uspF:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|uspF}}{{Tab On|Gene|uspF}}{{Tab|Gene Product(s)|uspF}}{{Tab|Expression|uspF}}{{Tab|Evolution|uspF}}{{Tab|On One Page|uspF}}{{TabsBottom}}
{{Tab|Quickview|uspF}}{{Tab On|Gene|uspF}}{{Tab|Gene Product(s)|uspF}}{{Tab|Expression|uspF}}{{Tab|Evolution|uspF}}{{Tab|On One Page|uspF}}{{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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==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''uspF''  
''uspF''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Universal stress protein
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1371, b1376, JW1370, ynaF, yzzL, up03''<ref name='LIB:Riley_2006'/>
''ECK1371, b1376, JW1370, ynaF, yzzL, up03''<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="D46a9c5becc814"  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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30.89 minutes&nbsp;
30.89 minutes&nbsp;
|
|
MG1655: 1433643..1433209<br />{{GBrowseFigureByCoord|1432209|1434643|ecoli|MG1655}}
MG1655: 1433643..1433209<br /><gbrowseImage>
name=NC_000913:1433209..1433643
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6699 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6699 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1432209..1434643 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1432209|1434643|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1433209..1433643&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1433209|1433643|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6699 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6699 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 1325268..1325702<br /><gbrowseImage>
name=NC_012759:1325268..1325702
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1325268|1325702|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1325268|1325702|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1437333..1436899<br />{{GBrowseFigureByCoord|1435899|1438333|ecoli_W3110|W3110}}  
W3110: 1437333..1436899<br /><gbrowseImage>
name=NC_007779:1436899..1437333
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1435899|1438333|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|1436899|1437333|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1435899..1438333 GBrowse(W3110)]
DH10B: 1524238..1523804<br /><gbrowseImage>
name=NC_010473:1523804..1524238
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1436899..1437333&plugin_action=Go FASTA Dump]
{{GBrowseLink|DH10B|NC_010473|1522936|1525106|GBrowse(DH10B)}}
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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="C46a9c5bf7b1f3"  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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Coding Start (SO:0000323)
|
[[MG1655]]
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1433209
|
Edman degradation
|
PMID:8740179<br />PMID:9298646<br />
|
 
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<protect><!--Sequence_notes--></protect>
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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="N46a9c5bfbd17a"  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
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&Delta;uspF (Keio:JW1370)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|-
|
&Delta;yzzL::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|D-Mannose]]
|
PMID:16095938
|
 
|
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13319.H4e04c55dcf26b-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H4e04c55dcf26b"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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JW1370
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAACAGAACGATTCTTGTCCC
 
Primer 2:CCGCGCACAACCAGCACGGAGCA
|-
|
[[:Category:Kohara_Phage:4E7|4E7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=264 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1E7|1E7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=265 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: 43% <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: 99% <ref name='LIB:Nichols_linked_Tn'/>
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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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=G6699 EcoCyc:G6699] 
EcoCyc:G6699
|
|
''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=EB2539 EchoBASE:EB2539] 
EcoGene:EG12674
|
|
''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=b1376 EcoliGenExpDB:b1376] 
RegulonDB:ECK120003294
|
|
''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=C1821 ECOL199310CYC:C1821]
[http://www.ncbi.nlm.nih.gov/gene?term=945948 GeneID:945948]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12674 EcoGene:EG12674] 
EchoBASE:EB2539
|
|
''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=YNAF ECOO157CYC:YNAF] 
ASAP:ABE-0004605
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
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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:usp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[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

uspF

Mnemonic

Universal stress protein

Synonyms

ECK1371, b1376, JW1370, ynaF, yzzL, up03[1]

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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

30.89 minutes 

MG1655: 1433643..1433209
<gbrowseImage> name=NC_000913:1433209..1433643 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1325268..1325702
<gbrowseImage> name=NC_012759:1325268..1325702 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1437333..1436899
<gbrowseImage> name=NC_007779:1436899..1437333 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1524238..1523804
<gbrowseImage> name=NC_010473:1523804..1524238 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

Coding Start (SO:0000323)

MG1655

1433209

Edman degradation

PMID:8740179[2]
PMID:9298646[3]


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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

ΔuspF (Keio:JW1370)

deletion

deletion

PMID:16738554[4]

Shigen

ΔyzzL::kan

deletion

Biolog:respiration

unable to respire D-Mannose

PMID:16095938[5]


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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

JW1370

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAACAGAACGATTCTTGTCCC

Primer 2:CCGCGCACAACCAGCACGGAGCA

4E7

Kohara Phage

Genobase

PMID:3038334[7]

1E7

Kohara Phage

Genobase

PMID:3038334[7]

recT3061::Tn10

Linked marker

CAG12081 = CGSC7375[8]

est. P1 cotransduction: 43% [9]
Synonyms:zcj-3061::Tn10, zda-3061::Tn10

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[8]

est. P1 cotransduction: 99% [9]

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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:G6699

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12674

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003294

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945948

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2539

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004605

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. ↑ Pasquali, C et al. (1996) Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 17 547-55 PubMed
  3. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  4. ↑ 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
  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 CGSC: The Coli Genetics Stock Center
  9. ↑ 9.0 9.1 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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