icdC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|icdC}}{{Tab On|Gene|icdC}}{{Tab|Gene Product(s)|icdC}}{{Tab|Expression|icdC}}{{Tab|Evolution|icdC}}{{Tab|On One Page|icdC}}{{TabsBottom}}
{{Tab|Quickview|icdC}}{{Tab On|Gene|icdC}}{{Tab|Gene Product(s)|icdC}}{{Tab|Expression|icdC}}{{Tab|Evolution|icdC}}{{Tab|On One Page|icdC}}{{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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{{BacktoTop}}
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{|  id="G46a9c0d66c811"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''icdC''  
''icdC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1146, b4519, JW5173''<ref name='LIB:Riley_2006'/>
''ECK1146, b4519, JW5173''<ref name='LIB:Riley_2006'/>, icd, JW5173''
|-
 
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<!--Nomenclature_notes--></protect>
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===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="X46a9c0d6e6c73"  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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26.09 minutes&nbsp;
26.09 minutes&nbsp;
|
|
MG1655: 1210648..1210800<br />{{GBrowseFigureByCoord|1209648|1211800|ecoli|MG1655}}
MG1655: 1210648..1210800<br /><gbrowseImage>
name=NC_000913:1210648..1210800
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10556 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10556 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1209648..1211800 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1209648|1211800|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1210648..1210800&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1210648|1210800|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G0-10556 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-10556 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1213002..1213154<br />{{GBrowseFigureByCoord|1212002|1214154|ecoli_W3110|W3110}}
W3110: 1213002..1213154<br /><gbrowseImage>
name=NC_007779:1213002..1213154
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1212002..1214154 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|1212002|1214154|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1213002..1213154&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|1213002|1213154|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="N46a9c0d798a2e"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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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="P46a9c0d7da192"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!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'
|-
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..Z469f9e0496529&page=&pagename={{FULLPAGENAMEE}} edit table] || || || || || ||
|
&Delta;icdC (Keio:JW5173)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109501 CGSC11220]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;icdC748::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:101522|CGSC:101522]]
|
 
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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="F4e04bd945617a"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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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="M46a9c0d888640"  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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|
JW5173
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCGGTTGGACTGAAGCGGCTGA
 
Primer 2:CCCATGTTTTCGATGATCGCTTC
|-
|
[[:Category:Kohara_Phage:3E11|3E11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=241 Genobase]
|
PMID:3038334
|-
|
[[yceG:Gene|zce-726::Tn10]]
|
Linked marker
|
CAG12078 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39418 CGSC7361]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[elbA:Gene|zcf-117::Tn10]]
|
Linked marker
|
CAG18463 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39422 CGSC7363]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 99% <ref name='LIB:Nichols_linked_Tn'/>
 
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===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="K46a9c0d92046b"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=4056026 GeneID:4056026]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120026447
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10556 EcoCyc:G0-10556] 
EchoBASE:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[ASAP]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10009 EcoGene:EG10009] 
ASAP:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:icd genes]]

Latest revision as of 20:30, 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

icdC

Mnemonic
Synonyms

ECK1146, b4519, JW5173[1], icd, JW5173

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Notes

Location(s) and DNA Sequence

[back to top]


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

26.09 minutes 

MG1655: 1210648..1210800
<gbrowseImage> name=NC_000913:1210648..1210800 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1213002..1213154
<gbrowseImage> name=NC_007779:1213002..1213154 source=W3110 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

ΔicdC (Keio:JW5173)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11220[3]

ΔicdC748::kan

PMID:16738554[2]

CGSC:101522


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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

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW5173

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGGTTGGACTGAAGCGGCTGA

Primer 2:CCCATGTTTTCGATGATCGCTTC

3E11

Kohara Phage

Genobase

PMID:3038334[5]

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[3]

est. P1 cotransduction: 7% [6]

zcf-117::Tn10

Linked marker

CAG18463 = CGSC7363[3]

est. P1 cotransduction: 99% [6]

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:4056026

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120026447

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  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. ↑ 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).

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