dmlR:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{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}}
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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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="U46a9cf2f19004"  class=" tableEdit Gene_nomenclature_table"   
{|   id="U46a9cf2f19004"  class=" tableEdit Gene_nomenclature_table"   


|-
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!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''yeaT''
''dmlR''
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|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1797, b1799, JW1788''<ref name='LIB:Riley_2006'/>
''ECK1797, b1799, JW1788''<ref name='LIB:Riley_2006'/>, yeaT, JW1788''


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{|   id="M46a9cf2f94731"  class=" tableEdit Gene_location_table"   
{| 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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40.5 minutes&nbsp;
40.5 minutes&nbsp;
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MG1655: 1879833..1878910<br />{{GBrowseFigureByCoord|1878910|1879833|ecoli|MG1655}}
MG1655: 1879833..1878910<br /><gbrowseImage>
name=NC_000913:1878910..1879833
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[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]
{{GBrowseLink|ecoli|NC_000913|1877910|1880833|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1877910|1880833|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1878910|1879833|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]  
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NC_012967: 1860387..1859464<br />{{GBrowseFigureByCoord|1859464|1860387|REL606|NC_012967}}
NC_012967: 1860387..1859464<br /><gbrowseImage>
name=NC_012967:1859464..1860387
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|1859464|1860387|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|1859464|1860387|GBrowse (REL606)}}
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NC_012759: 1770969..1771892<br />{{GBrowseFigureByCoord|1770969|1771892|BW2952|NC_012759}}
NC_012759: 1770969..1771892<br /><gbrowseImage>
name=NC_012759:1770969..1771892
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|BW2952|012759|1770969|NC_1771892|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|1770969|1771892|GBrowse (BW2952)}}
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W3110: 1883523..1882600<br />{{GBrowseFigureByCoord|1882600|1883523|ecoli_W3110|W3110}}
W3110: 1883523..1882600<br /><gbrowseImage>
name=NC_007779:1882600..1883523
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|1881600|1884523|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1881600|1884523|GBrowse(W3110)}}  
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DH10B: 1970404..1969481<br />{{GBrowseFigureByCoord|1969481|1970404|ecoli_DH10B|DH10B}}
DH10B: 1970404..1969481<br /><gbrowseImage>
name=NC_010473:1969481..1970404
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|1967635|1972250|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1967635|1972250|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1967635|1972250|FASTA Dump}}  
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{|   id="Z46a9cf3047214"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9cf3047214"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="U46a9cf308abaf"  class=" tableEdit Gene_allele_table dataTable"   
{| 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"   
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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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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14169.M4e04c835d1bad-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M4e04c835d1bad"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.14169.M4e04c835d1bad&page=14169&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="N46a9cf313d697"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9cf313d697"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
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{|   id="N46a9cf31ceb8b"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9cf31ceb8b"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6985 EcoCyc:G6985]
EcoCyc:G6985
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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]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3279 EchoBASE:EB3279]
EcoGene:EG13506
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1799 EcoliGenExpDB:b1799]
RegulonDB:ECK120003572
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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]])
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[http://ecogene.org/geneinfo.php?eg_id=EG13506 EcoGene:EG13506]
[http://www.ncbi.nlm.nih.gov/gene?term=946316 GeneID:946316]
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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=YEAT ECOO157CYC:YEAT]
EchoBASE:EB3279
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0005987&formSubmitReturn=1 ASAP:ABE-0005987]
ASAP:ABE-0005987
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:39, 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

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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

edit table


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
edit table


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]

edit table


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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<protect>

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).

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