argF:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|argF}}{{Tab On|Gene|argF}}{{Tab|Gene Product(s)|argF}}{{Tab|Expression|argF}}{{Tab|Evolution|argF}}{{Tab|On One Page|argF}}{{TabsBottom}}
{{Tab|Quickview|argF}}{{Tab On|Gene|argF}}{{Tab|Gene Product(s)|argF}}{{Tab|Expression|argF}}{{Tab|Evolution|argF}}{{Tab|On One Page|argF}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''argF''  
''argF''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Arginine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0274, b0273, JW0266, Arg5''<ref name='LIB:Riley_2006'/>, Arg5, argD''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11125.L46a9ac537a3da&page=11125&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0274, b0273, JW0266, Arg5, argD''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9ac53f34a0"  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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MG1655
MG1655
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6.22 minutes&nbsp;
6.22 minutes&nbsp;
|
|
MG1655: 289529..288525<br />{{GBrowseFigureByCoord|287525|290529|ecoli|MG1655}}
MG1655: 289529..288525<br /><gbrowseImage>
name=NC_000913:288525..289529
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10067 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10067 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:287525..290529 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|287525|290529|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:288525..289529&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|288525|289529|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10067 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10067 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 289529..288525<br />{{GBrowseFigureByCoord|287525|290529|ecoli_W3110|W3110}}  
W3110: 289529..288525<br /><gbrowseImage>
name=NC_007779:288525..289529
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|287525|290529|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|288525|289529|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 265079..264075<br /><gbrowseImage>
name=NC_010473:264075..265079
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:287525..290529 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|262067|267087|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:288525..289529&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|262067|267087|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9ac549cebb"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
288528
|
Edman degradation
|
PMID:3968036<br />
|
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9ac54ddc8f"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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ΔargF (Keio:JW0266)
|
deletion
|
deletion
|
Auxotrophies
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106763 CGSC8482]<ref name='LIB:cgsc'/>
|
|-
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''argF45''
|
 
|
 
|
Auxotrophies
|
 
|
 
|
[[cgscmutation:5160|CGSC:5160]]
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|-
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''argF58''
|
 
|
 
|
Auxotrophies
|
 
|
PMID:4873401
|
[[cgscmutation:5173|CGSC:5173]]
|
|-
|
''argF80''
|
 
|
 
|
Auxotrophies
|
 
|
 
|
[[cgscmutation:5196|CGSC:5196]]
|
|-
|
''ΔargF788::kan''
|
deletion
|
deletion
|
Auxotrophies
|
 
|
PMID:16738554
|
[[cgscmutation:100046|CGSC:100046]]
|
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S4e04b78556988"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0266
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCTCCGATTTATACAAAAAACA
 
Primer 2:CCCTCCCCAAGCGTTGCCATCAT
|-
|
[[:Category:Kohara_Phage:3C7|3C7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=130 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:21C10|21C10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=131 Genobase]
|
PMID:3038334
|-
|
[[proA:Gene|proA81::Tn10]]
|
Linked marker
|
CAG18447 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38993 CGSC7330]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 33% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[lacI:Gene|lacI3042::Tn10]]
|
Linked marker
|
CAG18439 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39002 CGSC7334]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
|
EcoCyc:EG10067
|
''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=EG10067 EcoCyc:EG10067] 
EcoGene:EG10067
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0065 EchoBASE:EB0065]
[http://www.ncbi.nlm.nih.gov/gene?term=944844 GeneID:944844]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0273 EcoliGenExpDB:b0273] 
RegulonDB:ECK120000063
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10067 EcoGene:EG10067] 
EchoBASE:EB0065
|
|
''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/1016 CGSC:1016] 
ASAP:ABE-0000939
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Gene List:CP4-6 prophage]]
[[Category:arg genes]][[Category:Gene_List:DH10B]]

Latest revision as of 20:37, 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

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

Standard name

argF

Mnemonic

Arginine

Synonyms

ECK0274, b0273, JW0266, Arg5[1], Arg5, argD

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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

6.22 minutes 

MG1655: 289529..288525
<gbrowseImage> name=NC_000913:288525..289529 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 289529..288525
<gbrowseImage> name=NC_007779:288525..289529 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 265079..264075
<gbrowseImage> name=NC_010473:264075..265079 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

Coding Start (SO:0000323)

MG1655

288528

Edman degradation

PMID:3968036[2]


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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

ΔargF (Keio:JW0266)

deletion

deletion

Auxotrophies

PMID:16738554[3]

Shigen

CGSC8482[4]

argF45

Auxotrophies

CGSC:5160

argF58

Auxotrophies

PMID:4873401[5]

CGSC:5173

argF80

Auxotrophies

CGSC:5196

ΔargF788::kan

deletion

deletion

Auxotrophies

PMID:16738554[3]

CGSC:100046


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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

JW0266

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTCCGATTTATACAAAAAACA

Primer 2:CCCTCCCCAAGCGTTGCCATCAT

3C7

Kohara Phage

Genobase

PMID:3038334[7]

21C10

Kohara Phage

Genobase

PMID:3038334[7]

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[4]

est. P1 cotransduction: 33% [8]

lacI3042::Tn10

Linked marker

CAG18439 = CGSC7334[4]

est. P1 cotransduction: % [8]
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).

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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:EG10067

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10067

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944844

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000063

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0065

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000939

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. ↑ Falmagne, P et al. (1985) Immunological and structural relatedness of catabolic ornithine carbamoyltransferases and the anabolic enzymes of enterobacteria. J. Bacteriol. 161 714-9 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ Glansdorff, N et al. () The dual genetic control of ornithine transcarbamylase synthesis in Escherichia coli K12. Mutat. Res. 4 743-51 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).

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