scpC: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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''scpC''  
''scpC''
|-
!align=left {{table_heading_style}} |Mnemonic
||
SuCcinate to Proprionate conversion
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ygfH, ECK2916, b2920, JW2887''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, JW2887''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16407.E46a9e96876ba7&page=16407&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ygfH, ECK2916, b2920, JW2887''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
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===Notes===
===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="G46a9e96901e22"  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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66.01 minutes&nbsp;
66.01 minutes&nbsp;
|
|
MG1655: 3062824..3064302<br />{{GBrowseFigureByCoord|3061824|3065302|ecoli|MG1655}}
MG1655: 3062824..3064302<br /><gbrowseImage>
name=NC_000913:3062824..3064302
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7517 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7517 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3061824..3065302 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3061824|3065302|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3062824..3064302&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3062824|3064302|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7517 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7517 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2950553..2952031<br /><gbrowseImage>
name=NC_012967:2950553..2952031
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2950553|2952031|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2950553|2952031|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2949972..2951450<br /><gbrowseImage>
name=NC_012759:2949972..2951450
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2949972|2951450|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2949972|2951450|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 3063458..3064936<br />{{GBrowseFigureByCoord|3062458|3065936|ecoli_W3110|W3110}}
W3110: 3063458..3064936<br /><gbrowseImage>
name=NC_007779:3063458..3064936
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3062458..3065936 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3062458|3065936|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3063458..3064936&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3063458|3064936|FASTA Dump}}
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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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="T46a9e96a05e2f"  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;scpC (Keio:)
''&#916;scpC771::kan''
|
|
deletion
 
|
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deletion
 
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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]
[[cgscmutation:106344|CGSC:106344]]
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==
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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]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:
Status:
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Primer 2:  
Primer 2:  
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[[:Category:Kohara_Phage:1A2|1A2]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=471 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6C5|6C5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=472 Genobase]
|
PMID:3038334
 
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
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EcoCyc:G7517
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7517 EcoCyc:G7517] 
EcoGene:EG12973
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2800 EchoBASE:EB2800] 
RegulonDB:ECK120004079
|
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2920 EcoliGenExpDB:b2920]
[http://www.ncbi.nlm.nih.gov/gene?term=947402 GeneID:947402]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12973 EcoGene:EG12973] 
EchoBASE:EB2800
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YGFH ECOO157CYC:YGFH] 
ASAP:ABE-0009583
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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{{RefHelp}}
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<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:scp genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:45, 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

scpC

Mnemonic

SuCcinate to Proprionate conversion

Synonyms

ygfH, ECK2916, b2920, JW2887[1][2], JW2887

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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

66.01 minutes 

MG1655: 3062824..3064302
<gbrowseImage> name=NC_000913:3062824..3064302 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2950553..2952031
<gbrowseImage> name=NC_012967:2950553..2952031 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2949972..2951450
<gbrowseImage> name=NC_012759:2949972..2951450 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3063458..3064936
<gbrowseImage> name=NC_007779:3063458..3064936 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

ΔscpC771::kan

PMID:16738554[3]

CGSC:106344


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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

Plasmid clone

Shigen

PMID:16769691[4]

Status:

Primer 1:

Primer 2:

1A2

Kohara Phage

Genobase

PMID:3038334[5]

6C5

Kohara Phage

Genobase

PMID:3038334[5]

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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:G7517

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12973

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004079

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947402

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2800

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009583

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. ↑ EcoCyc (release 11.1; 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

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