ydjO: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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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1728, b1730, JW1719''<ref name='LIB:Riley_2006'/>
''ECK1728, b1730, JW1719''<ref name='LIB:Riley_2006'/>, JW1719''


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{|   id="D46a9cd986ca95"  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="D46a9cd986ca95"  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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39.02 minutes, 39.02 minutes&nbsp;
39.02 minutes, 39.02 minutes&nbsp;
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MG1655: 1811168..1810353<br />{{GBrowseFigureByCoord|1810353|1811168|ecoli|MG1655}}
MG1655: 1811168..1810353<br /><gbrowseImage>
name=NC_000913:1810353..1811168
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6935 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6935 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1809353|1812168|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1809353|1812168|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1810353|1811168|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1810353|1811168|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6935 EcoCyc Sequence Dump]  
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NC_012967: 1790409..1789615<br />{{GBrowseFigureByCoord|1789615|1790409|REL606|NC_012967}}
NC_012967: 1790409..1789615<br /><gbrowseImage>
name=NC_012967:1789615..1790409
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|1789615|1790409|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|1789615|1790409|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|1789615|1790409|FASTA Dump}}  
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[[BW2952]]
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NC_012759: 1702412..1703227<br /><gbrowseImage>
name=NC_012759:1702412..1703227
source=BW2952
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|BW2952|NC_012759|1702412|1703227|GBrowse (BW2952)}}
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&nbsp;
&nbsp;
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W3110: 1814858..1814043<br />{{GBrowseFigureByCoord|1814043|1814858|ecoli_W3110|W3110}}
W3110: 1814858..1814043<br /><gbrowseImage>
name=NC_007779:1814043..1814858
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|1813043|1815858|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1813043|1815858|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|NC_007779|1814043|1814858|FASTA Dump}}  
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DH10B: 1901739..1900924<br />{{GBrowseFigureByCoord|1900924|1901739|ecoli_DH10B|DH10B}}
DH10B: 1901739..1900924<br /><gbrowseImage>
name=NC_010473:1900924..1901739
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|1899294|1903369|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1899294|1903369|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1899294|1903369|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1899294|1903369|FASTA Dump}}  


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{|   id="J46a9cd991e5f3"  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="J46a9cd991e5f3"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
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!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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{| {{Prettytable}} id="Z46a9cd9961971"  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="Z46a9cd9961971"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
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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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ydjO
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deletion
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Sensitivity to
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decreases sensitivity to bicyclomycin
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PMID:21357484
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mutation didn't affect sensitivity of any of 22 other antibiotics tested.
fig 2


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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14031.V4e04c81f78f5e-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V4e04c81f78f5e"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="Z46a9cd9a13791"  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="Z46a9cd9a13791"  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:CCTGCTGGCAACGGTCCGTTTTG  
Primer 2:CCTGCTGGCAACGGTCCGTTTTG  
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[[:Category:Kohara_Phage:8A4|8A4]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=324 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:19B6|19B6]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=325 Genobase]
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PMID:3038334
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{|   id="A46a9cd9aa3a12"  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="A46a9cd9aa3a12"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
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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=G6935 EcoCyc:G6935]
EcoCyc:G6935
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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=EB3747 EchoBASE:EB3747]
EcoGene:EG13991
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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=b1730 EcoliGenExpDB:b1730]
RegulonDB:ECK120003523
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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=EG13991 EcoGene:EG13991]
[http://www.ncbi.nlm.nih.gov/gene?term=946237 GeneID:946237]
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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=Z2759 ECOO157CYC:Z2759]
EchoBASE:EB3747
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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=0005773&formSubmitReturn=1 ASAP:ABE-0005773]
ASAP:ABE-0005773
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:y genes]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:38, 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

ydjO

Mnemonic

Systematic nomenclature

Synonyms

ECK1728, b1730, JW1719[1], JW1719

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

39.02 minutes, 39.02 minutes 

MG1655: 1811168..1810353
<gbrowseImage> name=NC_000913:1810353..1811168 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1790409..1789615
<gbrowseImage> name=NC_012967:1789615..1790409 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1702412..1703227
<gbrowseImage> name=NC_012759:1702412..1703227 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1814858..1814043
<gbrowseImage> name=NC_007779:1814043..1814858 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1901739..1900924
<gbrowseImage> name=NC_010473:1900924..1901739 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


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

ΔydjO (Keio:JW1719)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9451[3]

ΔydjO729::kan

PMID:16738554[2]

CGSC:104364

ydjO

deletion

Sensitivity to

decreases sensitivity to bicyclomycin

PMID:21357484[4]

mutation didn't affect sensitivity of any of 22 other antibiotics tested. fig 2

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

JW1719

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGGCGGGAGATGTTTTCTAC

Primer 2:CCTGCTGGCAACGGTCCGTTTTG

8A4

Kohara Phage

Genobase

PMID:3038334[6]

19B6

Kohara Phage

Genobase

PMID:3038334[6]

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[3]

est. P1 cotransduction: 26% [7]
Synonyms:zdh-925::Tn10

zdj-276::Tn10

Linked marker

CAG18464 = CGSC7387[3]

est. P1 cotransduction: 44% [7]
Synonyms:zdi-276::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:G6935

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13991

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003523

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946237

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3747

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005773

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. ↑ 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
  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 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
  7. ↑ 7.0 7.1 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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