dusB: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="Q46a9f17ed6498"  class=" tableEdit Gene_nomenclature_table"   
{|   id="Q46a9f17ed6498"  class=" tableEdit Gene_nomenclature_table"   


|-
|-
!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''dusB''  
''dusB''
|-
|-
!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Dihydrouridine synthase B
|-
|-
!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3247, b3260, JW3228, yhdG''<ref name='LIB:Riley_2006'/>
''ECK3247, b3260, JW3228, yhdG''<ref name='LIB:Riley_2006'/>, yhdG''


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{|   id="R46a9f17f6821b"  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="R46a9f17f6821b"  class=" tableEdit Gene_location_table"   
|-
|- {{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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73.46 minutes&nbsp;
73.46 minutes&nbsp;
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|
MG1655: 3408302..3409267<br />{{GBrowseFigureByCoord|3408302|3409267|ecoli|MG1655}}
MG1655: 3408302..3409267<br /><gbrowseImage>
name=NC_000913:3408302..3409267
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11311 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11311 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3407302|3410267|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3407302|3410267|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3408302|3409267|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3408302|3409267|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11311 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11311 EcoCyc Sequence Dump]  
|-
|
[[BW2952]]
|
|
NC_012759: 3295450..3296415<br /><gbrowseImage>
name=NC_012759:3295450..3296415
source=BW2952
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|BW2952|NC_012759|3295450|3296415|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|3295450|3296415|FASTA Dump}}
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&nbsp;
&nbsp;
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W3110: 3410135..3411100<br />{{GBrowseFigureByCoord|3410135|3411100|ecoli_W3110|W3110}}
W3110: 3410135..3411100<br /><gbrowseImage>
name=NC_007779:3410135..3411100
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3409135|3412100|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3409135|3412100|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3410135|3411100|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3410135|3411100|FASTA Dump}}  
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DH10B: 3506047..3507012<br />{{GBrowseFigureByCoord|3506047|3507012|ecoli_DH10B|DH10B}}
DH10B: 3506047..3507012<br /><gbrowseImage>
name=NC_010473:3506047..3507012
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_DH10B|NC_010473|3504117|3508942|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3504117|3508942|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3504117|3508942|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3504117|3508942|FASTA Dump}}  


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{|   id="A46a9f18028ecd"  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="A46a9f18028ecd"  class=" tableEdit Gene_sequence_features_table"   
|-
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17069.A46a9f18028ecd&page=17069&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
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*  
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{|   id="H46a9f18073be6"  class=" tableEdit Gene_allele_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9f18073be6"  class=" tableEdit Gene_allele_table dataTable"   
|-
|- {{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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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q4e04ba2a05715"  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.17069.Q4e04ba2a05715&page=17069&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="Y46a9f1813348a"  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="Y46a9f1813348a"  class=" tableEdit Gene_resource_table"   
|-
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCgGCAAAATTTTCGAAGTATGC  
Primer 2:CCgGCAAAATTTTCGAAGTATGC  
|-
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[[:Category:Kohara_Phage:6G3|6G3]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=529 Genobase]
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PMID:3038334
|-
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[[:Category:Kohara_Phage:6G9|6G9]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=530 Genobase]
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PMID:3038334
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{|   id="H46a9f181cea47"  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="H46a9f181cea47"  class=" tableEdit Gene_accessions_table"   
|-
|- {{table_heading_style}}
!|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=EG11311 EcoCyc:EG11311]
EcoCyc:EG11311
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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=EB1287 EchoBASE:EB1287]
EcoGene:EG11311
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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=b3260 EcoliGenExpDB:b3260]
RegulonDB:ECK120001282
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[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=C4026 ECOL199310CYC:C4026]
[http://www.ncbi.nlm.nih.gov/gene?term=947707 GeneID:947707]
|
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
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[http://ecogene.org/geneinfo.php?eg_id=EG11311 EcoGene:EG11311]
EchoBASE:EB1287
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
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[http://BioCyc.org/ECOO157/new-image?object=YHDG ECOO157CYC:YHDG]
ASAP:ABE-0010700
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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]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0010700&formSubmitReturn=1 ASAP:ABE-0010700]
|


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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:dus genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:dus genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:46, 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

dusB

Mnemonic

Dihydrouridine synthase B

Synonyms

ECK3247, b3260, JW3228, yhdG[1], yhdG

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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

73.46 minutes 

MG1655: 3408302..3409267
<gbrowseImage> name=NC_000913:3408302..3409267 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3295450..3296415
<gbrowseImage> name=NC_012759:3295450..3296415 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3410135..3411100
<gbrowseImage> name=NC_007779:3410135..3411100 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3506047..3507012
<gbrowseImage> name=NC_010473:3506047..3507012 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

ΔdusB (Keio:JW3228)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10442[3]

ΔdusB778::kan

PMID:16738554[2]

CGSC:100666


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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

JW3228

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCGCATCGGACAATATCAGCT

Primer 2:CCgGCAAAATTTTCGAAGTATGC

6G3

Kohara Phage

Genobase

PMID:3038334[5]

6G9

Kohara Phage

Genobase

PMID:3038334[5]

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[3]

est. P1 cotransduction: 14% [6]
Synonyms:zha-6::Tn10

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[3]

est. P1 cotransduction: 80% [6]
Synonyms:zhd-3083::Tn10, zhe-3083::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:EG11311

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11311

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001282

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947707

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1287

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010700

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. ↑ 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
  5. ↑ 5.0 5.1 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
  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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