argT:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|argT}}{{Tab On|Gene|argT}}{{Tab|Gene Product(s)|argT}}{{Tab|Expression|argT}}{{Tab|Evolution|argT}}{{Tab|On One Page|argT}}{{TabsBottom}}
{{Tab|Quickview|argT}}{{Tab On|Gene|argT}}{{Tab|Gene Product(s)|argT}}{{Tab|Expression|argT}}{{Tab|Evolution|argT}}{{Tab|On One Page|argT}}{{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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{|   id="A46a9db0b0be65"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''argT''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''argT''
Arginine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2304, b2310, JW2307, G388, G7989''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15183.A46a9db0b0be65&page=15183&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2304, b2310, JW2307, G388, G7989, argP''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===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="U46a9db0b8962b"  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
|-
|-  
|
|
MG1655
MG1655
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52.27 minutes&nbsp;
52.27 minutes&nbsp;
|
|
MG1655: 2425813..2425031<br />{{GBrowseFigureByCoord|2424031|2426813|ecoli|MG1655}}
MG1655: 2425813..2425031<br /><gbrowseImage>
name=NC_000913:2425031..2425813
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10072 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10072 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2424031..2426813 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2424031|2426813|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2425031..2425813&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2425031|2425813|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10072 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10072 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2371383..2370601<br /><gbrowseImage>
name=NC_012967:2370601..2371383
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2370601|2371383|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2370601|2371383|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2310836..2311618<br /><gbrowseImage>
name=NC_012759:2310836..2311618
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2310836|2311618|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2310836|2311618|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2433237..2432455<br />{{GBrowseFigureByCoord|2431455|2434237|ecoli_W3110|W3110}}  
W3110: 2433237..2432455<br /><gbrowseImage>
name=NC_007779:2432455..2433237
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2431455|2434237|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2432455|2433237|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2431455..2434237 GBrowse(W3110)]
DH10B: 2517578..2516796<br /><gbrowseImage>
name=NC_010473:2516796..2517578
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2432455..2433237&plugin_action=Go FASTA Dump]
{{GBrowseLink|DH10B|NC_010473|2515232|2519142|GBrowse(DH10B)}}
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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="F46a9db0c409ea"  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]]
|
2425034
|
Edman degradation
|
PMID:3040734<br />PMID:9298646<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="L46a9db0c85b52"  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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ΔargT (Keio:JW2307)
|
deletion
|
deletion
|
Auxotrophies
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007621 argT::Tn5KAN-2] (FB20757)
|
Insertion at nt 661 in Minus orientation
|
 
|
Auxotrophies
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20757]
|
contains [[pKD46]]
 
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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="Z4e04b795e9f09"  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
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JW2307
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAAGAAGTCGATTCTCGCTCT
 
Primer 2:CCGTCACCGTAGACATTAAAGTC
|-
|
[[:Category:Kohara_Phage:9D2|9D2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=406 Genobase]
|
PMID:3038334
|-
|
[[yfbO:Gene|zfb-223::Tn10]]
|
Linked marker
|
CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 23% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zej-223::Tn10
|-
|
zfd-1::Tn10
|
Linked marker
|
CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zfb-1::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
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|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10072 EcoCyc:EG10072] 
EcoCyc:EG10072
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0070 EchoBASE:EB0070] 
EcoGene:EG10072
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2310 EcoliGenExpDB:b2310] 
RegulonDB:ECK120000068
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10072 EcoGene:EG10072]
[http://www.ncbi.nlm.nih.gov/gene?term=949030 GeneID:949030]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=ARGT ECOO157CYC:ARGT] 
EchoBASE:EB0070
|
|
''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/18529 CGSC:18529] 
ASAP:ABE-0007621
|
|
''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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==References==
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:arg genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 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

argT

Mnemonic

Arginine

Synonyms

ECK2304, b2310, JW2307, G388, G7989[1][2]

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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

52.27 minutes 

MG1655: 2425813..2425031
<gbrowseImage> name=NC_000913:2425031..2425813 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2371383..2370601
<gbrowseImage> name=NC_012967:2370601..2371383 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2310836..2311618
<gbrowseImage> name=NC_012759:2310836..2311618 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2433237..2432455
<gbrowseImage> name=NC_007779:2432455..2433237 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2517578..2516796
<gbrowseImage> name=NC_010473:2516796..2517578 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

2425034

Edman degradation

PMID:3040734[3]
PMID:9298646[4]


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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

ΔargT (Keio:JW2307)

deletion

deletion

Auxotrophies

PMID:16738554[5]

Shigen

argT::Tn5KAN-2 (FB20757)

Insertion at nt 661 in Minus orientation

Auxotrophies

PMID:15262929[6]

E. coli Genome Project:FB20757

contains pKD46

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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

JW2307

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAAGAAGTCGATTCTCGCTCT

Primer 2:CCGTCACCGTAGACATTAAAGTC

9D2

Kohara Phage

Genobase

PMID:3038334[8]

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[9]

est. P1 cotransduction: 23% [10]
Synonyms:zej-223::Tn10

zfd-1::Tn10

Linked marker

CAG18467 = CGSC7408[9]

est. P1 cotransduction: 2% [10]
Synonyms:zfb-1::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:EG10072

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10072

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000068

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949030

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0070

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007621

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Nonet, ML et al. (1987) The hisT-purF region of the Escherichia coli K-12 chromosome. Identification of additional genes of the hisT and purF operons. J. Biol. Chem. 262 12209-17 PubMed
  4. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  5. ↑ 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
  6. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  7. ↑ 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
  8. ↑ 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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