prfB:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2886, b2891, JW5847, supK''<ref name='LIB:Riley_2006'/>
''ECK2886, b2891, JW5847, supK''<ref name='LIB:Riley_2006'/>, supK''


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{|   id="Q46a9e8af35b9e"  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="Q46a9e8af35b9e"  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: 3034938..3033840<br /><gbrowseImage>
W3110: 3034938..3033840<br /><gbrowseImage>
name=AC_000091:3033840..3034938
name=NC_007779:3033840..3034938
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|3032840|3035938|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3032840|3035938|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|3033840|3034938|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3033840|3034938|FASTA Dump}}  
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{|   id="V46a9e8afe6625"  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="V46a9e8afe6625"  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="H46a9e8b0399db"  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="H46a9e8b0399db"  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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&Delta;prfB (Keio:JW5847)
''prfB(del)'' (Keio:JW5847)
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deletion
deletion
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[[cgscmutation:81433|CGSC:81433]]
[[cgscmutation:81433|CGSC:81433]]
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''prfB'' neg40
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Resistant to
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Negamycin resistance
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PMID:7028032
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Parental with resistance: RIB40
Experimental strain: RIB185-1
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{|   id="L4e04c16eb6758"  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="L4e04c16eb6758"  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="M46a9e8b0eaba6"  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="M46a9e8b0eaba6"  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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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=467 Genobase]
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=467 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:22H4|22H4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=468 Genobase]
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PMID:3038334  
PMID:3038334  
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est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/> <br />  
est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/> <br />  
Synonyms:zgd-210::Tn10, zgf-210::Tn10  
Synonyms:zgd-210::Tn10, zgf-210::Tn10  
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[[:Category:Kohara_Phage:22H4|22H4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=468 Genobase]
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PMID:3038334


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{|   id="R46a9e8b18f76b"  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="R46a9e8b18f76b"  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=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]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0755 EchoBASE:EB0755]
EcoGene:EG10762
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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]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2891 EcoliGenExpDB:b2891]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10762 EcoGene:EG10762]
RegulonDB:ECK120000753
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=PRFB ECOO157CYC:PRFB]
[http://www.ncbi.nlm.nih.gov/gene?term=947369 GeneID:947369]
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Escherichia coli str. K-12 substr. MG1655
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/17635 CGSC:17635]
EchoBASE:EB0755
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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]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009488&formSubmitReturn=1 ASAP:ABE-0009488]
ASAP:ABE-0009488
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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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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<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. ↑ 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).

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