kilR:Gene: Difference between revisions

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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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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{| id="L46a9c554a7e9a"  class=" tableEdit Gene_nomenclature_table"   
{|   id="L46a9c554a7e9a"  class=" tableEdit Gene_nomenclature_table"   


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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''kil, ECK1350, b1352, JW1347, ydaD''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
''kil, ECK1350, b1352, JW1347, ydaD''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, ydaD''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="V46a9c5552df49"  class=" tableEdit Gene_location_table"   
{| 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
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30.52 minutes&nbsp;
30.52 minutes&nbsp;
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MG1655: 1416253..1416032<br />{{GBrowseFigureByCoord|1416032|1416253|ecoli|MG1655}}
MG1655: 1416253..1416032<br /><gbrowseImage>
name=NC_000913:1416032..1416253
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[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]
{{GBrowseLink|ecoli|NC_000913|1415032|1417253|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1415032|1417253|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1416032|1416253|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]  
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NC_012967: 1415178..1415399<br />{{GBrowseFigureByCoord|1415178|1415399|REL606|NC_012967}}
NC_012967: 1415178..1415399<br /><gbrowseImage>
name=NC_012967:1415178..1415399
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|1415178|1415399|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|1415178|1415399|GBrowse (REL606)}}
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NC_012759: 1308091..1308312<br />{{GBrowseFigureByCoord|1308091|1308312|BW2952|NC_012759}}
NC_012759: 1308091..1308312<br /><gbrowseImage>
name=NC_012759:1308091..1308312
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|1308091|NC_1308312|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|1308091|1308312|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|1308091|NC_1308312|FASTA Dump}}  
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&nbsp;
&nbsp;
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W3110: 1419943..1419722<br />{{GBrowseFigureByCoord|1419722|1419943|ecoli_W3110|W3110}}
W3110: 1419943..1419722<br /><gbrowseImage>
name=NC_007779:1419722..1419943
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|1418722|1420943|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1418722|1420943|GBrowse(W3110)}}  
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DH10B: 1505649..1505428<br />{{GBrowseFigureByCoord|1505428|1505649|ecoli_DH10B|DH10B}}
DH10B: 1505649..1505428<br /><gbrowseImage>
name=NC_010473:1505428..1505649
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|1504986|1506091|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1504986|1506091|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1504986|1506091|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1504986|1506091|FASTA Dump}}  


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{|   id="K46a9c555d0a21"  class=" tableEdit Gene_sequence_features_table"   
{| 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!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="O46a9c5561e824"  class=" tableEdit Gene_allele_table dataTable"   
{| 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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kil
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BCM sensitivity, cell death
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PMID:21357484
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<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}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.13277.P4e04be3243839&page=13277&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13277.P4e04be3243839--></protect>
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="D46a9c556c1603"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9c556c1603"  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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{|   id="R46a9c5575ab59"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9c5575ab59"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12155 EcoCyc:EG12155]
EcoCyc: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]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2075 EchoBASE:EB2075]
EcoGene:EG12155
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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]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1352 EcoliGenExpDB:b1352]
RegulonDB:ECK120002054
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG12155 EcoGene:EG12155]
[http://www.ncbi.nlm.nih.gov/gene?term=945921 GeneID:945921]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=YDAD ECOO157CYC:YDAD]
EchoBASE:EB2075
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''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]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004537&formSubmitReturn=1 ASAP:ABE-0004537]
ASAP:ABE-0004537
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:29, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

edit table


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>

edit table


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]


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


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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<protect>

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

Categories

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