ycbB: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
|
||
''ycbB''  
''ycbB''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
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Systematic nomenclature
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0916, b0925, JW0908, ycbB'''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK0916, b0925, JW0908, ycbB'''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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<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="G46a9bbcab444c"  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
|-
|-  
|
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MG1655
MG1655
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21.13 minutes&nbsp;
21.13 minutes&nbsp;
|
|
MG1655: 980270..982117<br />{{GBrowseFigureByCoord|979270|983117|ecoli|MG1655}}
MG1655: 980270..982117<br /><gbrowseImage>
name=NC_000913:980270..982117
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11253 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11253 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:979270..983117 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|979270|983117|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:980270..982117&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|980270|982117|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11253 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11253 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 998139..999986<br /><gbrowseImage>
name=NC_012967:998139..999986
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|998139|999986|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|998139|999986|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 883238..885085<br /><gbrowseImage>
name=NC_012759:883238..885085
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|883238|885085|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|883238|885085|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 981469..983316<br />{{GBrowseFigureByCoord|980469|984316|ecoli_W3110|W3110}}
W3110: 981469..983316<br /><gbrowseImage>
name=NC_007779:981469..983316
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:980469..984316 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|980469|984316|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:981469..983316&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|981469|983316|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 1034198..1036045<br /><gbrowseImage>
name=NC_010473:1034198..1036045
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|1030504|1039739|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1030504|1039739|FASTA Dump}}
 
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<!--Location_notes--></protect>
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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="G46a9bbcb5ebb9"  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
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<protect><!--Sequence_notes--></protect>
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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="I46a9bbcb9f281"  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
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;ycbB (Keio:JW0908)
&Delta;ycbB (Keio:JW0908)
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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=107202 CGSC8921]<ref name='LIB:cgsc'/>  
|
|-
|
&Delta;ycbB::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]  
''&#916;ycbB742::kan''
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PMID:16738554
|
[[cgscmutation:103916|CGSC:103916]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


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


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0908
JW0908
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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:Clone OK
Status:Clone OK
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Primer 2:CCCCTGATTAATTGTTCCGCTTT  
Primer 2:CCCCTGATTAATTGTTCCGCTTT  
|-
|-
|
[[:Category:Kohara_Phage:E1D1|E1D1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=218 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:11F5|11F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=219 Genobase]
|
PMID:3038334
|-  
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zca-1230::Tn10
zca-1230::Tn10
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CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 26% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 26% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zbj-1230::Tn10  
Synonyms:zbj-1230::Tn10  
|-
|-  
|
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[[ycbS:Gene|zcb-3059::Tn10]]
[[ycbS:Gene|zcb-3059::Tn10]]
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est. P1 cotransduction: 45% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 45% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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|- {{table_heading_style}}
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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=EG11253 EcoCyc:EG11253] 
EcoCyc:EG11253
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|
''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=EB1233 EchoBASE:EB1233] 
EcoGene:EG11253
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|
''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=b0925 EcoliGenExpDB:b0925] 
RegulonDB:ECK120001228
|
|
''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=C1067 ECOL199310CYC:C1067]
[http://www.ncbi.nlm.nih.gov/gene?term=945541 GeneID:945541]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11253 EcoGene:EG11253] 
EchoBASE:EB1233
|
|
''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=YCBB ECOO157CYC:YCBB] 
ASAP:ABE-0003142
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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:ycb genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 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

ycbB

Mnemonic

Systematic nomenclature

Synonyms

ECK0916, b0925, JW0908, ycbB'[1][2]

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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

21.13 minutes 

MG1655: 980270..982117
<gbrowseImage> name=NC_000913:980270..982117 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 998139..999986
<gbrowseImage> name=NC_012967:998139..999986 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 883238..885085
<gbrowseImage> name=NC_012759:883238..885085 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 981469..983316
<gbrowseImage> name=NC_007779:981469..983316 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1034198..1036045
<gbrowseImage> name=NC_010473:1034198..1036045 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

ΔycbB (Keio:JW0908)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8921[4]

ΔycbB::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

ΔycbB742::kan

PMID:16738554[3]

CGSC:103916


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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

JW0908

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTTGCTTAATATGATGTGTGG

Primer 2:CCCCTGATTAATTGTTCCGCTTT

E1D1

Kohara Phage

Genobase

PMID:3038334[7]

11F5

Kohara Phage

Genobase

PMID:3038334[7]

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[4]

est. P1 cotransduction: 26% [8]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[4]

est. P1 cotransduction: 45% [8]

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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:EG11253

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11253

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001228

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945541

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1233

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003142

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 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. ↑ Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 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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