ybcC: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="T46a9b3117e5c1"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ybcC''  
''ybcC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0531, b0539, JW0526, exo(Lam.)''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK0531, b0539, JW0526, exo(Lam.)''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='128117'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9b31202234"  class=" tableEdit Gene_location_table" 
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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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12.18 minutes&nbsp;
12.18 minutes&nbsp;
|
|
MG1655: 565584..565321<br />{{GBrowseFigureByCoord|564321|566584|ecoli|MG1655}}
MG1655: 565584..565321<br /><gbrowseImage>
name=NC_000913:565321..565584
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6295 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6295 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:564321..566584 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|564321|566584|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:565321..565584&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|565321|565584|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6295 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6295 EcoCyc Sequence Dump]  
|-
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 565584..565321<br />{{GBrowseFigureByCoord|564321|566584|ecoli_W3110|W3110}}  
W3110: 565584..565321<br /><gbrowseImage>
name=NC_007779:565321..565584
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|564321|566584|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|565321|565584|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 504916..504653<br /><gbrowseImage>
name=NC_010473:504653..504916
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:564321..566584 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|504127|505442|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:565321..565584&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|504127|505442|FASTA Dump}}
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===Notes===
===Notes===
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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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|- {{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;ybcC (Keio:JW0526)
&Delta;ybcC (Keio:JW0526)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106943 CGSC8662]<ref name='LIB:cgsc'/>  
|
|-
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''&#916;ybcC747::kan''
|
 
|
 
|
 
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
|
PMID:16738554
|
[[cgscmutation:103674|CGSC:103674]]
|
|
   
   
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0526
JW0526
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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:CCTCGCCATTGCTCCCCAAATAC  
Primer 2:CCTCGCCATTGCTCCCCAAATAC  
|-
|-
|
[[:Category:Kohara_Phage:2C4|2C4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=158 Genobase]
|
PMID:3038334
|-  
|
|
[[purK:Gene|purK79::Tn10]]
[[purK:Gene|purK79::Tn10]]
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CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 63% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 63% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:purE79::Tn10  
Synonyms:purE79::Tn10  
|-
|-  
|
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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: 1% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 1% <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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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6295 EcoCyc:G6295] 
EcoCyc:G6295
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2253 EchoBASE:EB2253] 
EcoGene:EG12349
|
|
''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=b0539 EcoliGenExpDB:b0539] 
RegulonDB:ECK120002903
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C1534 ECOL199310CYC:C1534] 
EchoBASE:EB2253
|
|
''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=Z3367 ECOO157CYC:Z3367] 
ASAP:ABE-0001850
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[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:ybc genes]][[Category:Gene_List:DH10B]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:33, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ybcC

Mnemonic
Synonyms

ECK0531, b0539, JW0526, exo(Lam.)[1][2]

edit table


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

12.18 minutes 

MG1655: 565584..565321
<gbrowseImage> name=NC_000913:565321..565584 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 565584..565321
<gbrowseImage> name=NC_007779:565321..565584 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 504916..504653
<gbrowseImage> name=NC_010473:504653..504916 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔybcC (Keio:JW0526)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8662[4]

ΔybcC747::kan

PMID:16738554[3]

CGSC:103674


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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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Resource Resource Type Source Notes/Reference

JW0526

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAATTCCGGCTCGGTGGTTT

Primer 2:CCTCGCCATTGCTCCCCAAATAC

2C4

Kohara Phage

Genobase

PMID:3038334[6]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[4]

est. P1 cotransduction: 63% [7]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[4]

est. P1 cotransduction: 1% [7]
Synonyms:zbd-601::Tn10, zbe-601::Tn10

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:G6295

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12349

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002903

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2253

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001850

Escherichia coli str. K-12 substr. MG1655

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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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 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
  7. ↑ 7.0 7.1 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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