rpsF: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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*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="G46aa09b910930" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''rpsF''  
''rpsF''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Ribosomal protein, small
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK4196, b4200, JW4158, sdgH''<ref name='LIB:Riley_2006'/>
''ECK4196, b4200, JW4158, sdgH''<ref name='LIB:Riley_2006'/>, sdgH''


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*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46aa09b9940f5"  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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95.33 minutes, 95.33 minutes&nbsp;
95.33 minutes, 95.33 minutes&nbsp;
|
|
MG1655: 4423141..4423536<br />{{GBrowseFigureByCoord|4422141|4424536|ecoli|MG1655}}
MG1655: 4423141..4423536<br /><gbrowseImage>
name=NC_000913:4423141..4423536
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10905 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10905 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4422141|4424536|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4422141|4424536|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|4423141|4423536|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|4423141|4423536|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10905 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10905 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 4403273..4403668<br /><gbrowseImage>
name=NC_012967:4403273..4403668
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|4403273|4403668|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4403273|4403668|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 4361876..4362271<br /><gbrowseImage>
name=NC_012759:4361876..4362271
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|4361876|4362271|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4361876|4362271|FASTA Dump}}
|-  
|-  
|
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&nbsp;
&nbsp;
|
|
W3110: 4429798..4430193<br />{{GBrowseFigureByCoord|4428798|4431193|ecoli_W3110|W3110}}
W3110: 4429798..4430193<br /><gbrowseImage>
name=NC_007779:4429798..4430193
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|4428798|4431193|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|4428798|4431193|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|4429798|4430193|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|4429798|4430193|FASTA Dump}}  
|-  
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|
|
DH10B: 4523503..4523898<br />{{GBrowseFigureByCoord|4522713|4524688|ecoli_DH10B|DH10B}}
DH10B: 4523503..4523898<br /><gbrowseImage>
name=NC_010473:4523503..4523898
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|4522713|4524688|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4522713|4524688|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4522713|4524688|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|4522713|4524688|FASTA Dump}}  


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*  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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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;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46aa09ba5c300"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
4423141
|
Edman degradation
|
PMID:328274<br />PMID:8740179<br />PMID:9298646<br />PMID:9600841<br />PMID:9740056<br />PMID:9868784<br />
|
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
4423153
|
Edman degradation
|
PMID:328274<br />PMID:8740179<br />PMID:9298646<br />PMID:9600841<br />PMID:9740056<br />PMID:9868784<br />
|


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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|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="H46aa09baa7db3"  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
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|
|
   
   
|-
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rpsF
|
deletion
|


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Sensitivity to
|
increases sensitivity to bicyclomycin
|
PMID:21357484
|
 
|
fig 2
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18965.D4e04c304e9bf6-->
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|- {{table_heading_style}}
!|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
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Primer 2:CCtTCTTCAGAATCCCCAGCTTC  
Primer 2:CCtTCTTCAGAATCCCCAGCTTC  
|-
|
[[:Category:Kohara_Phage:1G10|1G10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=654 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7E9|7E9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=655 Genobase]
|
PMID:3038334
|-  
|-  
|
|
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est. P1 cotransduction: 90% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 90% <ref name='LIB:Nichols_linked_Tn'/>  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10905 EcoCyc:EG10905]
EcoCyc:EG10905
|
|
''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=EB0898 EchoBASE:EB0898]
EcoGene:EG10905
|
|
''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=b4200 EcoliGenExpDB:b4200]
RegulonDB:ECK120000896
|
|
''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=C5291 ECOL199310CYC:C5291]
[http://www.ncbi.nlm.nih.gov/gene?term=948723 GeneID:948723]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10905 EcoGene:EG10905]
EchoBASE:EB0898
|
|
''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=RPSF ECOO157CYC:RPSF]
ASAP:ABE-0013740
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/225 CGSC:225]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0013740&formSubmitReturn=1 ASAP:ABE-0013740]
|


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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:rps genes]][[Category:Gene_List:DH10B]]
[[Category:rps genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:52, 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

[back to top]


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

Standard name

rpsF

Mnemonic

Ribosomal protein, small

Synonyms

ECK4196, b4200, JW4158, sdgH[1], sdgH

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

95.33 minutes, 95.33 minutes 

MG1655: 4423141..4423536
<gbrowseImage> name=NC_000913:4423141..4423536 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4403273..4403668
<gbrowseImage> name=NC_012967:4403273..4403668 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4361876..4362271
<gbrowseImage> name=NC_012759:4361876..4362271 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4429798..4430193
<gbrowseImage> name=NC_007779:4429798..4430193 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4523503..4523898
<gbrowseImage> name=NC_010473:4523503..4523898 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

4423141

Edman degradation

PMID:328274[2]
PMID:8740179[3]
PMID:9298646[4]
PMID:9600841[5]
PMID:9740056[6]
PMID:9868784[7]

Coding Start (SO:0000323)

MG1655

4423153

Edman degradation

PMID:328274[2]
PMID:8740179[3]
PMID:9298646[4]
PMID:9600841[5]
PMID:9740056[6]
PMID:9868784[7]


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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

ΔrpsF (Keio:JW4158)

deletion

deletion

PMID:16738554[8]

Shigen
CGSC10995[9]

ΔrpsF750::kan

PMID:16738554[8]

CGSC:102798

rpsF

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[10]

fig 2

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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

JW4158

Plasmid clone

Shigen

PMID:16769691[11]

Status:Clone OK

Primer 1:GCCCGTCATTACGAAATCGTTTT

Primer 2:CCtTCTTCAGAATCCCCAGCTTC

1G10

Kohara Phage

Genobase

PMID:3038334[12]

7E9

Kohara Phage

Genobase

PMID:3038334[12]

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[9]

est. P1 cotransduction: 2% [13]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[9]

est. P1 cotransduction: 90% [13]

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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:EG10905

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10905

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000896

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948723

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0898

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013740

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 Hitz, H et al. (1977) Determination of the complete amino-acid sequence of protein S6 from the wild-type and a mutant of Escherichia coli. Eur. J. Biochem. 75 497-512 PubMed
  3. ↑ 3.0 3.1 Pasquali, C et al. (1996) Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 17 547-55 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 Wilkins, MR et al. (1998) Protein identification with N and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278 599-608 PubMed
  6. ↑ 6.0 6.1 Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  7. ↑ 7.0 7.1 Wasinger, VC & Humphery-Smith, I (1998) Small genes/gene-products in Escherichia coli K-12. FEMS Microbiol. Lett. 169 375-82 PubMed
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 9.2 CGSC: The Coli Genetics Stock Center
  10. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  11. ↑ 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
  12. ↑ 12.0 12.1 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
  13. ↑ 13.0 13.1 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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