dcuC: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="V46a9b524ce4b4"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''dcuC''  
''dcuC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Dicarboxylate uptake
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0614, b0621, JW0616, JW0613, JW0613+JW0616''<ref name='LIB:Riley_2006'/>
''ECK0614, b0621, JW0616, JW0613, JW0613+JW0616''<ref name='LIB:Riley_2006'/>
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='128615'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9b5257da42"  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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14.09 minutes&nbsp;
14.09 minutes&nbsp;
|
|
MG1655: 655191..653806<br />{{GBrowseFigureByCoord|652806|656191|ecoli|MG1655}}
MG1655: 655191..653806<br /><gbrowseImage>
name=NC_000913:653806..655191
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6347 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6347 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:652806..656191 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|652806|656191|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:653806..655191&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|653806|655191|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6347 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6347 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 638556..637171<br /><gbrowseImage>
name=NC_012967:637171..638556
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|637171|638556|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|637171|638556|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 556566..557951<br /><gbrowseImage>
name=NC_012759:556566..557951
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|556566|557951|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|556566|557951|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 656390..655299<br />{{GBrowseFigureByCoord|654299|657390|ecoli_W3110|W3110}}
W3110: 656390..655299<br /><gbrowseImage>
name=NC_007779:655299..656390
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:654299..657390 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|654299|657390|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:655299..656390&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|655299|656390|FASTA Dump}}
|-
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 654282..653806<br />{{GBrowseFigureByCoord|652806|655282|ecoli_W3110|W3110}}
W3110: 654282..653806<br /><gbrowseImage>
name=NC_007779:653806..654282
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:652806..655282 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|652806|655282|GBrowse (W3110)}}<br \>
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:653806..654282&plugin_action=Go FASTA Dump]
*{{GBrowseFastaLink|W3110|NC_007779|653806|654282|FASTA Dump}}<br \>
|-
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 656390..653806<br />{{GBrowseFigureByCoord|652806|657390|ecoli_W3110|W3110}}
W3110: 656390..653806<br /><gbrowseImage>
name=NC_007779:653806..656390
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:652806..657390 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|652806|657390|GBrowse (W3110)}}<br \>
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:653806..656390&plugin_action=Go FASTA Dump]
*{{GBrowseFastaLink|W3110|NC_007779|653806|656390|FASTA Dump}}<br \>
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[[DH10B]]
|
 
|
DH10B: 594523..593138<br /><gbrowseImage>
name=NC_010473:593138..594523
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|590368|597293|GBrowse(DH10B)}}
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[[DH10B]]
|
 
|
DH10B: 707783..706398<br /><gbrowseImage>
name=NC_010473:706398..707783
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|703628|710553|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|703628|710553|FASTA Dump}}
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='128616'
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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====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9b52839a29"  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;dcuC (Keio:JW0613)
&Delta;dcuC (Keio:JW0613)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
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&Delta;dcuC (Keio:JW0616)
&Delta;dcuC (Keio:JW0616)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|
   
   
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11805.T4e04b99cd43c9-->
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0613
JW0613
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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:CCCTTGCCTGTGACCGCTGCTGC  
Primer 2:CCCTTGCCTGTGACCGCTGCTGC  
|-
|-
|
[[:Category:Kohara_Phage:3G5|3G5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=167 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1G6|1G6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=168 Genobase]
|
PMID:3038334
|-  
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JW0616
JW0616
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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
Line 240: Line 371:


Primer 2:CCAATAGGCTGATTCAAGGCATT  
Primer 2:CCAATAGGCTGATTCAAGGCATT  
|-
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[[dsbG:Gene|dsbG601::Tn10]]
[[dsbG:Gene|dsbG601::Tn10]]
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CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 52% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 52% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zbd-601::Tn10, zbe-601::Tn10  
Synonyms:zbd-601::Tn10, zbe-601::Tn10  
|-
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|
|
[[crcA:Gene|crcA280::Tn10]]
[[crcA:Gene|crcA280::Tn10]]
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CAG12077 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39388 CGSC7347]<ref name='LIB:cgsc'/>
CAG12077 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39388 CGSC7347]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 99% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 99% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbe-280::Tn10


Synonyms:zbe-280::Tn10
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===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]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6347 EcoCyc:G6347] 
EcoCyc:G6347
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3315 EchoBASE:EB3315] 
EcoGene:EG13545
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0621 EcoliGenExpDB:b0621] 
RegulonDB:ECK120002954
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0712 ECOL199310CYC:C0712]
[http://www.ncbi.nlm.nih.gov/gene?term=945000 GeneID:945000]
|
|
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=EG13545 EcoGene:EG13545] 
EchoBASE:EB3315
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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=DCUC ECOO157CYC:DCUC] 
ASAP:ABE-0002133
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
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[[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:dcu genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:34, 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

dcuC

Mnemonic

Dicarboxylate uptake

Synonyms

ECK0614, b0621, JW0616, JW0613, JW0613+JW0616[1]

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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

14.09 minutes 

MG1655: 655191..653806
<gbrowseImage> name=NC_000913:653806..655191 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 638556..637171
<gbrowseImage> name=NC_012967:637171..638556 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 556566..557951
<gbrowseImage> name=NC_012759:556566..557951 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 656390..655299
<gbrowseImage> name=NC_007779:655299..656390 source=W3110 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 654282..653806
<gbrowseImage> name=NC_007779:653806..654282 source=W3110 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 656390..653806
<gbrowseImage> name=NC_007779:653806..656390 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 594523..593138
<gbrowseImage> name=NC_010473:593138..594523 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 707783..706398
<gbrowseImage> name=NC_010473:706398..707783 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

ΔdcuC (Keio:JW0613)

deletion

deletion

PMID:16738554[2]

Shigen

ΔdcuC (Keio:JW0616)

deletion

deletion

PMID:16738554[2]

Shigen


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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

JW0613

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCATGAACCCTGTTCTATGGCT

Primer 2:CCCTTGCCTGTGACCGCTGCTGC

3G5

Kohara Phage

Genobase

PMID:3038334[4]

1G6

Kohara Phage

Genobase

PMID:3038334[4]

JW0616

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCCTGACATTCATTGAGCTCCT

Primer 2:CCAATAGGCTGATTCAAGGCATT

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[5]

est. P1 cotransduction: 52% [6]
Synonyms:zbd-601::Tn10, zbe-601::Tn10

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[5]

est. P1 cotransduction: 99% [6]
Synonyms:zbe-280::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:G6347

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13545

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002954

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945000

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3315

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002133

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. ↑ 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 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
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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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