prfB: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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
!align=left {{table_heading_style}} |Standard name
||
''prfB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''prfB''
Protein release factor
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2886, b2891, JW5847, supK''<ref name='LIB:Riley_2006'/>, supK''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16347.F46a9e8aeaa09e&page=16347&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2886, b2891, JW5847, supK''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9e8af35b9e"  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
|-
|-  
|
|
MG1655
MG1655
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65.38 minutes&nbsp;
65.38 minutes&nbsp;
|
|
MG1655: 3034304..3033206<br />{{GBrowseFigureByCoord|3032206|3035304|ecoli|MG1655}}
MG1655: 3034304..3033206<br /><gbrowseImage>
name=NC_000913:3033206..3034304
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10762 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10762 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3032206..3035304 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3032206|3035304|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3033206..3034304&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3033206|3034304|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10762 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10762 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2921959..2920937<br /><gbrowseImage>
name=NC_012967:2920937..2921959
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2920937|2921959|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2920937|2921959|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2920354..2921452<br /><gbrowseImage>
name=NC_012759:2920354..2921452
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2920354|2921452|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2920354|2921452|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3034938..3033840<br />{{GBrowseFigureByCoord|3032840|3035938|ecoli_W3110|W3110}}  
W3110: 3034938..3033840<br /><gbrowseImage>
name=NC_007779:3033840..3034938
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3032840|3035938|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3033840|3034938|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 3128098..3127076<br /><gbrowseImage>
name=NC_010473:3127076..3128098
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3032840..3035938 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3125032|3130142|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3033840..3034938&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3125032|3130142|FASTA Dump}}
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9e8afe6625"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
3033206
|
Edman degradation
|
PMID:3889910<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9e8b0399db"  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
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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|
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&Delta;prfB (Keio:JW5847)
''prfB(del)'' (Keio:JW5847)
|
|
deletion
deletion
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|
   
   
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prfBT246A
|
 
|
T246A
|
 
|
(in strain: BL21 and MRE-600; increased termination efficiency)
|
 
|
 
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P07012 UniProt:P07012]
|-
|
''prfB11''(UGAs)
|
 
|
 
|
 
|
UGA (opal) suppressor
|
 
|
[[cgscmutation:81433|CGSC:81433]]
|
|-
|
''prfB'' neg40
|
 
|
 
|
Resistant to
|
Negamycin resistance
|
PMID:7028032
|
Parental with resistance: RIB40
 
Experimental strain: RIB185-1
|
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
The Keio collection<ref name='PMID:16738554'/> lists a deletion of ''prfB''.  The insertion in this strain is a duplication of the ''prfB'' region.<ref name='PMID:20029369'/>
==Genetic Interactions==
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|- {{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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!|Resource!!Resource Type!!Source!!Notes/Reference
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JW5847
JW5847
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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:Clone OK
Status:Clone OK
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Primer 2:CCTAACCCTGCTTTCAAACTTGC  
Primer 2:CCTAACCCTGCTTTCAAACTTGC  
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[[:Category:Kohara_Phage:5B4|5B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=467 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:22H4|22H4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=468 Genobase]
|
PMID:3038334
|-
|
[[recD:Gene|recD1901::Tn10]]
|
Linked marker
|
CAG12135 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40106 CGSC7429]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[speA:Gene|speA210::Tn10]]
|
Linked marker
|
CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgd-210::Tn10, zgf-210::Tn10
 
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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10762 EcoCyc:EG10762] 
EcoCyc:EG10762
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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]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0755 EchoBASE:EB0755] 
EcoGene:EG10762
|
|
''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=b2891 EcoliGenExpDB:b2891] 
RegulonDB:ECK120000753
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[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=EG10762 EcoGene:EG10762]
[http://www.ncbi.nlm.nih.gov/gene?term=947369 GeneID:947369]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=PRFB ECOO157CYC:PRFB] 
EchoBASE:EB0755
|
|
''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/17635 CGSC:17635] 
ASAP:ABE-0009488
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:prf genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:44, 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

prfB

Mnemonic

Protein release factor

Synonyms

ECK2886, b2891, JW5847, supK[1], supK

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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

65.38 minutes 

MG1655: 3034304..3033206
<gbrowseImage> name=NC_000913:3033206..3034304 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2921959..2920937
<gbrowseImage> name=NC_012967:2920937..2921959 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2920354..2921452
<gbrowseImage> name=NC_012759:2920354..2921452 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3034938..3033840
<gbrowseImage> name=NC_007779:3033840..3034938 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3128098..3127076
<gbrowseImage> name=NC_010473:3127076..3128098 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

3033206

Edman degradation

PMID:3889910[2]


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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

prfB(del) (Keio:JW5847)

deletion

deletion

PMID:16738554[3]

Shigen

prfBT246A

T246A

(in strain: BL21 and MRE-600; increased termination efficiency)

Strain variation; seeded from UniProt:P07012

prfB11(UGAs)

UGA (opal) suppressor

CGSC:81433

prfB neg40

Resistant to

Negamycin resistance

PMID:7028032[4]

Parental with resistance: RIB40

Experimental strain: RIB185-1


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Notes

The Keio collection[3] lists a deletion of prfB. The insertion in this strain is a duplication of the prfB region.[5]


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

JW5847

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTTTGAAATTAATCCGGTAAA

Primer 2:CCTAACCCTGCTTTCAAACTTGC

5B4

Kohara Phage

Genobase

PMID:3038334[7]

22H4

Kohara Phage

Genobase

PMID:3038334[7]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[8]

est. P1 cotransduction: % [9]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[8]

est. P1 cotransduction: 8% [9]
Synonyms:zgd-210::Tn10, zgf-210::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:EG10762

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10762

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000753

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947369

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0755

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009488

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. ↑ Craigen, WJ et al. (1985) Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2. Proc. Natl. Acad. Sci. U.S.A. 82 3616-20 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ Corchuelo, MC et al. (1981) Resistance to the peptide-like antibiotic negamycin in Escherichia coli. Biochem. Biophys. Res. Commun. 100 1497-503 PubMed
  5. ↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 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).

Categories

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