znuB: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="J46a9d0a013e7d"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''znuB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''znuB''
Zn uptake
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1860, b1859, JW1848, yebI''<ref name='LIB:Riley_2006'/>, yebI''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
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''ECK1860, b1859, JW1848, yebI''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='136086'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9d0a08ff39"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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
MG1655
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41.84 minutes, 41.84 minutes&nbsp;
41.84 minutes, 41.84 minutes&nbsp;
|
|
MG1655: 1941438..1942223<br />{{GBrowseFigureByCoord|1940438|1943223|ecoli|MG1655}}
MG1655: 1941438..1942223<br /><gbrowseImage>
name=NC_000913:1941438..1942223
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12368 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12368 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1940438|1943223|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1940438|1943223|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1941438..1942223&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1941438|1942223|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12368 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12368 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1921990..1922775<br /><gbrowseImage>
name=NC_012967:1921990..1922775
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1921990|1922775|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1921990|1922775|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 1833497..1834282<br /><gbrowseImage>
name=NC_012759:1833497..1834282
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1833497|1834282|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1833497|1834282|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1945128..1945913<br />{{GBrowseFigureByCoord|1944128|1946913|ecoli_W3110|W3110}}  
W3110: 1945128..1945913<br /><gbrowseImage>
name=NC_007779:1945128..1945913
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1944128|1946913|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1945128|1945913|FASTA Dump}}  
|-
|
[[DH10B]]
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1944128|1946913|GBrowse(W3110)}}
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1945128..1945913&plugin_action=Go FASTA Dump]
DH10B: 2032009..2032794<br /><gbrowseImage>
|-class='sortbottom'
name=NC_010473:2032009..2032794
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2030439|2034364|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2030439|2034364|FASTA Dump}}
 
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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<protect><!--Sequence_notes--></protect>
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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="W46a9d0a186f01"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107823 CGSC9542]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107823 CGSC9542]<ref name='LIB:cgsc'/>  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:106108|CGSC:106108]]
[[cgscmutation:106108|CGSC:106108]]
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14295.D4e04cd3305948-->
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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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JW1848
JW1848
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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:Clone OK
Status:Clone OK
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Primer 2:CCGCTGGCCTGCTTTTTCATCAT  
Primer 2:CCGCTGGCCTGCTTTTTCATCAT  
|-
|-
|
[[:Category:Kohara_Phage:20H4|20H4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=337 Genobase]
|
PMID:3038334
|-  
|
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[[eda:Gene|eda-51::Tn10]]
[[eda:Gene|eda-51::Tn10]]
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|
|
est. P1 cotransduction: 68% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 68% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[uvrC:Gene|uvrC279::Tn10]]
[[uvrC:Gene|uvrC279::Tn10]]
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est. P1 cotransduction: 11% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 11% <ref name='LIB:Nichols_linked_Tn'/>  
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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="I46a9d0a2caddb"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12368 EcoCyc:EG12368]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2271 EchoBASE:EB2271]
EcoCyc:EG12368
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1859 EcoliGenExpDB:b1859]
EcoGene:EG12368
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2273 ECOL199310CYC:C2273]
RegulonDB:ECK120002236
|
|
''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=EG12368 EcoGene:EG12368]
[http://www.ncbi.nlm.nih.gov/gene?term=946372 GeneID:946372]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YEBI ECOO157CYC:YEBI]
EchoBASE:EB2271
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0006201&formSubmitReturn=1 ASAP:ABE-0006201] 
ASAP:ABE-0006201
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
===Notes===
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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 in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:znu genes]]
[[Category:znu genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:39, 19 September 2013

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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

znuB

Mnemonic

Zn uptake

Synonyms

ECK1860, b1859, JW1848, yebI[1], yebI

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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

41.84 minutes, 41.84 minutes 

MG1655: 1941438..1942223
<gbrowseImage> name=NC_000913:1941438..1942223 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1921990..1922775
<gbrowseImage> name=NC_012967:1921990..1922775 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1833497..1834282
<gbrowseImage> name=NC_012759:1833497..1834282 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1945128..1945913
<gbrowseImage> name=NC_007779:1945128..1945913 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2032009..2032794
<gbrowseImage> name=NC_010473:2032009..2032794 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

ΔznuB (Keio:JW1848)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9542[3]

ΔznuB784::kan

PMID:16738554[2]

CGSC:106108


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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

JW1848

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCATTGAATTATTATTTCCCGG

Primer 2:CCGCTGGCCTGCTTTTTCATCAT

20H4

Kohara Phage

Genobase

PMID:3038334[5]

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[3]

est. P1 cotransduction: 68% [6]

uvrC279::Tn10

Linked marker

CAG12156 = CGSC7394[3]

est. P1 cotransduction: 11% [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:EG12368

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12368

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002236

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946372

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2271

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006201

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. ↑ 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 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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