445

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001409

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947412

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1415

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009579

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. ↑ 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
  4. ↑ 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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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