trxA: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="N46a9fec0da414" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''trxA''  
''trxA''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Thioredoxin
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3773, b3781, JW5856, fipA, tsnC, dasC''<ref name='LIB:Riley_2006'/>
''ECK3773, b3781, JW5856, fipA, tsnC, dasC''<ref name='LIB:Riley_2006'/>, dasC''


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****************************************************************************************** -->{{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="Z46a9fec168863"  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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85.43 minutes, 85.43 minutes&nbsp;
85.43 minutes, 85.43 minutes&nbsp;
|
|
MG1655: 3963784..3964113<br />{{GBrowseFigureByCoord|3963784|3964113|ecoli|MG1655}}
MG1655: 3963784..3964113<br /><gbrowseImage>
name=NC_000913:3963784..3964113
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11031 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11031 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3962784|3965113|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3962784|3965113|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3963784|3964113|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3963784|3964113|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11031 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11031 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 3927561..3927890<br /><gbrowseImage>
name=NC_012967:3927561..3927890
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|3927561|3927890|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3927561|3927890|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 3853453..3853782<br /><gbrowseImage>
name=NC_012759:3853453..3853782
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|3853453|3853782|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3853453|3853782|FASTA Dump}}
|-  
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&nbsp;
&nbsp;
|
|
W3110: 3670920..3670591<br />{{GBrowseFigureByCoord|3670591|3670920|ecoli_W3110|W3110}}
W3110: 3670920..3670591<br /><gbrowseImage>
name=NC_007779:3670591..3670920
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3669591|3671920|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3669591|3671920|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3670591|3670920|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3670591|3670920|FASTA Dump}}  
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|
|
DH10B: 4062704..4063033<br />{{GBrowseFigureByCoord|4062704|4063033|ecoli_DH10B|DH10B}}
DH10B: 4062704..4063033<br /><gbrowseImage>
name=NC_010473:4062704..4063033
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|4062046|4063691|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4062046|4063691|GBrowse(DH10B)}}
|
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4062046|4063691|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|4062046|4063691|FASTA Dump}}  


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9fec22d042"  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]]
|
3963787
|
Edman degradation
|
PMID:4883076<br />
|


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*  
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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="N46a9fec2776b4"  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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|
|
   
   
|-
|
trxA
|
deletion
|
|
Sensitivity to
|
increases sensitivity to bicyclomycin
|
PMID:21357484
|


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fig 2
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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Primer 2:CCtGCCAGGTTAGCGTCGAGGAA  
Primer 2:CCtGCCAGGTTAGCGTCGAGGAA  
|-
|
[[:Category:Kohara_Phage:7B1|7B1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=555 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:2A8|2A8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=556 Genobase]
|
PMID:3038334
|-  
|-  
|
|
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Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.  
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.  


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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=EG11031 EcoCyc:EG11031]
EcoCyc:EG11031
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1024 EchoBASE:EB1024]
EcoGene:EG11031
|
|
''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=b3781 EcoliGenExpDB:b3781]
RegulonDB:ECK120001020
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4701 ECOL199310CYC:C4701]
[http://www.ncbi.nlm.nih.gov/gene?term=948289 GeneID:948289]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11031 EcoGene:EG11031]
EchoBASE:EB1024
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=TRXA ECOO157CYC:TRXA]
ASAP:ABE-0012357
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/65 CGSC:65]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012357&formSubmitReturn=1 ASAP:ABE-0012357]
|


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

Latest revision as of 20:49, 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

trxA

Mnemonic

Thioredoxin

Synonyms

ECK3773, b3781, JW5856, fipA, tsnC, dasC[1], dasC

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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

85.43 minutes, 85.43 minutes 

MG1655: 3963784..3964113
<gbrowseImage> name=NC_000913:3963784..3964113 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3927561..3927890
<gbrowseImage> name=NC_012967:3927561..3927890 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3853453..3853782
<gbrowseImage> name=NC_012759:3853453..3853782 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3670920..3670591
<gbrowseImage> name=NC_007779:3670591..3670920 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4062704..4063033
<gbrowseImage> name=NC_010473:4062704..4063033 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

[back to top]


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

3963787

Edman degradation

PMID:4883076[2]


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Notes

Alleles and Phenotypes

[back to top]


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

ΔtrxA (Keio:JW5856)

deletion

deletion

PMID:16738554[3]

Shigen

trxA1(Am)

PMID:337124[4] PMID:3881756[5]

CGSC:5031

amber (UAG) mutation

ΔtrxA307

CGSC:10957

trxA11(ts)

temperature sensitive

PMID:3881756[5]

CGSC:88597

trxA

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[6]

fig 2

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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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Resource Resource Type Source Notes/Reference

JW5856

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAGCGATAAAATTATTCACCT

Primer 2:CCtGCCAGGTTAGCGTCGAGGAA

7B1

Kohara Phage

Genobase

PMID:3038334[8]

2A8

Kohara Phage

Genobase

PMID:3038334[8]

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[9]

est. P1 cotransduction: 69% [10]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[9]

est. P1 cotransduction: 14% [10]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:EG11031

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11031

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001020

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948289

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1024

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012357

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Holmgren, A (1968) Thioredoxin. 6. The amino acid sequence of the protein from escherichia coli B. Eur. J. Biochem. 6 475-84 PubMed
  3. ↑ 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. ↑ Mark, DF et al. (1977) Genetic mapping of trxA, a gene affecting thioredoxin in Escherichia coli K12. Mol. Gen. Genet. 155 145-52 PubMed
  5. ↑ 5.0 5.1 Russel, M & Model, P (1985) Thioredoxin is required for filamentous phage assembly. Proc. Natl. Acad. Sci. U.S.A. 82 29-33 PubMed
  6. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 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. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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