efeO:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1008, b1018, JW1003'', ycdO<ref name='LIB:Riley_2006'/>
''ECK1008, b1018, JW1003'', ycdO<ref name='LIB:Riley_2006'/>, JW1003, ycdO''


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{|   id="I46a9bdd0a8a62"  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="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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W3110: 1082665..1083792<br /><gbrowseImage>
W3110: 1082665..1083792<br /><gbrowseImage>
name=AC_000091:1082665..1083792
name=NC_007779:1082665..1083792
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|1081665|1084792|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1081665|1084792|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|1082665|1083792|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1082665|1083792|FASTA Dump}}  
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{|   id="B46a9bdd153808"  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="B46a9bdd153808"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="J46a9bdd19409c"  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="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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{|   id="O4e04ba44a71cf"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O4e04ba44a71cf"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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{|   id="C46a9bdd2c963a"  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="C46a9bdd2c963a"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
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EcoCyc:G6527
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG13861
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[RegulonDB]]
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RegulonDB:ECK120003125
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[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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[[EchoBASE]]
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EchoBASE:EB3621
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0003448
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:31, 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

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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<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. ↑ 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).

Categories

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