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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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****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
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{|   id="N46a9c6a3aa5c0" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''trg''  
''trg''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Taxis to ribose and galactose
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK1415, b1421, JW1417''<ref name='LIB:Riley_2006'/>
''ECK1415, b1421, JW1417''<ref name='LIB:Riley_2006'/>, JW1417''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9c6a43061e"  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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32.12 minutes&nbsp;
32.12 minutes&nbsp;
|
|
MG1655: 1490494..1492134<br />{{GBrowseFigureByCoord|1490494|1492134|ecoli|MG1655}}
MG1655: 1490494..1492134<br /><gbrowseImage>
name=NC_000913:1490494..1492134
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11018 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11018 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1489494|1493134|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1489494|1493134|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|1490494|1492134|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1490494|1492134|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11018 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11018 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 1462579..1464219<br /><gbrowseImage>
name=NC_012967:1462579..1464219
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|1462579|1464219|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1462579|1464219|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 1382553..1384193<br /><gbrowseImage>
name=NC_012759:1382553..1384193
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|1382553|1384193|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1382553|1384193|FASTA Dump}}
|-  
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&nbsp;
&nbsp;
|
|
W3110: 1494184..1495824<br />{{GBrowseFigureByCoord|1494184|1495824|ecoli_W3110|W3110}}
W3110: 1494184..1495824<br /><gbrowseImage>
name=NC_007779:1494184..1495824
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1493184|1496824|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1493184|1496824|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|1494184|1495824|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1494184|1495824|FASTA Dump}}  
|-  
|-  
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|
|
DH10B: 1581089..1582729<br />{{GBrowseFigureByCoord|1581089|1582729|ecoli_DH10B|DH10B}}
DH10B: 1581089..1582729<br /><gbrowseImage>
name=NC_010473:1581089..1582729
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|1577809|1586009|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1577809|1586009|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1577809|1586009|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1577809|1586009|FASTA Dump}}  


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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;"   
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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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="M46a9c6a52184e"  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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|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004744 trg]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004744 trg::Tn5KAN-2] (FB20316)
|
|
 
Insertion at nt 509 in Minus orientation
|
|


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|
|
PMID:12519969
PMID:15262929
|
|
[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20316]
|
|
At position 509 in Minus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB20316
contains [[pKD46]]  
|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004744 trg]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004744 trg::Tn5KAN-2] (FB20317)
|
|
 
Insertion at nt 509 in Minus orientation
|
|


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|
|
PMID:12519969
PMID:15262929
|
|
[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20317]
|
|
At position 509 in Minus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB20317
does not contain [[pKD46]]  
|-  
|-  
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13407.L4e04c4df6595f-->
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===Notes===


==Genetic Resources==
==Genetic Resources==
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Primer 2:CCaACCGTAGCGAAACTAACTGG  
Primer 2:CCaACCGTAGCGAAACTAACTGG  
|-
|
[[:Category:Kohara_Phage:24D6|24D6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=270 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1A6|1A6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=271 Genobase]
|
PMID:3038334
|-  
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Synonyms:zdc-235::Tn10  
Synonyms:zdc-235::Tn10  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11018 EcoCyc:EG11018]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1011 EchoBASE:EB1011]
EcoCyc:EG11018
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1421 EcoliGenExpDB:b1421]
EcoGene:EG11018
|
|
''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=EG11018 EcoGene:EG11018]
RegulonDB:ECK120001007
|
|
''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=TRG ECOO157CYC:TRG]
[http://www.ncbi.nlm.nih.gov/gene?term=945995 GeneID:945995]
|
|
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/85 CGSC:85]
EchoBASE:EB1011
|
|
''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=0004744&formSubmitReturn=1 ASAP:ABE-0004744]
ASAP:ABE-0004744
|
|
''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:trg genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:trg genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:29, 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

trg

Mnemonic

Taxis to ribose and galactose

Synonyms

ECK1415, b1421, JW1417[1], JW1417

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

32.12 minutes 

MG1655: 1490494..1492134
<gbrowseImage> name=NC_000913:1490494..1492134 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1462579..1464219
<gbrowseImage> name=NC_012967:1462579..1464219 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1382553..1384193
<gbrowseImage> name=NC_012759:1382553..1384193 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1494184..1495824
<gbrowseImage> name=NC_007779:1494184..1495824 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1581089..1582729
<gbrowseImage> name=NC_010473:1581089..1582729 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


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
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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

Δtrg (Keio:JW1417)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9242[3]

trg::Tn5KAN-2 (FB20316)

Insertion at nt 509 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20316

contains pKD46

trg::Tn5KAN-2 (FB20317)

Insertion at nt 509 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20317

does not contain pKD46

trg-2::Tn10

Insertion at 1,491,930 bp in MG1655 (NC_000913)

adapted from Nichols et al.[5]

CAG12026 = CGSC7376[3]

Synonyms:

trg-1::Tn5

CGSC:9685

trg-2::Tn10

PMID:2540407[6]

CGSC:10754

trg-3120::Tn10kan

PMID:2540407[6]

CGSC:39820

Δtrg-782::kan

PMID:16738554[2]

CGSC:103208


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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

JW1417

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAATACAACTCCCTCACAGCG

Primer 2:CCaACCGTAGCGAAACTAACTGG

24D6

Kohara Phage

Genobase

PMID:3038334[8]

1A6

Kohara Phage

Genobase

PMID:3038334[8]

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[3]

est. P1 cotransduction: 6% [5]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[3]

est. P1 cotransduction: 13% [5]
Synonyms:zdc-235::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:EG11018

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11018

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001007

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945995

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1011

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004744

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 3.3 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 5.0 5.1 5.2 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).
  6. ↑ 6.0 6.1 Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 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

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