fre: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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{|   id="G46aa005b24cb4" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''fre''  
''fre''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Flavin reductase
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3836, b3844, JW3820, fsrC, flrd, luxG, G2019, lux''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3836, b3844, JW3820, fsrC, flrd, luxG, G2019, lux''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, fadI, flrD''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46aa005ba7af0"  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
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86.74 minutes&nbsp;
86.74 minutes&nbsp;
|
|
MG1655: 4024550..4025251<br />{{GBrowseFigureByCoord|4024550|4025251|ecoli|MG1655}}
MG1655: 4024550..4025251<br /><gbrowseImage>
name=NC_000913:4024550..4025251
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10334 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10334 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4023550|4026251|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4023550|4026251|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|4024550|4025251|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|4024550|4025251|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10334 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10334 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 4004998..4005699<br /><gbrowseImage>
name=NC_012967:4004998..4005699
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|4004998|4005699|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4004998|4005699|FASTA Dump}}
|-
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[[BW2952]]
|
|
NC_012759: 3914219..3914920<br /><gbrowseImage>
name=NC_012759:3914219..3914920
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|3914219|3914920|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|3914219|3914920|FASTA Dump}}
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&nbsp;
&nbsp;
|
|
W3110: 3610154..3609453<br />{{GBrowseFigureByCoord|3609453|3610154|ecoli_W3110|W3110}}
W3110: 3610154..3609453<br /><gbrowseImage>
name=NC_007779:3609453..3610154
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3608453|3611154|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3608453|3611154|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3609453|3610154|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3609453|3610154|FASTA Dump}}  
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|
|
DH10B: 4123470..4124171<br />{{GBrowseFigureByCoord|4123470|4124171|ecoli_DH10B|DH10B}}
DH10B: 4123470..4124171<br /><gbrowseImage>
name=NC_010473:4123470..4124171
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|4122068|4125573|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4122068|4125573|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4122068|4125573|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|4122068|4125573|FASTA Dump}}  


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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46aa005c6d02b"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
4024553
|
Edman degradation
|
PMID:2050627<br />
|


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****************************************************************************************** -->{{Gene_alleles_help}}
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="U46aa005cb77ac"  class=" tableEdit Gene_allele_table dataTable" 
|- {{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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|
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&Delta;fre (Keio:JW3820)
''fre(del)'' (Keio:JW3820)
|
|
deletion
deletion
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PMID:16738554
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109044 CGSC10763]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=109044 CGSC10763]<ref name='LIB:cgsc'/>  
|
|
   
   
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|-  
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''&#916;fre-784::kan''
''fre-784(del)::kan''
|
|


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''fre784(del)''::FRTKanFRT
|


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|
Mutagenesis rate
|
Decreased stress-induced mutagenesis (SIM) phenotype.
|
PMID:23224554
|
Parental Strain: SMR4562
 
Experimental Strain: SMR12007
|
Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
|-
|
SMR4562 yiaG-yfp FRTcatFRT ''fre784(del)''::FRTKanFRT
|
Deletion & Insertion
|
 
|
Sigma <sup>S</sup> activity
|
Decrease in Sigma <sup>S</sup> activity
 
 
 
|
PMID:23224554
|
Parental Strain: SMR10582
Experimental Strain: SMR14267
|
See table S8 for full experimental results. 
|-
|
CAG45114 ''fre784(del)''::FRTKanFRT
|
deletion
|
 
|
Sigma<sup>E</sup> activity
|
Decrease in sigma<sup>E</sup> activity
|
PMID:23224554
|
Parental Strain: CAG45114
Experimental Strain: SMR15362
|
See table S11 for experimental results. 
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18247.M4e04bb6cd9110-->
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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Primer 2:CCGATAAATGCAAACGCATCGCC  
Primer 2:CCGATAAATGCAAACGCATCGCC  
|-
|
[[:Category:Kohara_Phage:16G1|16G1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=550 Genobase]
|
PMID:3038334
|-  
|-  
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Synonyms:fadAB101::Tn10  
Synonyms:fadAB101::Tn10  


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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=EG10334 EcoCyc:EG10334]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0330 EchoBASE:EB0330]
|
|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3844 EcoliGenExpDB:b3844]
EcoCyc:EG10334
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4791 ECOL199310CYC:C4791]
EcoGene:EG10334
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10334 EcoGene:EG10334]
RegulonDB:ECK120000328
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOO157/new-image?object=UBIB ECOO157CYC:UBIB]
[http://www.ncbi.nlm.nih.gov/gene?term=948325 GeneID:948325]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/49 CGSC:49]
EchoBASE:EB0330
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012559&formSubmitReturn=1 ASAP:ABE-0012559]
ASAP:ABE-0012559
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:fre genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:fre genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:50, 19 September 2013

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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

fre

Mnemonic

Flavin reductase

Synonyms

ECK3836, b3844, JW3820, fsrC, flrd, luxG, G2019, lux[1][2], fadI, flrD

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

86.74 minutes 

MG1655: 4024550..4025251
<gbrowseImage> name=NC_000913:4024550..4025251 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4004998..4005699
<gbrowseImage> name=NC_012967:4004998..4005699 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3914219..3914920
<gbrowseImage> name=NC_012759:3914219..3914920 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3610154..3609453
<gbrowseImage> name=NC_007779:3609453..3610154 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4123470..4124171
<gbrowseImage> name=NC_010473:4123470..4124171 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

4024553

Edman degradation

PMID:2050627[3]


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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

fre(del) (Keio:JW3820)

deletion

deletion

PMID:16738554[4]

Shigen

CGSC10763[5]

fre-352

CGSC:5420

fre-784(del)::kan

PMID:16738554[4]

CGSC:101000

fre784(del)::FRTKanFRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[6]

Parental Strain: SMR4562

Experimental Strain: SMR12007

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

SMR4562 yiaG-yfp FRTcatFRT fre784(del)::FRTKanFRT

Deletion & Insertion

Sigma S activity

Decrease in Sigma S activity


PMID:23224554[6]

Parental Strain: SMR10582 Experimental Strain: SMR14267

See table S8 for full experimental results.

CAG45114 fre784(del)::FRTKanFRT

deletion

SigmaE activity

Decrease in sigmaE activity

PMID:23224554[6]

Parental Strain: CAG45114 Experimental Strain: SMR15362

See table S11 for experimental results.

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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

JW3820

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCACAACCTTAAGCTGTAAAGT

Primer 2:CCGATAAATGCAAACGCATCGCC

16G1

Kohara Phage

Genobase

PMID:3038334[8]

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[5]

est. P1 cotransduction: 57% [9]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

fad-751::Tn10

Linked marker

CAG18496 = CGSC7465[5]

est. P1 cotransduction: 92% [9]
Synonyms:fadAB101::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:EG10334

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10334

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000328

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948325

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0330

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012559

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 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Spyrou, G et al. (1991) Characterization of the flavin reductase gene (fre) of Escherichia coli and construction of a plasmid for overproduction of the enzyme. J. Bacteriol. 173 3673-9 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 6.2 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  7. ↑ 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
  8. ↑ 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
  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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