tsf:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0169, b0170, JW0165''<ref name='LIB:Riley_2006'/>
''ECK0169, b0170, JW0165''<ref name='LIB:Riley_2006'/>, JW0165''


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{|   id="F46a9aa0093b80"  class=" tableEdit Gene_location_table"   
{| 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"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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W3110: 190857..191708<br /><gbrowseImage>
W3110: 190857..191708<br /><gbrowseImage>
name=AC_000091:190857..191708
name=NC_007779:190857..191708
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|189857|192708|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|189857|192708|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|190857|191708|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|190857|191708|FASTA Dump}}  
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{|   id="R46a9aa013c7b2"  class=" tableEdit Gene_sequence_features_table"   
{| 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"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="L46a9aa017d22f"  class=" tableEdit Gene_allele_table dataTable"   
{| 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"   
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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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{|   id="H4e04c50344ced"  class=" tableEdit Genetic_interaction_table dataTable"   
{| 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"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="N46a9aa022625c"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9aa022625c"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCAGACTGCTTGGACATCGCAGC  
Primer 2:CCAGACTGCTTGGACATCGCAGC  
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[[:Category:Kohara_Phage:21C8|21C8]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=119 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:12D5|12D5]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=120 Genobase]
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PMID:3038334
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{|   id="L46a9aa02aff0a"  class=" tableEdit Gene_accessions_table"   
{| 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"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11033 EcoCyc:EG11033]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1026 EchoBASE:EB1026]
EcoCyc:EG11033
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0170 EcoliGenExpDB:b0170]
EcoGene:EG11033
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C0206 ECOL199310CYC:C0206]
RegulonDB:ECK120001022
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11033 EcoGene:EG11033]
[http://www.ncbi.nlm.nih.gov/gene?term=944866 GeneID:944866]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=TSF ECOO157CYC:TSF]
EchoBASE:EB1026
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/64 CGSC:64]
ASAP:ABE-0000579
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000579&formSubmitReturn=1 ASAP:ABE-0000579]
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{|   id="Y46a6773ae9c8e"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
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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

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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

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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

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>

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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

190860

Edman degradation

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


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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

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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<protect>

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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