dmlR:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|yeaT}}{{Tab On|Gene|yeaT}}{{Tab|Gene Product(s)|yeaT}}{{Tab|Expression|yeaT}}{{Tab|Evolution|yeaT}}{{Tab|On One Page|yeaT}}{{TabsBottom}}
{{Tab|Quickview|dmlR}}{{Tab On|Gene|dmlR}}{{Tab|Gene Product(s)|dmlR}}{{Tab|Expression|dmlR}}{{Tab|Evolution|dmlR}}{{Tab|On One Page|dmlR}}{{TabsBottom}}
{|
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|{{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="U46a9cf2f19004"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''dmlR''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''yeaT''
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1797, b1799, JW1788''<ref name='LIB:Riley_2006'/>, yeaT, JW1788''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14169.U46a9cf2f19004&page=14169&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK1797, b1799, JW1788''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='135708'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9cf2f94731"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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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40.5 minutes&nbsp;
40.5 minutes&nbsp;
|
|
MG1655: 1879833..1878910<br />{{GBrowseFigureByCoord|1877910|1880833|ecoli|MG1655}}
MG1655: 1879833..1878910<br /><gbrowseImage>
name=NC_000913:1878910..1879833
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6985 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6985 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1877910..1880833 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1877910|1880833|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1878910..1879833&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1878910|1879833|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6985 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6985 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1860387..1859464<br /><gbrowseImage>
name=NC_012967:1859464..1860387
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1859464|1860387|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1859464|1860387|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 1770969..1771892<br /><gbrowseImage>
name=NC_012759:1770969..1771892
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1770969|1771892|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1770969|1771892|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1883523..1882600<br />{{GBrowseFigureByCoord|1881600|1884523|ecoli_W3110|W3110}}  
W3110: 1883523..1882600<br /><gbrowseImage>
name=NC_007779:1882600..1883523
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1881600|1884523|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1882600|1883523|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 1970404..1969481<br /><gbrowseImage>
name=NC_010473:1969481..1970404
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1881600..1884523 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1967635|1972250|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1882600..1883523&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1967635|1972250|FASTA Dump}}
|-class='sortbottom'
 
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14169.M46a9cf2f94731&page=14169&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14169.M46a9cf2f94731&page=14169&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
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===Notes===
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{|class = 'sortable' {{Prettytable}} id='135709'
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{|class = 'sortable' {{Prettytable}} id='135710'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9cf308abaf"  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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&Delta;yeaT (Keio:JW1788)
&Delta;yeaT (Keio:JW1788)
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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=107780 CGSC9499]<ref name='LIB:cgsc'/>  
|
|-
|
&Delta;yeaT::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;yeaT::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Bromosuccinate]]
|
PMID:16095938
|
 
|
|-
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107780 CGSC9499]<ref name='LIB:cgsc'/> 
''&#916;yeaT724::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:104396|CGSC:104396]]
|
|
   
   
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14169.U46a9cf308abaf&page=14169&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14169.M4e04c835d1bad-->
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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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JW1788
JW1788
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCGGCATGCTCCAGTGAAAAATT  
Primer 2:CCGGCATGCTCCAGTGAAAAATT  
|-
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[[yeaI:Gene|zea-225::Tn10]]
[[yeaI:Gene|zea-225::Tn10]]
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CAG18465 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39973 CGSC7388]<ref name='LIB:cgsc'/>
CAG18465 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39973 CGSC7388]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 73% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 73% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zdj-225::Tn10  
Synonyms:zdj-225::Tn10  
|-
|-  
|
|
[[eda:Gene|eda-51::Tn10]]
[[eda:Gene|eda-51::Tn10]]
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|
|
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>  
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<protect><!--Gene_resources_notes--></protect>
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='135712'
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-
|
[[EcoCyc]]
|
EcoCyc:G6985
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6985 EcoCyc:G6985] 
EcoGene:EG13506
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3279 EchoBASE:EB3279] 
RegulonDB:ECK120003572
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1799 EcoliGenExpDB:b1799]
[http://www.ncbi.nlm.nih.gov/gene?term=946316 GeneID:946316]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13506 EcoGene:EG13506] 
EchoBASE:EB3279
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YEAT ECOO157CYC:YEAT] 
ASAP:ABE-0005987
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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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:yea genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:39, 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

dmlR

Mnemonic

Systematic nomenclature

Synonyms

ECK1797, b1799, JW1788[1], yeaT, JW1788

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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

40.5 minutes 

MG1655: 1879833..1878910
<gbrowseImage> name=NC_000913:1878910..1879833 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1860387..1859464
<gbrowseImage> name=NC_012967:1859464..1860387 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1770969..1771892
<gbrowseImage> name=NC_012759:1770969..1771892 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1883523..1882600
<gbrowseImage> name=NC_007779:1882600..1883523 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1970404..1969481
<gbrowseImage> name=NC_010473:1969481..1970404 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

ΔyeaT (Keio:JW1788)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9499[3]

ΔyeaT::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔyeaT::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[4]

ΔyeaT724::kan

PMID:16738554[2]

CGSC:104396


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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

JW1788

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAATAATTTACCGCTGCTGAA

Primer 2:CCGGCATGCTCCAGTGAAAAATT

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[3]

est. P1 cotransduction: 73% [6]
Synonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[3]

est. P1 cotransduction: 9% [6]

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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:G6985

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13506

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003572

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946316

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3279

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005987

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. ↑ 4.0 4.1 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ 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
  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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