zapA: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="A46a9e928243f3"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''zapA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''zapA''
Z-ring-associated protein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2905, b2910, JW2878, ygfE''<ref name='LIB:Riley_2006'/>, ygfE''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16385.A46a9e928243f3&page=16385&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2905, b2910, JW2878, ygfE''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='142352'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9e928a36bd"  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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65.82 minutes&nbsp;
65.82 minutes&nbsp;
|
|
MG1655: 3053634..3053963<br />{{GBrowseFigureByCoord|3052634|3054963|ecoli|MG1655}}
MG1655: 3053634..3053963<br /><gbrowseImage>
name=NC_000913:3053634..3053963
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12878 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12878 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3052634|3054963|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3052634|3054963|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3053634..3053963&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3053634|3053963|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12878 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12878 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 2941363..2941692<br /><gbrowseImage>
name=NC_012967:2941363..2941692
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2941363|2941692|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2941363|2941692|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2940782..2941111<br /><gbrowseImage>
name=NC_012759:2940782..2941111
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2940782|2941111|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2940782|2941111|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 3054268..3054597<br />{{GBrowseFigureByCoord|3053268|3055597|ecoli_W3110|W3110}}
W3110: 3054268..3054597<br /><gbrowseImage>
name=NC_007779:3054268..3054597
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3053268..3055597 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3053268|3055597|GBrowse(W3110)}}
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3054268..3054597&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3054268|3054597|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 3147504..3147833<br /><gbrowseImage>
name=NC_010473:3147504..3147833
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3146846|3148491|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3146846|3148491|FASTA Dump}}
 
|- class="tableEdit_footer"
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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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====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="O46a9e929a8bb9"  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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[[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=108513 CGSC10232]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108513 CGSC10232]<ref name='LIB:cgsc'/>  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
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[[cgscmutation:106100|CGSC:106100]]
[[cgscmutation:106100|CGSC:106100]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16385.O46a9e929a8bb9&page=16385&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16385.M4e04cd26c6599-->
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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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JW2878
JW2878
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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]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTTCAAAGTTTTGGTTAGTTTT  
Primer 2:CCTTCAAAGTTTTGGTTAGTTTT  
|-
|-
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[[:Category:Kohara_Phage:10B4|10B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=470 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1A2|1A2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=471 Genobase]
|
PMID:3038334
|-  
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[[recD:Gene|recD1901::Tn10]]
[[recD:Gene|recD1901::Tn10]]
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
|-
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[[speA:Gene|speA210::Tn10]]
[[speA:Gene|speA210::Tn10]]
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CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgd-210::Tn10, zgf-210::Tn10


Synonyms:zgd-210::Tn10, zgf-210::Tn10
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===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="K46a9e92b0a1ca"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12878 EcoCyc:EG12878]
EcoCyc:EG12878
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2716 EchoBASE:EB2716]
EcoGene:EG12878
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2910 EcoliGenExpDB:b2910]
RegulonDB:ECK120002417
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://BioCyc.org/ECOL199310/new-image?object=C3492 ECOL199310CYC:C3492]
[http://www.ncbi.nlm.nih.gov/gene?term=947404 GeneID:947404]
|
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG12878 EcoGene:EG12878]
EchoBASE:EB2716
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=YGFE ECOO157CYC:YGFE]
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ASAP:ABE-0009554
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009554&formSubmitReturn=1 ASAP:ABE-0009554]
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===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:zap genes]]
[[Category:zap genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:45, 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

zapA

Mnemonic

Z-ring-associated protein

Synonyms

ECK2905, b2910, JW2878, ygfE[1], ygfE

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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

65.82 minutes 

MG1655: 3053634..3053963
<gbrowseImage> name=NC_000913:3053634..3053963 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2941363..2941692
<gbrowseImage> name=NC_012967:2941363..2941692 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2940782..2941111
<gbrowseImage> name=NC_012759:2940782..2941111 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3054268..3054597
<gbrowseImage> name=NC_007779:3054268..3054597 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3147504..3147833
<gbrowseImage> name=NC_010473:3147504..3147833 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

ΔzapA (Keio:JW2878)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10232[3]

ΔzapA761::kan

PMID:16738554[2]

CGSC:106100


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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

JW2878

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTCTGCACAACCCGTCGATAT

Primer 2:CCTTCAAAGTTTTGGTTAGTTTT

10B4

Kohara Phage

Genobase

PMID:3038334[5]

1A2

Kohara Phage

Genobase

PMID:3038334[5]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: % [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: 28% [6]
Synonyms:zgd-210::Tn10, zgf-210::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:EG12878

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12878

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002417

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947404

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2716

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009554

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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