citC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|citC}}{{Tab On|Gene|citC}}{{Tab|Gene Product(s)|citC}}{{Tab|Expression|citC}}{{Tab|Evolution|citC}}{{Tab|On One Page|citC}}{{TabsBottom}}
{{Tab|Quickview|citC}}{{Tab On|Gene|citC}}{{Tab|Gene Product(s)|citC}}{{Tab|Expression|citC}}{{Tab|Evolution|citC}}{{Tab|On One Page|citC}}{{TabsBottom}}
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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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</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|   id="E46a9b50b4cf64"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''citC''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''citC''
Citrate
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0611, b0618, JW0610, ybeO''<ref name='LIB:Riley_2006'/>, ybeO''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11799.E46a9b50b4cf64&page=11799&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0611, b0618, JW0610, ybeO''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<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="D46a9b50bef685"  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
Line 52: Line 76:
14.01 minutes&nbsp;
14.01 minutes&nbsp;
|
|
MG1655: 651079..650021<br />{{GBrowseFigureByCoord|649021|652079|ecoli|MG1655}}
MG1655: 651079..650021<br /><gbrowseImage>
name=NC_000913:650021..651079
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6344 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6344 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:649021..652079 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|649021|652079|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:650021..651079&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|650021|651079|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6344 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6344 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 633907..632849<br /><gbrowseImage>
name=NC_012967:632849..633907
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|632849|633907|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|632849|633907|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 552781..553839<br /><gbrowseImage>
name=NC_012759:552781..553839
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|552781|553839|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|552781|553839|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 651079..650021<br />{{GBrowseFigureByCoord|649021|652079|ecoli_W3110|W3110}}  
W3110: 651079..650021<br /><gbrowseImage>
name=NC_007779:650021..651079
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|649021|652079|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|650021|651079|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 590411..589353<br /><gbrowseImage>
name=NC_010473:589353..590411
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|587237|592527|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|587237|592527|FASTA Dump}}
|-
|
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:649021..652079 GBrowse(W3110)]
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:650021..651079&plugin_action=Go FASTA Dump]
DH10B: 703671..702613<br /><gbrowseImage>
|-class='sortbottom'
name=NC_010473:702613..703671
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..G469f9cabc4696&page=&pagename={{FULLPAGENAMEE}} edit table] || || || ||
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|700497|705787|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|700497|705787|FASTA Dump}}
 
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<!--Location_notes--></protect>
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9b50d02b61"  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
|-class='sortbottom'
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9b50d6f471"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;citC (Keio:JW0610)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107005 CGSC8724]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;citC756::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100320|CGSC:100320]]
|
 
|- class="tableEdit_footer"
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C4e04b8c004e89"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9b50e88d1f"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-class='sortbottom'
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JW0610
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCTTCGGCAATGATATTTTCAC
 
Primer 2:CCTGCGGGGGTCTTTTGACGAGC
|-
|
[[: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
|-
|
[[dsbG:Gene|dsbG601::Tn10]]
|
Linked marker
|
CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 60% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbd-601::Tn10, zbe-601::Tn10
|-
|
[[crcA:Gene|crcA280::Tn10]]
|
Linked marker
|
CAG12077 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39388 CGSC7347]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbe-280::Tn10
 
|- class="tableEdit_footer"
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<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9b50f7e792"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6344 EcoCyc:G6344] 
EcoCyc:G6344
|
|
''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=EB3409 EchoBASE:EB3409] 
EcoGene:EG13645
|
|
''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=b0618 EcoliGenExpDB:b0618] 
RegulonDB:ECK120002951
|
|
''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=C0709 ECOL199310CYC:C0709]
[http://www.ncbi.nlm.nih.gov/gene?term=945231 GeneID:945231]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13645 EcoGene:EG13645] 
EchoBASE:EB3409
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=CITC ECOO157CYC:CITC] 
ASAP:ABE-0002126
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
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===Notes===
===Notes===
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==Links==
==Links==
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==References==
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:cit 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

citC

Mnemonic

Citrate

Synonyms

ECK0611, b0618, JW0610, ybeO[1], ybeO

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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

14.01 minutes 

MG1655: 651079..650021
<gbrowseImage> name=NC_000913:650021..651079 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 633907..632849
<gbrowseImage> name=NC_012967:632849..633907 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 552781..553839
<gbrowseImage> name=NC_012759:552781..553839 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 651079..650021
<gbrowseImage> name=NC_007779:650021..651079 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 590411..589353
<gbrowseImage> name=NC_010473:589353..590411 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 703671..702613
<gbrowseImage> name=NC_010473:702613..703671 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

ΔcitC (Keio:JW0610)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8724[3]

ΔcitC756::kan

PMID:16738554[2]

CGSC:100320


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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

JW0610

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTTCGGCAATGATATTTTCAC

Primer 2:CCTGCGGGGGTCTTTTGACGAGC

3G5

Kohara Phage

Genobase

PMID:3038334[5]

1G6

Kohara Phage

Genobase

PMID:3038334[5]

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[3]

est. P1 cotransduction: 60% [6]
Synonyms:zbd-601::Tn10, zbe-601::Tn10

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[3]

est. P1 cotransduction: 87% [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:G6344

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13645

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002951

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945231

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3409

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002126

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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