tfaX: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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{|{{Prettytable}}
{|  id="L46a9b38ad528e"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''tfaX''  
''tfaX''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ylcE, ECK0555, b0563, JW0552''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
''ylcE, ECK0555, b0563, JW0552''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, JW0552''
|-
 
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===Notes===
===Notes===
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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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|
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MG1655
MG1655
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12.55 minutes&nbsp;
12.55 minutes&nbsp;
|
|
MG1655: 582098..582283<br />{{GBrowseFigureByCoord|581098|583283|ecoli|MG1655}}
MG1655: 582098..582283<br /><gbrowseImage>
name=NC_000913:582098..582283
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6317 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6317 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:581098..583283 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|581098|583283|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:582098..582283&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|582098|582283|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6317 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6317 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 582098..582283<br />{{GBrowseFigureByCoord|581098|583283|ecoli_W3110|W3110}}  
W3110: 582098..582283<br /><gbrowseImage>
name=NC_007779:582098..582283
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|581098|583283|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|582098|582283|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 521430..521615<br /><gbrowseImage>
name=NC_010473:521430..521615
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|521060|521985|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|521060|521985|FASTA Dump}}
|-
|
[[DH10B]]
|
 
|
DH10B: 634690..634875<br /><gbrowseImage>
name=NC_010473:634690..634875
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:581098..583283 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|634320|635245|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:582098..582283&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|634320|635245|FASTA Dump}}
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===Notes===
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====Notes====
====Notes====
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{|class = 'sortable' {{Prettytable}} id='128263'
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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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''&#916;ylcE772::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:105700|CGSC:105700]]
|
 
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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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:
Status:
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Primer 2:  
Primer 2:  
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|
[[:Category:Kohara_Phage:23E10|23E10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=160 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12A1|12A1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=161 Genobase]
|
PMID:3038334
 
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===Notes===
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6317 EcoCyc:G6317] 
EcoCyc:G6317
|
|
''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=EB4064 EchoBASE:EB4064] 
EcoGene:EG14317
|
|
''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=b0563 EcoliGenExpDB:b0563] 
RegulonDB:ECK120002925
|
|
''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=C1475 ECOL199310CYC:C1475]
[http://www.ncbi.nlm.nih.gov/gene?term=945183 GeneID:945183]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14317 EcoGene:EG14317] 
EchoBASE:EB4064
|
|
''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=Z1926 ECOO157CYC:Z1926] 
ASAP:ABE-0001926
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{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:Gene List:DLP12 prophage]]
[[Category:tfa genes]]

Latest revision as of 20:33, 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

tfaX

Mnemonic
Synonyms

ylcE, ECK0555, b0563, JW0552[1][2], JW0552

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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

12.55 minutes 

MG1655: 582098..582283
<gbrowseImage> name=NC_000913:582098..582283 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 582098..582283
<gbrowseImage> name=NC_007779:582098..582283 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 521430..521615
<gbrowseImage> name=NC_010473:521430..521615 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 634690..634875
<gbrowseImage> name=NC_010473:634690..634875 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

[back to top]


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

ΔylcE772::kan

PMID:16738554[3]

CGSC:105700


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Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

Plasmid clone

Shigen

PMID:16769691[4]

Status:

Primer 1:

Primer 2:

23E10

Kohara Phage

Genobase

PMID:3038334[5]

12A1

Kohara Phage

Genobase

PMID:3038334[5]

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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:G6317

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14317

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002925

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945183

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4064

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001926

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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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
  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

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