tsf: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}}
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{|   id="E46a9aa001b639" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''tsf''  
''tsf''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Translation stable factor
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK0169, b0170, JW0165''<ref name='LIB:Riley_2006'/>
''ECK0169, b0170, JW0165''<ref name='LIB:Riley_2006'/>, JW0165''


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*  
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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="F46a9aa0093b80"  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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4.11 minutes&nbsp;
4.11 minutes&nbsp;
|
|
MG1655: 190857..191708<br />{{GBrowseFigureByCoord|189857|192708|ecoli|MG1655}}
MG1655: 190857..191708<br /><gbrowseImage>
name=NC_000913:190857..191708
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11033 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11033 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|189857|192708|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|189857|192708|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|190857|191708|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|190857|191708|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11033 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11033 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 193699..194550<br /><gbrowseImage>
name=NC_012967:193699..194550
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|193699|194550|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|193699|194550|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 190856..191707<br /><gbrowseImage>
name=NC_012759:190856..191707
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|190856|191707|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|190856|191707|FASTA Dump}}
|-  
|-  
|
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&nbsp;
&nbsp;
|
|
W3110: 190857..191708<br />{{GBrowseFigureByCoord|189857|192708|ecoli_W3110|W3110}}  
W3110: 190857..191708<br /><gbrowseImage>
name=NC_007779:190857..191708
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|189857|192708|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|190857|191708|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 164961..165812<br /><gbrowseImage>
name=NC_010473:164961..165812
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|189857|192708|GBrowse(W3110)}}  
{{GBrowseLink|DH10B|NC_010473|163259|167514|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|190857|191708|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|163259|167514|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="R46a9aa013c7b2"  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]]
|
190860
|
Edman degradation
|
PMID:8740179<br />PMID:9298646<br />PMID:9600841<br />PMID:9740056<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="L46a9aa017d22f"  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
|-
|
tsfF82A
|
|
F82A
|
|
2 to 3-fold less active in promoting GDP exchange and 6-fold less active in binding to EF-Tu
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A6P1 UniProt:P0A6P1]
|-
|
tsfH148A
|
|
H148A
|
|
At least 100-fold decrease in affinity between EF-Ts and EF-Tu and only small amount of GDP exchange activity
|
|
|
seeded from [http://www.uniprot.org/uniprot/P0A6P1 UniProt:P0A6P1]
|-
|
tsfK24A
|


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K24A
|
 
|
No change in binding to EF-Tu and in promoting GDP exchange
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A6P1 UniProt:P0A6P1]
|-
|
tsfD81A
|
 
|
D81A
|
 
|
2 to 3-fold less active in promoting GDP exchange and slightly lower binding constant for interaction with EF- Tu
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A6P1 UniProt:P0A6P1]
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10915.H4e04c50344ced-->
<!--
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*
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H4e04c50344ced"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCAGACTGCTTGGACATCGCAGC  
Primer 2:CCAGACTGCTTGGACATCGCAGC  
|-
|
[[:Category:Kohara_Phage:21C8|21C8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=119 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12D5|12D5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=120 Genobase]
|
PMID:3038334
|-  
|-  
|
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Synonyms:zae-502::Tn10  
Synonyms:zae-502::Tn10  


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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="L46a9aa02aff0a"  class=" tableEdit Gene_accessions_table"   
|- {{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=EG11033 EcoCyc:EG11033]
EcoCyc:EG11033
|
|
''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=EB1026 EchoBASE:EB1026]
EcoGene:EG11033
|
|
''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=b0170 EcoliGenExpDB:b0170]
RegulonDB:ECK120001022
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C0206 ECOL199310CYC:C0206]
|
|-  
|-  
|
|
[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=EG11033 EcoGene:EG11033]
[http://www.ncbi.nlm.nih.gov/gene?term=944866 GeneID:944866]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=TSF ECOO157CYC:TSF]
EchoBASE:EB1026
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/64 CGSC:64]
ASAP:ABE-0000579
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000579&formSubmitReturn=1 ASAP:ABE-0000579]
|


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{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:tsf genes]][[Category:Gene_List:DH10B]]
[[Category:tsf genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:37, 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

tsf

Mnemonic

Translation stable factor

Synonyms

ECK0169, b0170, JW0165[1], JW0165

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

4.11 minutes 

MG1655: 190857..191708
<gbrowseImage> name=NC_000913:190857..191708 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 193699..194550
<gbrowseImage> name=NC_012967:193699..194550 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 190856..191707
<gbrowseImage> name=NC_012759:190856..191707 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 190857..191708
<gbrowseImage> name=NC_007779:190857..191708 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 164961..165812
<gbrowseImage> name=NC_010473:164961..165812 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

190860

Edman degradation

PMID:8740179[2]
PMID:9298646[3]
PMID:9600841[4]
PMID:9740056[5]


edit table


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

tsfF82A

F82A

2 to 3-fold less active in promoting GDP exchange and 6-fold less active in binding to EF-Tu

seeded from UniProt:P0A6P1

tsfH148A

H148A

At least 100-fold decrease in affinity between EF-Ts and EF-Tu and only small amount of GDP exchange activity

seeded from UniProt:P0A6P1

tsfK24A

K24A

No change in binding to EF-Tu and in promoting GDP exchange

seeded from UniProt:P0A6P1

tsfD81A

D81A

2 to 3-fold less active in promoting GDP exchange and slightly lower binding constant for interaction with EF- Tu

seeded from UniProt:P0A6P1

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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

JW0165

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGCTGAAATTACCGCATCCCT

Primer 2:CCAGACTGCTTGGACATCGCAGC

21C8

Kohara Phage

Genobase

PMID:3038334[7]

12D5

Kohara Phage

Genobase

PMID:3038334[7]

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[8]

est. P1 cotransduction: 16% [9]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[8]

est. P1 cotransduction: 17% [9]
Synonyms:zae-502::Tn10

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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:EG11033

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11033

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001022

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944866

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1026

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000579

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. ↑ Wilkins, MR et al. (1998) Protein identification with N and C-terminal sequence tags in proteome projects. J. Mol. Biol. 278 599-608 PubMed
  5. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 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).

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