bssR: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="P46a9b9c734c00"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''bssR''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''bssR''
regulator of Biofilm through Signal Secretion
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''yliH, ECK0826, b0836, JW0820''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, JW0820''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12229.P46a9b9c734c00&page=12229&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''yliH, ECK0826, b0836, JW0820''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='129887'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9b9c7acb5b"  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
|-
|-  
|
|
MG1655
MG1655
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18.91 minutes&nbsp;
18.91 minutes&nbsp;
|
|
MG1655: 877471..877854<br />{{GBrowseFigureByCoord|876471|878854|ecoli|MG1655}}
MG1655: 877471..877854<br /><gbrowseImage>
name=NC_000913:877471..877854
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6436 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6436 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:876471..878854 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|876471|878854|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:877471..877854&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|877471|877854|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6436 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6436 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 870800..871183<br /><gbrowseImage>
name=NC_012967:870800..871183
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|870800|871183|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|870800|871183|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 780439..780822<br /><gbrowseImage>
name=NC_012759:780439..780822
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|780439|780822|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|780439|780822|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 878670..879053<br />{{GBrowseFigureByCoord|877670|880053|ecoli_W3110|W3110}}  
W3110: 878670..879053<br /><gbrowseImage>
name=NC_007779:878670..879053
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|877670|880053|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|878670|879053|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 931399..931782<br /><gbrowseImage>
name=NC_010473:931399..931782
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:877670..880053 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|930633|932548|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:878670..879053&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|930633|932548|FASTA Dump}}
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===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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{|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="K46a9b9c896bc6"  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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|
|
''&#916;bssR736::kan''
''bssR736(del)::kan''
|
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:106136|CGSC:106136]]
[[cgscmutation:106136|CGSC:106136]]
|
|
   
   
|-
|
''bssR(del)''
|
deletion
|
deletion
|
Colony Morphology
|
Mutant: table 2.


|-class='sortbottom'
*increase biofilm formation
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12229.K46a9b9c896bc6&page=12229&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
*increase biofilm mass
*increase surface coverage
*increase mean thickness
|
PMID:16597943
|
 
|
|-
|
''BssR(del)''
|
deletion
|
deletion
|
Motility
|
Deletion mutation led to an increase in motility, relative to the wild type in LB medium, fig 3A. Except when glucose was added where motility was inhibited.
|
PMID:16597943
|
 
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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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]
|
|
[[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:1E2|1E2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=208 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3H12|3H12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=209 Genobase]
|
PMID:3038334
 
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===Notes===
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|- {{table_heading_style}}
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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=G6436 EcoCyc:G6436] 
EcoCyc:G6436
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3252 EchoBASE:EB3252] 
EcoGene:EG13479
|
|
''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=b0836 EcoliGenExpDB:b0836] 
RegulonDB:ECK120003036
|
|
''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=C0921 ECOL199310CYC:C0921]
[http://www.ncbi.nlm.nih.gov/gene?term=945466 GeneID:945466]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13479 EcoGene:EG13479] 
EchoBASE:EB3252
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z1062 ECOO157CYC:Z1062] 
ASAP:ABE-0002849
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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 not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:bss genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

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

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

Standard name

bssR

Mnemonic

regulator of Biofilm through Signal Secretion

Synonyms

yliH, ECK0826, b0836, JW0820[1][2], JW0820

edit table


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

18.91 minutes 

MG1655: 877471..877854
<gbrowseImage> name=NC_000913:877471..877854 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 870800..871183
<gbrowseImage> name=NC_012967:870800..871183 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 780439..780822
<gbrowseImage> name=NC_012759:780439..780822 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 878670..879053
<gbrowseImage> name=NC_007779:878670..879053 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 931399..931782
<gbrowseImage> name=NC_010473:931399..931782 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

bssR736(del)::kan

PMID:16738554[3]

CGSC:106136

bssR(del)

deletion

deletion

Colony Morphology

Mutant: table 2.

  • increase biofilm formation
  • increase biofilm mass
  • increase surface coverage
  • increase mean thickness

PMID:16597943[4]

BssR(del)

deletion

deletion

Motility

Deletion mutation led to an increase in motility, relative to the wild type in LB medium, fig 3A. Except when glucose was added where motility was inhibited.

PMID:16597943[4]


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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[5]

Status:

Primer 1:

Primer 2:

1E2

Kohara Phage

Genobase

PMID:3038334[6]

3H12

Kohara Phage

Genobase

PMID:3038334[6]

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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:G6436

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13479

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003036

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945466

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3252

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002849

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. ↑ 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 Domka, J et al. (2006) YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling. Appl. Environ. Microbiol. 72 2449-59 PubMed
  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

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