kilR: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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|{{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="L46a9c554a7e9a"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''kilR''  
''kilR''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Killing function
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''kil, ECK1350, b1352, JW1347, ydaD''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, ydaD''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13277.L46a9c554a7e9a&page=13277&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''kil, ECK1350, b1352, JW1347, ydaD''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
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===Notes===
===Notes===
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<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="V46a9c5552df49"  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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30.52 minutes&nbsp;
30.52 minutes&nbsp;
|
|
MG1655: 1416253..1416032<br />{{GBrowseFigureByCoord|1415032|1417253|ecoli|MG1655}}
MG1655: 1416253..1416032<br /><gbrowseImage>
name=NC_000913:1416032..1416253
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12155 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12155 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1415032..1417253 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1415032|1417253|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1416032..1416253&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1416032|1416253|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12155 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12155 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1415178..1415399<br /><gbrowseImage>
name=NC_012967:1415178..1415399
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1415178|1415399|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1415178|1415399|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 1308091..1308312<br /><gbrowseImage>
name=NC_012759:1308091..1308312
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1308091|1308312|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1308091|1308312|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1419943..1419722<br />{{GBrowseFigureByCoord|1418722|1420943|ecoli_W3110|W3110}}  
W3110: 1419943..1419722<br /><gbrowseImage>
name=NC_007779:1419722..1419943
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1418722|1420943|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1419722|1419943|FASTA Dump}}  
|-
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1418722..1420943 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1419722..1419943&plugin_action=Go FASTA Dump]
 
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DH10B: 1505649..1505428<br /><gbrowseImage>
name=NC_010473:1505428..1505649
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|1504986|1506091|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1504986|1506091|FASTA Dump}}
 
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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="K46a9c555d0a21"  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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9c5561e824"  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!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;kilR (Keio:)
kil
|
|
deletion
 
|
deletion
|
|


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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
BCM sensitivity, cell death
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] 
PMID:21357484
|
 
|
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13277.P4e04be3243839-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P4e04be3243839"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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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:
Status:
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Primer 2:  
Primer 2:  
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
|
EcoCyc:EG12155
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12155 EcoCyc:EG12155] 
EcoGene:EG12155
|
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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]])
[[RegulonDB]]
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2075 EchoBASE:EB2075] 
RegulonDB:ECK120002054
|
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1352 EcoliGenExpDB:b1352]
[http://www.ncbi.nlm.nih.gov/gene?term=945921 GeneID:945921]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12155 EcoGene:EG12155] 
EchoBASE:EB2075
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YDAD ECOO157CYC:YDAD] 
ASAP:ABE-0004537
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
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{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Gene List:Rac prophage]]
[[Category:kil genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:29, 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

kilR

Mnemonic

Killing function

Synonyms

kil, ECK1350, b1352, JW1347, ydaD[1][2], ydaD

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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

30.52 minutes 

MG1655: 1416253..1416032
<gbrowseImage> name=NC_000913:1416032..1416253 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1415178..1415399
<gbrowseImage> name=NC_012967:1415178..1415399 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1308091..1308312
<gbrowseImage> name=NC_012759:1308091..1308312 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1419943..1419722
<gbrowseImage> name=NC_007779:1419722..1419943 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1505649..1505428
<gbrowseImage> name=NC_010473:1505428..1505649 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

kil

BCM sensitivity, cell death

PMID:21357484[3]


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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

Plasmid clone

Shigen

PMID:16769691[4]

Status:

Primer 1:

Primer 2:

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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:EG12155

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12155

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002054

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945921

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2075

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004537

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 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  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

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