bcsE: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="R46a9f85cded00"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''bcsE''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''bcsE''
Bacterial cellulose synthesis
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3521, b3536, JW3504, yhjS''<ref name='LIB:Riley_2006'/>, yhjS''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17617.R46a9f85cded00&page=17617&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3521, b3536, JW3504, yhjS''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='146055'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9f85d6bf58"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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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79.63 minutes, 79.63 minutes&nbsp;
79.63 minutes, 79.63 minutes&nbsp;
|
|
MG1655: 3694481..3696052<br />{{GBrowseFigureByCoord|3693481|3697052|ecoli|MG1655}}
MG1655: 3694481..3696052<br /><gbrowseImage>
name=NC_000913:3694481..3696052
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12263 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12263 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3693481..3697052 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3693481|3697052|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3694481..3696052&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3694481|3696052|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12263 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12263 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3625950..3627521<br /><gbrowseImage>
name=NC_012967:3625950..3627521
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3625950|3627521|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3625950|3627521|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3582975..3584546<br /><gbrowseImage>
name=NC_012759:3582975..3584546
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3582975|3584546|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3582975|3584546|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3943957..3942386<br />{{GBrowseFigureByCoord|3941386|3944957|ecoli_W3110|W3110}}
W3110: 3943957..3942386<br /><gbrowseImage>
name=NC_007779:3942386..3943957
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3941386..3944957 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3941386|3944957|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3942386..3943957&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3942386|3943957|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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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="U46a9f85e77d9e"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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
|-
|
Strain DH10B
|
|
G151E
|
|
Nonsynonomous mutation
|
PMID:18245285
|
[https://asap.ahabs.wisc.edu/asap/home.php ASAP]
|
This is a SNP in <i>E. coli</i> K-12 Strain [[DH10B]]
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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=108873 CGSC10592]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108873 CGSC10592]<ref name='LIB:cgsc'/>  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[[cgscmutation:100164|CGSC:100164]]
[[cgscmutation:100164|CGSC:100164]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17617.U46a9f85e77d9e&page=17617&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17617.O4e04b82349a5b-->
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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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JW3504
JW3504
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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:CCTGATGAGCGCTCCACAGCATC  
Primer 2:CCTGATGAGCGCTCCACAGCATC  
|-
|-
|
[[:Category:Kohara_Phage:1D1|1D1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=603 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:9H8|9H8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=604 Genobase]
|
PMID:3038334
|-  
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zhg-50::Tn10
zhg-50::Tn10
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CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zhf-50::Tn10, zhf-5::Tn10  
Synonyms:zhf-50::Tn10, zhf-5::Tn10  
|-
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|
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zic-4901::Tn10
zic-4901::Tn10
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|
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12263 EcoCyc:EG12263]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2172 EchoBASE:EB2172]
EcoCyc:EG12263
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3536 EcoliGenExpDB:b3536]
EcoGene:EG12263
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4348 ECOL199310CYC:C4348]
RegulonDB:ECK120002144
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12263 EcoGene:EG12263]
[http://www.ncbi.nlm.nih.gov/gene?term=948050 GeneID:948050]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YHJS ECOO157CYC:YHJS]
EchoBASE:EB2172
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011554&formSubmitReturn=1 ASAP:ABE-0011554] 
ASAP:ABE-0011554
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
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===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:bcs genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:48, 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

bcsE

Mnemonic

Bacterial cellulose synthesis

Synonyms

ECK3521, b3536, JW3504, yhjS[1], yhjS

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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

79.63 minutes, 79.63 minutes 

MG1655: 3694481..3696052
<gbrowseImage> name=NC_000913:3694481..3696052 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3625950..3627521
<gbrowseImage> name=NC_012967:3625950..3627521 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3582975..3584546
<gbrowseImage> name=NC_012759:3582975..3584546 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3943957..3942386
<gbrowseImage> name=NC_007779:3942386..3943957 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

Strain DH10B

G151E

Nonsynonomous mutation

PMID:18245285[2]

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔbcsE (Keio:JW3504)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10592[4]

ΔbcsE790::kan

PMID:16738554[3]

CGSC:100164


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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

JW3504

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGGGACATTGTGGACCCTGT

Primer 2:CCTGATGAGCGCTCCACAGCATC

1D1

Kohara Phage

Genobase

PMID:3038334[6]

9H8

Kohara Phage

Genobase

PMID:3038334[6]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: % [7]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

est. P1 cotransduction: % [7]

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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:EG12263

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12263

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002144

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948050

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2172

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011554

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. ↑ Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
  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. ↑ 6.0 6.1 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
  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).

Categories

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