stfR:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|stfR}}{{Tab On|Gene|stfR}}{{Tab|Gene Product(s)|stfR}}{{Tab|Expression|stfR}}{{Tab|Evolution|stfR}}{{Tab|On One Page|stfR}}{{TabsBottom}}
{{Tab|Quickview|stfR}}{{Tab On|Gene|stfR}}{{Tab|Gene Product(s)|stfR}}{{Tab|Expression|stfR}}{{Tab|Evolution|stfR}}{{Tab|On One Page|stfR}}{{TabsBottom}}
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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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</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|   id="D46a9c5a932aee"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''stfR''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''stfR''
Side-tail fiber
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1367, b1372, JW1366, ynaB''<ref name='LIB:Riley_2006'/>, ynaB''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13311.D46a9c5a932aee&page=13311&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1367, b1372, JW1366, ynaB''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<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="S46a9c5a9acca0"  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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30.76 minutes&nbsp;
30.76 minutes&nbsp;
|
|
MG1655: 1427073..1430435<br />{{GBrowseFigureByCoord|1426073|1431435|ecoli|MG1655}}
MG1655: 1427073..1430435<br /><gbrowseImage>
name=NC_000913:1427073..1430435
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6695 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6695 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1426073..1431435 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1426073|1431435|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1427073..1430435&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1427073|1430435|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6695 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6695 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 1319132..1322494<br /><gbrowseImage>
name=NC_012759:1319132..1322494
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1319132|1322494|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1319132|1322494|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1430763..1434125<br />{{GBrowseFigureByCoord|1429763|1435125|ecoli_W3110|W3110}}  
W3110: 1430763..1434125<br /><gbrowseImage>
name=NC_007779:1430763..1434125
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1429763|1435125|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|1430763|1434125|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 1516469..1519831<br /><gbrowseImage>
name=NC_010473:1516469..1519831
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1429763..1435125 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1509745|1526555|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1430763..1434125&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1509745|1526555|FASTA Dump}}
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<!--Location_notes--></protect>
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9c5aa5b4c2"  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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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9c5aa9d5a3"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-
|
&Delta;stfR (Keio:JW1366)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107491 CGSC9210]<ref name='LIB:cgsc'/>
|
|-  
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''&#916;stfR735::kan''
|
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&nbsp;
 
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&nbsp;
 
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&nbsp;
 
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&nbsp;
 
|
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&nbsp;
PMID:16738554
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&nbsp;
[[cgscmutation:103044|CGSC:103044]]
|
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&nbsp;
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13311.T4e04c43f8dc36-->
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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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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW1366
JW1366
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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:CCTGCAAGCCTCACAATATAGTT  
Primer 2:CCTGCAAGCCTCACAATATAGTT  
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[[:Category:Kohara_Phage:2C3|2C3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=263 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:4E7|4E7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=264 Genobase]
|
PMID:3038334
|-
|
[[recT:Gene|recT3061::Tn10]]
|
Linked marker
|
CAG12081 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39818 CGSC7375]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 55% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zcj-3061::Tn10, zda-3061::Tn10
|-
|
[[ompN:Gene|zhj-3076::Tn10]]
|
Linked marker
|
CAG18640 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40323 CGSC7453]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 80% <ref name='LIB:Nichols_linked_Tn'/>
 
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<protect><!--Gene_resources_notes--></protect>
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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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=G6695 EcoCyc:G6695] 
EcoCyc:G6695
|
|
''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=EB3152 EchoBASE:EB3152] 
EcoGene:EG13370
|
|
''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=b1372 EcoliGenExpDB:b1372] 
RegulonDB:ECK120003290
|
|
''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=C3150 ECOL199310CYC:C3150]
[http://www.ncbi.nlm.nih.gov/gene?term=945207 GeneID:945207]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13370 EcoGene:EG13370] 
EchoBASE:EB3152
|
|
''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=Z1918 ECOO157CYC:Z1918] 
ASAP:ABE-0004595
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<protect><!--Gene_accessions_notes--></protect>
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===Notes===
===Notes===
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==Links==
==Links==
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==References==
==References==
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[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Gene List:Rac prophage]]
[[Category:stf genes]][[Category:Gene_List:DH10B]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:29, 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

stfR

Mnemonic

Side-tail fiber

Synonyms

ECK1367, b1372, JW1366, ynaB[1], ynaB

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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

30.76 minutes 

MG1655: 1427073..1430435
<gbrowseImage> name=NC_000913:1427073..1430435 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1319132..1322494
<gbrowseImage> name=NC_012759:1319132..1322494 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1430763..1434125
<gbrowseImage> name=NC_007779:1430763..1434125 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1516469..1519831
<gbrowseImage> name=NC_010473:1516469..1519831 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

ΔstfR (Keio:JW1366)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9210[3]

ΔstfR735::kan

PMID:16738554[2]

CGSC:103044


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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

JW1366

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGCAGTAAAGATTTCAGGTGT

Primer 2:CCTGCAAGCCTCACAATATAGTT

2C3

Kohara Phage

Genobase

PMID:3038334[5]

4E7

Kohara Phage

Genobase

PMID:3038334[5]

recT3061::Tn10

Linked marker

CAG12081 = CGSC7375[3]

est. P1 cotransduction: 55% [6]
Synonyms:zcj-3061::Tn10, zda-3061::Tn10

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[3]

est. P1 cotransduction: 80% [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:G6695

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13370

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003290

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945207

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3152

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004595

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  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
  6. ↑ 6.0 6.1 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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