zraR:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|zraR}}{{Tab On|Gene|zraR}}{{Tab|Gene Product(s)|zraR}}{{Tab|Expression|zraR}}{{Tab|Evolution|zraR}}{{Tab|On One Page|zraR}}{{TabsBottom}}
{{Tab|Quickview|zraR}}{{Tab On|Gene|zraR}}{{Tab|Gene Product(s)|zraR}}{{Tab|Expression|zraR}}{{Tab|Evolution|zraR}}{{Tab|On One Page|zraR}}{{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
|
||
''zraR''  
''zraR''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Zn resistance-associated
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3996, b4004, JW3968, hydG''<ref name='LIB:Riley_2006'/>, hydG''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18567.D46aa04826cac0&page=18567&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3996, b4004, JW3968, hydG''<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="F46aa0482ef35d"  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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90.55 minutes, 90.55 minutes&nbsp;
90.55 minutes, 90.55 minutes&nbsp;
|
|
MG1655: 4201343..4202668<br />{{GBrowseFigureByCoord|4200343|4203668|ecoli|MG1655}}
MG1655: 4201343..4202668<br /><gbrowseImage>
name=NC_000913:4201343..4202668
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10482 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10482 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4200343..4203668 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4200343|4203668|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4201343..4202668&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4201343|4202668|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10482 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10482 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4182905..4184230<br /><gbrowseImage>
name=NC_012967:4182905..4184230
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4182905|4184230|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4182905|4184230|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 4091023..4092348<br /><gbrowseImage>
name=NC_012759:4091023..4092348
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4091023|4092348|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4091023|4092348|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3433361..3432036<br />{{GBrowseFigureByCoord|3431036|3434361|ecoli_W3110|W3110}}  
W3110: 3433361..3432036<br /><gbrowseImage>
name=NC_007779:3432036..3433361
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3431036|3434361|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3431036..3434361 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|3432036|3433361|FASTA Dump}}
|-  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3432036..3433361&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 4301039..4302364<br /><gbrowseImage>
name=NC_010473:4301039..4302364
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|4298389|4305014|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4298389|4305014|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="H46aa0483b5e73"  class=" tableEdit Gene_sequence_features_table" 
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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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==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="S46aa04840cee7"  class=" tableEdit Gene_allele_table dataTable" 
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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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&Delta;zraR (Keio:JW3968)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109135 CGSC10854]<ref name='LIB:cgsc'/>
|
|-
|
&Delta;hydG::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;hydG::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;hydG::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketoglutarate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;hydG::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Aspartate]]
|
PMID:16095938
|
 
|
|-
|
''&#916;zraR775::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:106114|CGSC:106114]]
|
 
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===Notes===
===Notes===


==Genetic Interactions==
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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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JW3968
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCACGCACGATAATATCGATAT
 
Primer 2:CCACGCGACAGTTTTGCCAATAG
|-
|
[[thiC:Gene|thiC39::Tn10]]
|
Linked marker
|
CAG18500 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40361 CGSC7472]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 79% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:thi-39::Tn10
|-
|
[[malF:Gene|malF3089::Tn10]]
|
Linked marker
|
CAG12164 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40371 CGSC7476]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 19% <ref name='LIB:Nichols_linked_Tn'/>
 
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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}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10482 EcoCyc:EG10482] 
|
|
[[EcoCyc]]
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
EcoCyc:EG10482
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0477 EchoBASE:EB0477]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[[EcoGene]]
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
EcoGene:EG10482
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4004 EcoliGenExpDB:b4004]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[[RegulonDB]]
|-
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
RegulonDB:ECK120000475
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4962 ECOL199310CYC:C4962]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|-
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[http://www.ncbi.nlm.nih.gov/gene?term=948505 GeneID:948505]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10482 EcoGene:EG10482] 
Escherichia coli str. K-12 substr. MG1655
|-
|
|
[[EchoBASE]]
|-
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
EchoBASE:EB0477
|
|
[http://BioCyc.org/ECOO157/new-image?object=HYDG ECOO157CYC:HYDG]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[[ASAP]]
|-
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
ASAP:ABE-0013093
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/34252 CGSC:34252]
''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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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:zra genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:50, 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

zraR

Mnemonic

Zn resistance-associated

Synonyms

ECK3996, b4004, JW3968, hydG[1], hydG

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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

90.55 minutes, 90.55 minutes 

MG1655: 4201343..4202668
<gbrowseImage> name=NC_000913:4201343..4202668 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4182905..4184230
<gbrowseImage> name=NC_012967:4182905..4184230 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4091023..4092348
<gbrowseImage> name=NC_012759:4091023..4092348 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3433361..3432036
<gbrowseImage> name=NC_007779:3432036..3433361 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4301039..4302364
<gbrowseImage> name=NC_010473:4301039..4302364 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

ΔzraR (Keio:JW3968)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10854[3]

ΔhydG::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔhydG::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

ΔhydG::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

ΔhydG::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[4]

ΔzraR775::kan

PMID:16738554[2]

CGSC:106114


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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

JW3968

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCACGCACGATAATATCGATAT

Primer 2:CCACGCGACAGTTTTGCCAATAG

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[3]

est. P1 cotransduction: 79% [6]
Synonyms:thi-39::Tn10

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[3]

est. P1 cotransduction: 19% [6]

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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:EG10482

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10482

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000475

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948505

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0477

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013093

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 4.2 4.3 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ 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
  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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