ymfR: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="V46a9c0a619b5b"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ymfR''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ymfR''
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1136, b1150, JW1136''<ref name='LIB:Riley_2006'/>, JW1136''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12849.V46a9c0a619b5b&page=12849&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1136, b1150, JW1136''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='131747'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9c0a6930cf"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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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MG1655
MG1655
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25.97 minutes&nbsp;
25.97 minutes&nbsp;
|
|
MG1655: 1204772..1204954<br />{{GBrowseFigureByCoord|1203772|1205954|ecoli|MG1655}}
MG1655: 1204772..1204954<br /><gbrowseImage>
name=NC_000913:1204772..1204954
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6594 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6594 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1203772..1205954 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1203772|1205954|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1204772..1204954&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1204772|1204954|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6594 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6594 EcoCyc Sequence Dump]  
|-
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 1207126..1207308<br />{{GBrowseFigureByCoord|1206126|1208308|ecoli_W3110|W3110}}
W3110: 1207126..1207308<br /><gbrowseImage>
name=NC_007779:1207126..1207308
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1206126..1208308 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|1206126|1208308|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1207126..1207308&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|1207126|1207308|FASTA Dump}}
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===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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{|class = 'sortable' {{Prettytable}} id='131749'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46a9c0a78343b"  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!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;ymfR (Keio:JW1136)
&Delta;ymfR (Keio:JW1136)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107340 CGSC9059]<ref name='LIB:cgsc'/>  
|
|-
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''&#916;ymfR738::kan''
|
 
|
 
|
 
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107340 CGSC9059]<ref name='LIB:cgsc'/> 
 
|
PMID:16738554
|
[[cgscmutation:105742|CGSC:105742]]
|
|
   
   
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12849.A4e04cc0be1099-->
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|class = 'sortable' {{Prettytable}} id='131750'
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JW1136
JW1136
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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]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTTTACCTCCGCCGACAGACGA  
Primer 2:CCTTTACCTCCGCCGACAGACGA  
|-
|-
|
[[:Category:Kohara_Phage:2E7|2E7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=240 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3E11|3E11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=241 Genobase]
|
PMID:3038334
|-  
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[[yceG:Gene|zce-726::Tn10]]
[[yceG:Gene|zce-726::Tn10]]
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est. P1 cotransduction: 10% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 10% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
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[[elbA:Gene|zcf-117::Tn10]]
[[elbA:Gene|zcf-117::Tn10]]
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est. P1 cotransduction: 81% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 81% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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{|class = 'sortable' {{Prettytable}} id='131751'
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:G6594
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[EcoGene]]
|
EcoGene:EG14336
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6594 EcoCyc:G6594] 
RegulonDB:ECK120003189
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4082 EchoBASE:EB4082]
[http://www.ncbi.nlm.nih.gov/gene?term=945700 GeneID:945700]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EchoBASE]]
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1150 EcoliGenExpDB:b1150] 
EchoBASE:EB4082
|
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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]])
[[ASAP]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14336 EcoGene:EG14336] 
ASAP:ABE-0003868
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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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:Gene List:e14 prophage]]
[[Category:ymf genes]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:31, 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

ymfR

Mnemonic

Systematic nomenclature

Synonyms

ECK1136, b1150, JW1136[1], JW1136

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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

25.97 minutes 

MG1655: 1204772..1204954
<gbrowseImage> name=NC_000913:1204772..1204954 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1207126..1207308
<gbrowseImage> name=NC_007779:1207126..1207308 source=W3110 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

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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

ΔymfR (Keio:JW1136)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9059[3]

ΔymfR738::kan

PMID:16738554[2]

CGSC:105742


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Notes

Genetic Interactions

[back to top]



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

JW1136

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCATCATGCTGATTCTCGCGCC

Primer 2:CCTTTACCTCCGCCGACAGACGA

2E7

Kohara Phage

Genobase

PMID:3038334[5]

3E11

Kohara Phage

Genobase

PMID:3038334[5]

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[3]

est. P1 cotransduction: 10% [6]

zcf-117::Tn10

Linked marker

CAG18463 = CGSC7363[3]

est. P1 cotransduction: 81% [6]

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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:G6594

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14336

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003189

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945700

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4082

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003868

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 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  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
  6. ↑ 6.0 6.1 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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