zapB:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|yiiU}}{{Tab On|Gene|yiiU}}{{Tab|Gene Product(s)|yiiU}}{{Tab|Expression|yiiU}}{{Tab|Evolution|yiiU}}{{Tab|On One Page|yiiU}}{{TabsBottom}}
{{Tab|Quickview|zapB}}{{Tab On|Gene|zapB}}{{Tab|Gene Product(s)|zapB}}{{Tab|Expression|zapB}}{{Tab|Evolution|zapB}}{{Tab|On One Page|zapB}}{{TabsBottom}}
{|
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
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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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|   id="Z46aa027f0d259"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''zapB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''yiiU''
Z-ring-associated protein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3920, b3928, JW3899'', yiiU<ref name='LIB:Riley_2006'/>, JW3899, yiiU''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18415.Z46aa027f0d259&page=18415&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3920, b3928, JW3899''<ref name='LIB:Riley_2006'/>
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{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
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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="W46aa027f8fe59"  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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88.72 minutes&nbsp;
88.72 minutes&nbsp;
|
|
MG1655: 4116538..4116783<br />{{GBrowseFigureByCoord|4115538|4117783|ecoli|MG1655}}
MG1655: 4116538..4116783<br /><gbrowseImage>
name=NC_000913:4116538..4116783
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11878 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11878 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4115538..4117783 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|4115538|4117783|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4116538..4116783&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|4116538|4116783|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11878 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11878 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4097998..4098243<br /><gbrowseImage>
name=NC_012967:4097998..4098243
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4097998|4098243|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4097998|4098243|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 4006207..4006452<br /><gbrowseImage>
name=NC_012759:4006207..4006452
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|012759|4006207|NC_4006452|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|4006207|NC_4006452|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 3518166..3517921<br />{{GBrowseFigureByCoord|3516921|3519166|ecoli_W3110|W3110}}  
W3110: 3518166..3517921<br /><gbrowseImage>
name=NC_007779:3517921..3518166
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|3516921|3519166|GBrowse(W3110)}}
|
{{GBrowseFastaLink|ecoli_W3110|NC_007779|3517921|3518166|FASTA Dump}}  
|-
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3516921..3519166 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3517921..3518166&plugin_action=Go FASTA Dump]
 
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DH10B: 4216235..4216480<br /><gbrowseImage>
name=NC_010473:4216235..4216480
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_DH10B|NC_010473|4215745|4216970|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4215745|4216970|FASTA Dump}}
 
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===Notes===
===Notes===
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{|  id="Q46aa028055b35"  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
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{| {{Prettytable}} id="M46aa0280a0618"  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
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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&Delta;yiiU (Keio:JW3899)
&Delta;yiiU (Keio:JW3899)
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]   
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109095 CGSC10814]<ref name='LIB:cgsc'/>
|
   
|-
|
''&#916;yiiU787::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:105434|CGSC:105434]]
|
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{{Gene_alleles_help}}
 
<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="A4e04cd27d6f8b"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|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.18415.A4e04cd27d6f8b&page=18415&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="Z46aa028165f3c"  class=" tableEdit Gene_resource_table" 
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW3899
JW3899
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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:CCGACCTCTTCCATGCGACCCAG  
Primer 2:CCGACCTCTTCCATGCGACCCAG  
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[[:Category:Kohara_Phage:12E3|12E3]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=538 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:4H12|4H12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=539 Genobase]
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PMID:3038334
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[[yihO:Gene|zih-35::Tn10]]
|
Linked marker
|
CAG18495 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37140 CGSC7467]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[pflD:Gene|pflD501::Tn10]]
|
Linked marker
|
CAG18477 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37152 CGSC7470]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 36% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).
 
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11878 EcoCyc:EG11878]
[http://chase.ou.edu/macro/searchlink.php?bnum=b3928 EcoliGenExpDB:b3928]
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|-
|-  
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1824 EchoBASE:EB1824]
[http://BioCyc.org/ECOL199310/new-image?object=C4880 ECOL199310CYC:C4880]
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|-
|-  
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3928 EcoliGenExpDB:b3928]
[http://BioCyc.org/ECOO157/new-image?object=YIIU ECOO157CYC:YIIU]
|
|
   
   
|-
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4880 ECOL199310CYC:C4880]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11878 ECOCYC:EG11878]
|
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Escherichia coli str. K-12 substr. 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=EG11878 EcoGene:EG11878]
[http://www.ncbi.nlm.nih.gov/gene?term=948420 GeneID:948420]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YIIU ECOO157CYC:YIIU] 
RegulonDB:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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:yii genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:zap genes]]
[[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

zapB

Mnemonic

Z-ring-associated protein

Synonyms

ECK3920, b3928, JW3899, yiiU[1], JW3899, yiiU

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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

88.72 minutes 

MG1655: 4116538..4116783
<gbrowseImage> name=NC_000913:4116538..4116783 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4097998..4098243
<gbrowseImage> name=NC_012967:4097998..4098243 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4006207..4006452
<gbrowseImage> name=NC_012759:4006207..4006452 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3518166..3517921
<gbrowseImage> name=NC_007779:3517921..3518166 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4216235..4216480
<gbrowseImage> name=NC_010473:4216235..4216480 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

ΔyiiU (Keio:JW3899)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10814[3]

ΔyiiU787::kan

PMID:16738554[2]

CGSC:105434


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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

JW3899

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCACAATGTCATTAGAAGTGTT

Primer 2:CCGACCTCTTCCATGCGACCCAG

12E3

Kohara Phage

Genobase

PMID:3038334[5]

4H12

Kohara Phage

Genobase

PMID:3038334[5]

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[3]

est. P1 cotransduction: 8% [6]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[3]

est. P1 cotransduction: 36% [6]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3928

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4880

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YIIU

EcoCyc (EcoliWiki Page)

ECOCYC:EG11878

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948420

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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. ↑ 5.0 5.1 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
  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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