citD:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|citD}}{{Tab On|Gene|citD}}{{Tab|Gene Product(s)|citD}}{{Tab|Expression|citD}}{{Tab|Evolution|citD}}{{Tab|On One Page|citD}}{{TabsBottom}}
{{Tab|Quickview|citD}}{{Tab On|Gene|citD}}{{Tab|Gene Product(s)|citD}}{{Tab|Expression|citD}}{{Tab|Evolution|citD}}{{Tab|On One Page|citD}}{{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="H46a9b503adccf"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''citD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''citD''
Citrate
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0610, b0617, JW0609, ybdX''<ref name='LIB:Riley_2006'/>, ybdX''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11797.H46a9b503adccf&page=11797&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0610, b0617, JW0609, ybdX''<ref name='LIB:Riley_2006'/>
|-
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{{Gene_nomenclature_help}}
 
<!--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="R46a9b5045c8a3"  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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14 minutes&nbsp;
14 minutes&nbsp;
|
|
MG1655: 650006..649710<br />{{GBrowseFigureByCoord|648710|651006|ecoli|MG1655}}
MG1655: 650006..649710<br /><gbrowseImage>
name=NC_000913:649710..650006
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6343 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6343 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:648710..651006 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|648710|651006|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:649710..650006&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|649710|650006|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6343 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6343 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 632834..632538<br /><gbrowseImage>
name=NC_012967:632538..632834
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|632538|632834|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|632538|632834|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 552470..552766<br /><gbrowseImage>
name=NC_012759:552470..552766
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|552470|552766|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|552470|552766|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 650006..649710<br />{{GBrowseFigureByCoord|648710|651006|ecoli_W3110|W3110}}  
W3110: 650006..649710<br /><gbrowseImage>
name=NC_007779:649710..650006
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|648710|651006|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|649710|650006|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 589338..589042<br /><gbrowseImage>
name=NC_010473:589042..589338
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|588450|589930|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|588450|589930|FASTA Dump}}
|-
|
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:648710..651006 GBrowse(W3110)]
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:649710..650006&plugin_action=Go FASTA Dump]
DH10B: 702598..702302<br /><gbrowseImage>
|-class='sortbottom'
name=NC_010473:702302..702598
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..I469f9cab3f4bc&page=&pagename={{FULLPAGENAMEE}} edit table] || || || ||
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|701710|703190|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|701710|703190|FASTA Dump}}
 
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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="T46a9b505648cc"  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="A46a9b505d01d6"  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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''(del)citD (Keio:JW0609)''
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=107004 CGSC8723]<ref name='LIB:cgsc'/>
|
|-
|
''citD755(del)::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100322|CGSC:100322]]
|
 
|- class="tableEdit_footer"
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===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="M4e04b8c14e689"  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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<!-- Genetic Interacdtions Notes -->
===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="U46a9b506d7816"  class=" tableEdit Gene_resource_table" 
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-class='sortbottom'
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|
JW0609
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAAAATAAACCAGCCCGCCGT
 
Primer 2:CCTTGGCAATCCTCCCATGGCAG
|-
|
[[: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: 61% <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: 86% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbe-280::Tn10
 
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{{Gene_resources_help}}
 
<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="K46a9b507cd304"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:G6343
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6343 EcoCyc:G6343] 
EcoGene:EG13543
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3313 EchoBASE:EB3313] 
RegulonDB:ECK120002950
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[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=b0617 EcoliGenExpDB:b0617]
[http://www.ncbi.nlm.nih.gov/gene?term=945415 GeneID:945415]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13543 EcoGene:EG13543] 
EchoBASE:EB3313
|
|
''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=CITD ECOO157CYC:CITD] 
ASAP:ABE-0002124
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<protect><!--Gene_accessions_notes--></protect>
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===Notes===
===Notes===
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==Links==
==Links==
{{BacktoTop}}
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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

citD

Mnemonic

Citrate

Synonyms

ECK0610, b0617, JW0609, ybdX[1], ybdX

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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 minutes 

MG1655: 650006..649710
<gbrowseImage> name=NC_000913:649710..650006 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 632834..632538
<gbrowseImage> name=NC_012967:632538..632834 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 552470..552766
<gbrowseImage> name=NC_012759:552470..552766 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 650006..649710
<gbrowseImage> name=NC_007779:649710..650006 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 589338..589042
<gbrowseImage> name=NC_010473:589042..589338 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 702598..702302
<gbrowseImage> name=NC_010473:702302..702598 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

(del)citD (Keio:JW0609)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8723[3]

citD755(del)::kan

PMID:16738554[2]

CGSC:100322


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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

JW0609

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAAATAAACCAGCCCGCCGT

Primer 2:CCTTGGCAATCCTCCCATGGCAG

3G5

Kohara Phage

Genobase

PMID:3038334[5]

1G6

Kohara Phage

Genobase

PMID:3038334[5]

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[3]

est. P1 cotransduction: 61% [6]
Synonyms:zbd-601::Tn10, zbe-601::Tn10

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[3]

est. P1 cotransduction: 86% [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:G6343

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13543

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002950

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945415

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3313

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002124

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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