argU: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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''ECK0529, b0536, JWR0010, dnaY, pin''<ref name='LIB:Riley_2006'/>
''ECK0529, b0536, JWR0010, dnaY, pin''<ref name='LIB:Riley_2006'/>, argW, fimU, pin''


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{|   id="Q46a9b3082cea4"  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="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
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MG1655: 563946..564022<br /><gbrowseImage>
MG1655: 563946..564022<br /><gbrowseImage>
name=NC_000913:563946..564022
name=NC_000913:563946..564022
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
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*[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]
{{GBrowseLink|ecoli|NC_000913|562946|565022|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|562946|565022|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|563946|564022|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]  
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{{GBrowseLink|BW2952|012759|466706|NC_466782|GBrowse (BW2952)}}
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W3110: 563946..564022<br /><gbrowseImage>
W3110: 563946..564022<br /><gbrowseImage>
name=AC_000091:563946..564022
name=NC_007779:563946..564022
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|562946|565022|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|562946|565022|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|563946|564022|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|563946|564022|FASTA Dump}}  
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DH10B: 503278..503354<br /><gbrowseImage>
DH10B: 503278..503354<br /><gbrowseImage>
name=NC_010473:503278..503354
name=NC_010473:503278..503354
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|503126|503506|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|503126|503506|GBrowse(DH10B)}}
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{|   id="D46a9b308c8d83"  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="D46a9b308c8d83"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="J46a9b309145e8"  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="J46a9b309145e8"  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.11635.M4e04b7976aa78-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M4e04b7976aa78"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|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.11635.M4e04b7976aa78&page=11635&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="J46a9b309b05e3"  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="J46a9b309b05e3"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:  
Primer 2:  
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[[:Category:Kohara_Phage:2C4|2C4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=158 Genobase]
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PMID:3038334
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{|   id="C46a9b30a447eb"  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="C46a9b30a447eb"  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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EcoCyc:EG30014
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[[EcoGene]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG30014 EcoCyc:EG30014]
EcoGene:EG30014
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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]])
[[RegulonDB]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4177 EchoBASE:EB4177]
RegulonDB:ECK120002457
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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=b0536 EcoliGenExpDB:b0536]
[http://www.ncbi.nlm.nih.gov/gene?term=945161 GeneID:945161]
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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=EG30014 EcoGene:EG30014]
EchoBASE:EB4177
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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]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/17755 CGSC:17755]
ASAP:ABE-0001840
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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 20:33, 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

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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<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. ↑ 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).

Categories

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