prfH: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="S46a9ab75705af"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''prfH''  
''prfH''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0237, b0236, JW0226''<ref name='LIB:Riley_2006'/>
''ECK0237, b0236, JW0226''<ref name='LIB:Riley_2006'/>, JW0226''
|-
 
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{{Gene_nomenclature_help}}
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='126351'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46a9ab75e8f17"  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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5.47 minutes&nbsp;
5.47 minutes&nbsp;
|
|
MG1655: 253702..254202<br />{{GBrowseFigureByCoord|252702|255202|ecoli|MG1655}}
MG1655: 253702..254202<br /><gbrowseImage>
name=NC_000913:253702..254202
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11496 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11496 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:252702..255202 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|252702|255202|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:253702..254202&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|253702|254202|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11496 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11496 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 258193..258693<br /><gbrowseImage>
name=NC_012967:258193..258693
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|258193|258693|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|258193|258693|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 253702..254202<br />{{GBrowseFigureByCoord|252702|255202|ecoli_W3110|W3110}}  
W3110: 253702..254202<br /><gbrowseImage>
name=NC_007779:253702..254202
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|252702|255202|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|253702|254202|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 227806..228306<br /><gbrowseImage>
name=NC_010473:227806..228306
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:252702..255202 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|226806|229306|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:253702..254202&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|226806|229306|FASTA Dump}}
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===Notes===
===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='126353'
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|- {{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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&Delta;prfH (Keio:JW0226)
''prfH(del)'' (Keio:JW0226)
|
|
deletion
deletion
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106742 CGSC8461]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106742 CGSC8461]<ref name='LIB:cgsc'/>  
|
|
   
   
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''prfH754(del)::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102452|CGSC:102452]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11051.K4e04c170e75c5-->
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0226
JW0226
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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:CCTCCTTCGATAAAAGCCATCCC  
Primer 2:CCTCCTTCGATAAAAGCCATCCC  
|-
|-
|
[[:Category:Kohara_Phage:8F9|8F9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=127 Genobase]
|
PMID:3038334
|-  
|
|
[[yafC:Gene|yafC502::Tn10]]
[[yafC:Gene|yafC502::Tn10]]
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CAG18436 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38989 CGSC7328]<ref name='LIB:cgsc'/>
CAG18436 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38989 CGSC7328]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 45% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 45% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zae-502::Tn10  
Synonyms:zae-502::Tn10  
|-
|-  
|
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[[proA:Gene|proA81::Tn10]]
[[proA:Gene|proA81::Tn10]]
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|
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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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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11496 EcoCyc:EG11496]
[http://www.ncbi.nlm.nih.gov/gene?term=947374 GeneID:947374]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1459 EchoBASE:EB1459] 
|
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0236 EcoliGenExpDB:b0236] 
EcoCyc:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0382 ECOL199310CYC:C0382] 
RegulonDB:ECK120001452
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11496 EcoGene:EG11496] 
EchoBASE:
|
|
''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=PRFH ECOO157CYC:PRFH] 
ASAP:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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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 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:prf genes]][[Category:Gene_List:REL606]]

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

prfH

Mnemonic
Synonyms

ECK0237, b0236, JW0226[1], JW0226

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

5.47 minutes 

MG1655: 253702..254202
<gbrowseImage> name=NC_000913:253702..254202 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 258193..258693
<gbrowseImage> name=NC_012967:258193..258693 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 253702..254202
<gbrowseImage> name=NC_007779:253702..254202 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 227806..228306
<gbrowseImage> name=NC_010473:227806..228306 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

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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

prfH(del) (Keio:JW0226)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC8461[3]

prfH754(del)::kan

PMID:16738554[2]

CGSC:102452


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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

JW0226

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCTGGAAACAGAAACGGGCCG

Primer 2:CCTCCTTCGATAAAAGCCATCCC

8F9

Kohara Phage

Genobase

PMID:3038334[5]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 45% [6]
Synonyms:zae-502::Tn10

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[3]

est. P1 cotransduction: 81% [6]

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Notes

Accessions in Other Databases

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Database Accession Notes

NCBI (EcoliWiki Page)

GeneID:947374

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001452

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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. ↑ 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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