rhaT: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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{|{{Prettytable}}
{|   id="W46aa01f645318"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''rhaT''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''rhaT''
Rhamnose
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3900, b3907, JW3878''<ref name='LIB:Riley_2006'/>, JW3878''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18375.W46aa01f645318&page=18375&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3900, b3907, JW3878''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='148331'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46aa01f6c76ab"  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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MG1655
MG1655
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88.31 minutes&nbsp;
88.31 minutes&nbsp;
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MG1655: 4098548..4097514<br />{{GBrowseFigureByCoord|4096514|4099548|ecoli|MG1655}}
MG1655: 4098548..4097514<br /><gbrowseImage>
name=NC_000913:4097514..4098548
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11313 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11313 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4096514..4099548 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4096514|4099548|GBrowse(MG1655)}}
   
   
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4097514..4098548&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4097514|4098548|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11313 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11313 EcoCyc Sequence Dump]  
|-
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[[REL606]]
|
 
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NC_012967: 4080007..4078973<br /><gbrowseImage>
name=NC_012967:4078973..4080007
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4078973|4080007|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|4078973|4080007|FASTA Dump}}
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[[BW2952]]
|
 
|
NC_012759: 3987183..3988217<br /><gbrowseImage>
name=NC_012759:3987183..3988217
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3987183|3988217|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|3987183|3988217|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 3536156..3537190<br />{{GBrowseFigureByCoord|3535156|3538190|ecoli_W3110|W3110}}  
W3110: 3536156..3537190<br /><gbrowseImage>
name=NC_007779:3536156..3537190
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3535156|3538190|GBrowse(W3110)}}  
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3535156..3538190 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|3536156|3537190|FASTA Dump}}
|-  
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3536156..3537190&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 4198245..4197211<br /><gbrowseImage>
name=NC_010473:4197211..4198245
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|4195143|4200313|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4195143|4200313|FASTA Dump}}
 
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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{|class = 'sortable' {{Prettytable}} id='148333'
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|- {{table_heading_style}}
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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;rhaT (Keio:JW3878)
&Delta;rhaT (Keio:JW3878)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109078 CGSC10797]<ref name='LIB:cgsc'/>
|
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''&#916;rhaT767::kan''
|
 
|
 
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PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109078 CGSC10797]<ref name='LIB:cgsc'/> 
[[cgscmutation:102688|CGSC:102688]]
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18375.V4e04c26786d46-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V4e04c26786d46"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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JW3878
JW3878
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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]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCATTCGCCATGCCGATGCCGAC  
Primer 2:CCATTCGCCATGCCGATGCCGAC  
|-
|-
|
[[:Category:Kohara_Phage:4B6|4B6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=541 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7G8|7G8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=542 Genobase]
|
PMID:3038334
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[[yihO:Gene|zih-35::Tn10]]
[[yihO:Gene|zih-35::Tn10]]
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est. P1 cotransduction: 27% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 27% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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[[pflD:Gene|pflD501::Tn10]]
[[pflD:Gene|pflD501::Tn10]]
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CAG18477 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37152 CGSC7470]<ref name='LIB:cgsc'/>
CAG18477 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37152 CGSC7470]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).
Synonyms:zij-501::Tn10  
 


CAG18477 also carries metF79(Am) (CGSC).
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===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=EG11313 EcoCyc:EG11313] 
EcoCyc:EG11313
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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]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1289 EchoBASE:EB1289] 
|
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3907 EcoliGenExpDB:b3907] 
EcoGene:EG11313
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C4857 ECOL199310CYC:C4857] 
RegulonDB:ECK120001284
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[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=EG11313 EcoGene:EG11313]
[http://www.ncbi.nlm.nih.gov/gene?term=948398 GeneID:948398]
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=RHAT ECOO157CYC:RHAT] 
EchoBASE:EB1289
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/34185 CGSC:34185] 
ASAP:ABE-0012749
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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{{BacktoTop}}
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<references />
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:rha 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

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

rhaT

Mnemonic

Rhamnose

Synonyms

ECK3900, b3907, JW3878[1], JW3878

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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

88.31 minutes 

MG1655: 4098548..4097514
<gbrowseImage> name=NC_000913:4097514..4098548 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4080007..4078973
<gbrowseImage> name=NC_012967:4078973..4080007 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3987183..3988217
<gbrowseImage> name=NC_012759:3987183..3988217 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3536156..3537190
<gbrowseImage> name=NC_007779:3536156..3537190 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4198245..4197211
<gbrowseImage> name=NC_010473:4197211..4198245 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
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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

ΔrhaT (Keio:JW3878)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10797[3]

ΔrhaT767::kan

PMID:16738554[2]

CGSC:102688


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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

JW3878

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAGTAACGCGATTACGATGGG

Primer 2:CCATTCGCCATGCCGATGCCGAC

4B6

Kohara Phage

Genobase

PMID:3038334[5]

7G8

Kohara Phage

Genobase

PMID:3038334[5]

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[3]

est. P1 cotransduction: 27% [6]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[3]

est. P1 cotransduction: 13% [6]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

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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:EG11313

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11313

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001284

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948398

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1289

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012749

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 CGSC: The Coli Genetics Stock Center
  4. ↑ 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
  5. ↑ 5.0 5.1 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
  6. ↑ 6.0 6.1 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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