dedD: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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{|   id="M46a9db24da7cf"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''dedD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''dedD''
Downstream E. coli DNA
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2308, b2314, JW5378''<ref name='LIB:Riley_2006'/>, JW5378''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15191.M46a9db24da7cf&page=15191&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2308, b2314, JW5378''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='138769'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9db2564565"  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
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MG1655
MG1655
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52.35 minutes&nbsp;
52.35 minutes&nbsp;
|
|
MG1655: 2429706..2429044<br />{{GBrowseFigureByCoord|2428044|2430706|ecoli|MG1655}}
MG1655: 2429706..2429044<br /><gbrowseImage>
name=NC_000913:2429044..2429706
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10218 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10218 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2428044..2430706 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2428044|2430706|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2429044..2429706&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2429044|2429706|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10218 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10218 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2375276..2374614<br /><gbrowseImage>
name=NC_012967:2374614..2375276
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2374614|2375276|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2374614|2375276|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2314849..2315511<br /><gbrowseImage>
name=NC_012759:2314849..2315511
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2314849|2315511|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2314849|2315511|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2437130..2436468<br />{{GBrowseFigureByCoord|2435468|2438130|ecoli_W3110|W3110}}
W3110: 2437130..2436468<br /><gbrowseImage>
name=NC_007779:2436468..2437130
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2435468..2438130 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2435468|2438130|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2436468..2437130&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2436468|2437130|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 2521471..2520809<br /><gbrowseImage>
name=NC_010473:2520809..2521471
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2519485|2522795|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2519485|2522795|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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&Delta;dedD (Keio:JW5378)
&Delta;dedD (Keio:JW5378)
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007643 dedD::Tn5KAN-2] (FB20761)
|
Insertion at nt 407 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20761]
|
contains [[pKD46]]
|-
|
&Delta;dedD::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
dedD
|
deletion
|
 
|
Sensitivity to
|
decreases sensitivity to bicyclomycin
|
PMID:21357484
|
 
|
fig 2
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15191.Z4e04b9af4aa39-->
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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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JW5378
JW5378
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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:CCATTCGGCGTATAGCCCATTAC  
Primer 2:CCATTCGGCGTATAGCCCATTAC  
|-
|-
|
[[:Category:Kohara_Phage:9D2|9D2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=406 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12F12|12F12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=407 Genobase]
|
PMID:3038334
|-  
|
|
[[yfbO:Gene|zfb-223::Tn10]]
[[yfbO:Gene|zfb-223::Tn10]]
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CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 19% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 19% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zej-223::Tn10  
Synonyms:zej-223::Tn10  
|-
|-  
|
|
zfd-1::Tn10
zfd-1::Tn10
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CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zfb-1::Tn10


Synonyms:zfb-1::Tn10
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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=EG10218 EcoCyc:EG10218] 
EcoCyc:EG10218
|
|
''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=EB0214 EchoBASE:EB0214] 
EcoGene:EG10218
|
|
''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=b2314 EcoliGenExpDB:b2314] 
RegulonDB:ECK120000212
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2859 ECOL199310CYC:C2859]
[http://www.ncbi.nlm.nih.gov/gene?term=944971 GeneID:944971]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10218 EcoGene:EG10218] 
EchoBASE:EB0214
|
|
''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=DEDD ECOO157CYC:DEDD] 
ASAP:ABE-0007643
|
|
''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:ded genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 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

dedD

Mnemonic

Downstream E. coli DNA

Synonyms

ECK2308, b2314, JW5378[1], JW5378

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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

52.35 minutes 

MG1655: 2429706..2429044
<gbrowseImage> name=NC_000913:2429044..2429706 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2375276..2374614
<gbrowseImage> name=NC_012967:2374614..2375276 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2314849..2315511
<gbrowseImage> name=NC_012759:2314849..2315511 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2437130..2436468
<gbrowseImage> name=NC_007779:2436468..2437130 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2521471..2520809
<gbrowseImage> name=NC_010473:2520809..2521471 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

ΔdedD (Keio:JW5378)

deletion

deletion

PMID:16738554[2]

Shigen

dedD::Tn5KAN-2 (FB20761)

Insertion at nt 407 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB20761

contains pKD46

ΔdedD::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

dedD

deletion

Sensitivity to

decreases sensitivity to bicyclomycin

PMID:21357484[5]

fig 2

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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

JW5378

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGCAAGTAAGTTTCAGAATCG

Primer 2:CCATTCGGCGTATAGCCCATTAC

9D2

Kohara Phage

Genobase

PMID:3038334[7]

12F12

Kohara Phage

Genobase

PMID:3038334[7]

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[8]

est. P1 cotransduction: 19% [9]
Synonyms:zej-223::Tn10

zfd-1::Tn10

Linked marker

CAG18467 = CGSC7408[8]

est. P1 cotransduction: 3% [9]
Synonyms:zfb-1::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:EG10218

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10218

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000212

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944971

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0214

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007643

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. ↑ 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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  4. ↑ 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. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 CGSC: The Coli Genetics Stock Center
  9. ↑ 9.0 9.1 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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