der: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="A46a9dfbbccc40"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''der''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''der''
Double ERa-like domains
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2507, b2511, JW5403, engA, yfgK''<ref name='LIB:Riley_2006'/>, yfgK''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15589.A46a9dfbbccc40&page=15589&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2507, b2511, JW5403, engA, yfgK''<ref name='LIB:Riley_2006'/>
|-
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{{Gene_nomenclature_help}}
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='139963'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9dfbc566a5"  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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56.77 minutes&nbsp;
56.77 minutes&nbsp;
|
|
MG1655: 2635378..2633906<br />{{GBrowseFigureByCoord|2632906|2636378|ecoli|MG1655}}
MG1655: 2635378..2633906<br /><gbrowseImage>
name=NC_000913:2633906..2635378
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7319 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7319 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2632906..2636378 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2632906|2636378|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2633906..2635378&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2633906|2635378|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7319 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7319 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 2519711..2521183<br /><gbrowseImage>
name=NC_012759:2519711..2521183
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2519711|2521183|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2519711|2521183|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2636012..2634540<br />{{GBrowseFigureByCoord|2633540|2637012|ecoli_W3110|W3110}}
W3110: 2636012..2634540<br /><gbrowseImage>
name=NC_007779:2634540..2636012
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2633540..2637012 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2633540|2637012|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2634540..2636012&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2634540|2636012|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 2727143..2725671<br /><gbrowseImage>
name=NC_010473:2725671..2727143
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2722727|2730087|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2722727|2730087|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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!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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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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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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JW5403
JW5403
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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:CCTTTATTTTTCTTGATGTGCTT  
Primer 2:CCTTTATTTTTCTTGATGTGCTT  
|-
|-
|
[[:Category:Kohara_Phage:8E3|8E3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=427 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:2D5|2D5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=428 Genobase]
|
PMID:3038334
|-  
|
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[[purC:Gene|purC80::Tn10]]
[[purC:Gene|purC80::Tn10]]
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|
|
est. P1 cotransduction: 18% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 18% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[hcaT:Gene|zfh-208::Tn10]]
[[hcaT:Gene|zfh-208::Tn10]]
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CAG18481 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40086 CGSC7417]<ref name='LIB:cgsc'/>
CAG18481 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40086 CGSC7417]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 32% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 32% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zff-208::Tn10


Synonyms:zff-208::Tn10
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===Notes===
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|- {{table_heading_style}}
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7319 EcoCyc:G7319]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3959 EchoBASE:EB3959]
EcoCyc:G7319
|
|
''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=b2511 EcoliGenExpDB:b2511]
EcoGene:EG14207
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3033 ECOL199310CYC:C3033]
RegulonDB:ECK120003891
|
|
''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=EG14207 EcoGene:EG14207]
[http://www.ncbi.nlm.nih.gov/gene?term=946983 GeneID:946983]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z3774 ECOO157CYC:Z3774]
EchoBASE:EB3959
|
|
''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=0008270&formSubmitReturn=1 ASAP:ABE-0008270] 
ASAP:ABE-0008270
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:der genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:42, 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

der

Mnemonic

Double ERa-like domains

Synonyms

ECK2507, b2511, JW5403, engA, yfgK[1], yfgK

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

56.77 minutes 

MG1655: 2635378..2633906
<gbrowseImage> name=NC_000913:2633906..2635378 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2519711..2521183
<gbrowseImage> name=NC_012759:2519711..2521183 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2636012..2634540
<gbrowseImage> name=NC_007779:2634540..2636012 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2727143..2725671
<gbrowseImage> name=NC_010473:2725671..2727143 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
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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

JW5403

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCGTACCTGTGGTCGCGCTTGT

Primer 2:CCTTTATTTTTCTTGATGTGCTT

8E3

Kohara Phage

Genobase

PMID:3038334[3]

2D5

Kohara Phage

Genobase

PMID:3038334[3]

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[4]

est. P1 cotransduction: 18% [5]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[4]

est. P1 cotransduction: 32% [5]
Synonyms:zff-208::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:G7319

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14207

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003891

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946983

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3959

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008270

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. ↑ 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
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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