dctR: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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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''yhiF, ECK3491, b3507, JW3475''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''yhiF, ECK3491, b3507, JW3475''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, JW3475''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="U46a9f79d0adf8"  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="U46a9f79d0adf8"  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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78.73 minutes&nbsp;
78.73 minutes&nbsp;
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|
MG1655: 3652706..3653236<br />{{GBrowseFigureByCoord|3652706|3653236|ecoli|MG1655}}
MG1655: 3652706..3653236<br /><gbrowseImage>
name=NC_000913:3652706..3653236
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11889 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11889 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3651706|3654236|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3651706|3654236|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3652706|3653236|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3652706|3653236|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11889 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11889 EcoCyc Sequence Dump]  
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NC_012759: 3541200..3541730<br />{{GBrowseFigureByCoord|3541200|3541730|BW2952|NC_012759}}
NC_012759: 3541200..3541730<br /><gbrowseImage>
name=NC_012759:3541200..3541730
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|BW2952|012759|3541200|NC_3541730|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3541200|3541730|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|3541200|NC_3541730|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|3541200|3541730|FASTA Dump}}  
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&nbsp;
&nbsp;
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W3110: 3985732..3985202<br />{{GBrowseFigureByCoord|3985202|3985732|ecoli_W3110|W3110}}
W3110: 3985732..3985202<br /><gbrowseImage>
name=NC_007779:3985202..3985732
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|3984202|3986732|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3984202|3986732|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3985202|3985732|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3985202|3985732|FASTA Dump}}  


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*  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="B46a9f79dc0db1"  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="B46a9f79dc0db1"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="G46a9f79e17f8c"  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="G46a9f79e17f8c"  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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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17557.O4e04b9997e0a8-->
<!--
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O4e04b9997e0a8"  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.17557.O4e04b9997e0a8&page=17557&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17557.O4e04b9997e0a8--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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*  
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****************************************************************************************** -->{{Gene_resources_help}}
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{|   id="Z46a9f79ecef2f"  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="Z46a9f79ecef2f"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:  
Primer 2:  
|-
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[[:Category:Kohara_Phage:4D9|4D9]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=607 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:12E4|12E4]]
|
Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=608 Genobase]
|
PMID:3038334


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*  
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****************************************************************************************** -->{{Gene_accessions_help}}
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{|   id="E46a9f79f781e1"  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="E46a9f79f781e1"  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=EG11889 EcoCyc:EG11889]
EcoCyc:EG11889
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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=EB1835 EchoBASE:EB1835]
EcoGene:EG11889
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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=b3507 EcoliGenExpDB:b3507]
RegulonDB:ECK120001819
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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=C4306 ECOL199310CYC:C4306]
[http://www.ncbi.nlm.nih.gov/gene?term=948021 GeneID:948021]
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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=EG11889 EcoGene:EG11889]
EchoBASE:EB1835
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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=YHIF ECOO157CYC:YHIF]
ASAP:ABE-0011454
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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]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011454&formSubmitReturn=1 ASAP:ABE-0011454]
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{|   id="Q46a7125eee25b"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a7125eee25b"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:48, 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

dctR

Mnemonic

Dicarboxylate transport regulator

Synonyms

yhiF, ECK3491, b3507, JW3475[1][2], JW3475

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

78.73 minutes 

MG1655: 3652706..3653236
<gbrowseImage> name=NC_000913:3652706..3653236 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3541200..3541730
<gbrowseImage> name=NC_012759:3541200..3541730 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3985732..3985202
<gbrowseImage> name=NC_007779:3985202..3985732 source=W3110 preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
edit table


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

ΔdctR762::kan

PMID:16738554[3]

CGSC:106154


edit table


Notes

Genetic Interactions

[back to top]



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


Notes

Genetic Resources

[back to top]


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:

4D9

Kohara Phage

Genobase

PMID:3038334[5]

12E4

Kohara Phage

Genobase

PMID:3038334[5]

edit table


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:EG11889

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11889

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001819

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948021

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1835

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011454

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

[back to top]


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 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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
  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

Categories

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