efeO:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|ycdO}}{{Tab On|Gene|ycdO}}{{Tab|Gene Product(s)|ycdO}}{{Tab|Expression|ycdO}}{{Tab|Evolution|ycdO}}{{Tab|On One Page|ycdO}}{{TabsBottom}}
{{Tab|Quickview|efeO}}{{Tab On|Gene|efeO}}{{Tab|Gene Product(s)|efeO}}{{Tab|Expression|efeO}}{{Tab|Evolution|efeO}}{{Tab|On One Page|efeO}}{{TabsBottom}}
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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="M46a9bdd02fc75"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''efeO''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ycdO''
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1008, b1018, JW1003'', ycdO<ref name='LIB:Riley_2006'/>, JW1003, ycdO''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12593.M46a9bdd02fc75&page=12593&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1008, b1018, JW1003''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='130979'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46a9bdd0a8a62"  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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23.31 minutes&nbsp;
23.31 minutes&nbsp;
|
|
MG1655: 1081466..1082593<br />{{GBrowseFigureByCoord|1080466|1083593|ecoli|MG1655}}
MG1655: 1081466..1082593<br /><gbrowseImage>
name=NC_000913:1081466..1082593
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6527 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6527 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1080466..1083593 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1080466|1083593|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1081466..1082593&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1081466|1082593|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6527 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6527 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 984434..985561<br /><gbrowseImage>
name=NC_012759:984434..985561
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|984434|985561|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|984434|985561|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 1082665..1083792<br />{{GBrowseFigureByCoord|1081665|1084792|ecoli_W3110|W3110}}
W3110: 1082665..1083792<br /><gbrowseImage>
name=NC_007779:1082665..1083792
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1081665..1084792 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|1081665|1084792|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1082665..1083792&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|1082665|1083792|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 1135394..1136521<br /><gbrowseImage>
name=NC_010473:1135394..1136521
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|1133140|1138775|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1133140|1138775|FASTA Dump}}
 
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{|class = 'sortable' {{Prettytable}} id='130981'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9bdd19409c"  class=" tableEdit Gene_allele_table dataTable" 
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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;ycdO (Keio:JW1003)
&Delta;ycdO (Keio:JW1003)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107265 CGSC8984]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107265 CGSC8984]<ref name='LIB:cgsc'/>  
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW1003
JW1003
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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:CCATCCAGTCCCAGCACACCGCG  
Primer 2:CCATCCAGTCCCAGCACACCGCG  
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[[yccE:Gene|zcc-282::Tn10]]
[[yccE:Gene|zcc-282::Tn10]]
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est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
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[[yceG:Gene|zce-726::Tn10]]
[[yceG:Gene|zce-726::Tn10]]
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est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6527 EcoCyc:G6527] 
EcoCyc:G6527
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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]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3621 EchoBASE:EB3621] 
EcoGene:EG13861
|
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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]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1018 EcoliGenExpDB:b1018] 
RegulonDB:ECK120003125
|
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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]])
|
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[http://BioCyc.org/ECOL199310/new-image?object=C1156 ECOL199310CYC:C1156]
[http://www.ncbi.nlm.nih.gov/gene?term=945603 GeneID:945603]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13861 EcoGene:EG13861] 
EchoBASE:EB3621
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YCDO ECOO157CYC:YCDO] 
ASAP:ABE-0003448
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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 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:ycd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:efe genes]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:31, 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

efeO

Mnemonic

Systematic nomenclature

Synonyms

ECK1008, b1018, JW1003, ycdO[1], JW1003, ycdO

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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

23.31 minutes 

MG1655: 1081466..1082593
<gbrowseImage> name=NC_000913:1081466..1082593 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 984434..985561
<gbrowseImage> name=NC_012759:984434..985561 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1082665..1083792
<gbrowseImage> name=NC_007779:1082665..1083792 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1135394..1136521
<gbrowseImage> name=NC_010473:1135394..1136521 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

ΔycdO (Keio:JW1003)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8984[3]


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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

JW1003

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCACCATTAACTTCCGCCGTAA

Primer 2:CCATCCAGTCCCAGCACACCGCG

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[3]

est. P1 cotransduction: 50% [5]

zce-726::Tn10

Linked marker

CAG12078 = CGSC7361[3]

est. P1 cotransduction: 1% [5]

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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:G6527

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13861

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003125

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945603

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3621

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003448

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. ↑ 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 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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