dmlR:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Added to the category for BW2952 genes.
touch
 
(20 intermediate revisions by 4 users not shown)
Line 9: Line 9:
-->{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
-->{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<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}}
{|
{|
|- 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]]
Line 31: Line 33:
*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{| id="U46a9cf2f19004"  class=" tableEdit Gene_nomenclature_table"   
{|   id="U46a9cf2f19004"  class=" tableEdit Gene_nomenclature_table"   


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''yeaT''
''dmlR''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
Line 44: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK1797, b1799, JW1788''<ref name='LIB:Riley_2006'/>
''ECK1797, b1799, JW1788''<ref name='LIB:Riley_2006'/>, yeaT, JW1788''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 65: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   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}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
Line 74: Line 76:
40.5 minutes&nbsp;
40.5 minutes&nbsp;
|
|
MG1655: 1879833..1878910<br />{{GBrowseFigureByCoord|1878910|1879833|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]
{{GBrowseLink|ecoli|NC_000913|1877910|1880833|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1877910|1880833|GBrowse(MG1655)}}
   
   
|
|
{{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]  
|-  
|-  
Line 88: Line 95:


|
|
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>
 
|
|
{{GBrowseLink|REL606|NC_012967|1859464|1860387|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|1859464|1860387|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|1859464|1860387|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|1859464|1860387|FASTA Dump}}  
|-
|
[[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}}
|-  
|-  
|
|
Line 99: Line 127:
&nbsp;
&nbsp;
|
|
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>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1881600|1884523|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1881600|1884523|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|1882600|1883523|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1882600|1883523|FASTA Dump}}  
|-  
|-  
|
|
Line 110: Line 143:


|
|
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>
 
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|1967635|1972250|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1967635|1972250|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1967635|1972250|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1967635|1972250|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 134: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   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"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14169.Z46a9cf3047214&page=14169&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.14169.Z46a9cf3047214&page=14169&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.14169.Z46a9cf3047214-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.14169.Z46a9cf3047214-->
Line 156: Line 194:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{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"   
|- {{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
Line 174: Line 212:
|
|
[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'/>  
[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
|
|
|
   
   
Line 202: Line 274:
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14169.M4e04c835d1bad-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{| 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
|- class="tableEdit_footer"
|<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> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14169.M4e04c835d1bad--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
Line 212: Line 306:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   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"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 268: Line 362:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   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"   
|- {{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=G6985 EcoCyc:G6985]
EcoCyc:G6985
|
|
''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=EB3279 EchoBASE:EB3279]
EcoGene:EG13506
|
|
''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=b1799 EcoliGenExpDB:b1799]
RegulonDB:ECK120003572
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[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=EG13506 EcoGene:EG13506]
[http://www.ncbi.nlm.nih.gov/gene?term=946316 GeneID:946316]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YEAT ECOO157CYC:YEAT]
EchoBASE:EB3279
|
|
''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=0005987&formSubmitReturn=1 ASAP:ABE-0005987]
ASAP:ABE-0005987
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 332: Line 426:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="P46a6ec8e97f9c"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46a6ec8e97f9c"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

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

[back to top]


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

[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

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>

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
edit table


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

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


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


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

[back to top]


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

edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=dmlR:Gene&oldid=1478258"