argU: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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{|{{Prettytable}}
{|   id="X46a9b307a917a"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''argU''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''argU''
Arginine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0529, b0536, JWR0010, dnaY, pin''<ref name='LIB:Riley_2006'/>, argW, fimU, pin''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11635.X46a9b307a917a&page=11635&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK0529, b0536, JWR0010, dnaY, pin''<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="Q46a9b3082cea4"  class=" tableEdit Gene_location_table" 
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
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12.15 minutes&nbsp;
12.15 minutes&nbsp;
|
|
MG1655: 563946..564022<br />{{GBrowseFigureByCoord|562946|565022|ecoli|MG1655}}
MG1655: 563946..564022<br /><gbrowseImage>
name=NC_000913:563946..564022
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG30014 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG30014 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:562946..565022 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|562946|565022|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:563946..564022&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|563946|564022|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG30014 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG30014 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 536837..536913<br /><gbrowseImage>
name=NC_012967:536837..536913
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|536837|536913|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|536837|536913|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 466706..466782<br /><gbrowseImage>
name=NC_012759:466706..466782
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|466706|466782|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|466706|466782|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 563946..564022<br />{{GBrowseFigureByCoord|562946|565022|ecoli_W3110|W3110}}  
W3110: 563946..564022<br /><gbrowseImage>
name=NC_007779:563946..564022
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|562946|565022|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|563946|564022|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 503278..503354<br /><gbrowseImage>
name=NC_010473:503278..503354
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:562946..565022 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|503126|503506|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:563946..564022&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|503126|503506|FASTA Dump}}
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===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="J46a9b309145e8"  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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|
|
 
Auxotrophies
|
|
temperature sensitive
growth inhibition at high temperatures caused by a reduced intracellular level of tRNA
|
|
[[PMID:15317788]]<ref name=PMID:15317788/>
PMID:15317788
 
PMID:15317795
|
|
[[cgscmutation:10700|CGSC:10700]]
[[cgscmutation:10700|CGSC:10700]]
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:
Status:
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Primer 2:  
Primer 2:  
|-
|-
|
[[:Category:Kohara_Phage:2C4|2C4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=158 Genobase]
|
PMID:3038334
|-  
|
|
[[purK:Gene|purK79::Tn10]]
[[purK:Gene|purK79::Tn10]]
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CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:purE79::Tn10  
Synonyms:purE79::Tn10  
|-
|-  
|
|
[[dsbG:Gene|dsbG601::Tn10]]
[[dsbG:Gene|dsbG601::Tn10]]
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CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbd-601::Tn10, zbe-601::Tn10


Synonyms:zbd-601::Tn10, zbe-601::Tn10
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===Notes===
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!Database!!Accession!!Notes
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[[EcoCyc]]
|
EcoCyc:EG30014
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG30014 EcoCyc:EG30014] 
EcoGene:EG30014
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4177 EchoBASE:EB4177] 
RegulonDB:ECK120002457
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0536 EcoliGenExpDB:b0536]
[http://www.ncbi.nlm.nih.gov/gene?term=945161 GeneID:945161]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG30014 EcoGene:EG30014] 
EchoBASE:EB4177
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/17755 CGSC:17755] 
ASAP:ABE-0001840
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:arg genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

argU

Mnemonic

Arginine

Synonyms

ECK0529, b0536, JWR0010, dnaY, pin[1], argW, fimU, pin

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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

12.15 minutes 

MG1655: 563946..564022
<gbrowseImage> name=NC_000913:563946..564022 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 536837..536913
<gbrowseImage> name=NC_012967:536837..536913 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 466706..466782
<gbrowseImage> name=NC_012759:466706..466782 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 563946..564022
<gbrowseImage> name=NC_007779:563946..564022 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 503278..503354
<gbrowseImage> name=NC_010473:503278..503354 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

argU110(ts)

Auxotrophies

growth inhibition at high temperatures caused by a reduced intracellular level of tRNA

PMID:15317788[2]

PMID:15317795[3]

CGSC:10700


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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

Plasmid clone

Shigen

PMID:16769691[4]

Status:

Primer 1:

Primer 2:

2C4

Kohara Phage

Genobase

PMID:3038334[5]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[6]

est. P1 cotransduction: 66% [7]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[6]

est. P1 cotransduction: 1% [7]
Synonyms:zbd-601::Tn10, zbe-601::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:EG30014

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG30014

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002457

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945161

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4177

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001840

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. ↑ Grass, G et al. (2004) Linkage between catecholate siderophores and the multicopper oxidase CueO in Escherichia coli. J. Bacteriol. 186 5826-33 PubMed
  3. ↑ Sakamoto, K et al. (2004) The Escherichia coli argU10(Ts) phenotype is caused by a reduction in the cellular level of the argU tRNA for the rare codons AGA and AGG. J. Bacteriol. 186 5899-905 PubMed
  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. ↑ 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
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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).

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