allB:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0505, b0512, JW0500, glxB3, ybbX''<ref name='LIB:Riley_2006'/>
''ECK0505, b0512, JW0500, glxB3, ybbX''<ref name='LIB:Riley_2006'/>, ybbX''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="O46a9b264a9fd1"  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="O46a9b264a9fd1"  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: 538371..539732<br /><gbrowseImage>
W3110: 538371..539732<br /><gbrowseImage>
name=AC_000091:538371..539732
name=NC_007779:538371..539732
source=W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|537371|540732|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|537371|540732|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|538371|539732|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|538371|539732|FASTA Dump}}  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="F46a9b26590baf"  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="F46a9b26590baf"  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="P46a9b2660a2d5"  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="P46a9b2660a2d5"  class=" tableEdit Gene_allele_table dataTable"   
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|- {{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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&Delta;allB (Keio:JW0500)
''allB(del)'' (Keio:JW0500)
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deletion
deletion
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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=106926 CGSC8645]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106926 CGSC8645]<ref name='LIB:cgsc'/>  
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''&#916;allB724::kan''
''allB724(del)::kan''
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{|   id="Z4e04b732c1cc9"  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="Z4e04b732c1cc9"  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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{|   id="E46a9b266e53ad"  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="E46a9b266e53ad"  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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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=156 Genobase]
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=156 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:6E7|6E7]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=157 Genobase]
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PMID:3038334  
PMID:3038334  
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est. P1 cotransduction: 62% <ref name='LIB:Nichols_linked_Tn'/> <br />  
est. P1 cotransduction: 62% <ref name='LIB:Nichols_linked_Tn'/> <br />  
Synonyms:purE79::Tn10  
Synonyms:purE79::Tn10  
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[[:Category:Kohara_Phage:6E7|6E7]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=157 Genobase]
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PMID:3038334


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****************************************************************************************** -->{{Gene_accessions_help}}
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{|   id="Z46a9b267cc295"  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="Z46a9b267cc295"  class=" tableEdit Gene_accessions_table"   
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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=G6281 EcoCyc:G6281]
EcoCyc:G6281
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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=EB3384 EchoBASE:EB3384]
EcoGene:EG13619
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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=b0512 EcoliGenExpDB:b0512]
RegulonDB:ECK120002889
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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=C0626 ECOL199310CYC:C0626]
[http://www.ncbi.nlm.nih.gov/gene?term=945134 GeneID:945134]
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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=EG13619 EcoGene:EG13619]
EchoBASE:EB3384
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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=Z0666 ECOO157CYC:Z0666]
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ASAP:ABE-0001768
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001768&formSubmitReturn=1 ASAP:ABE-0001768]
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{|   id="H46a6cfeee7757"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:32, 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

allB

Mnemonic

Allantoin

Synonyms

ECK0505, b0512, JW0500, glxB3, ybbX[1], ybbX

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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

11.6 minutes 

MG1655: 538371..539732
<gbrowseImage> name=NC_000913:538371..539732 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 511313..512674
<gbrowseImage> name=NC_012967:511313..512674 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 441130..442491
<gbrowseImage> name=NC_012759:441130..442491 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 538371..539732
<gbrowseImage> name=NC_007779:538371..539732 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 477702..479063
<gbrowseImage> name=NC_010473:477702..479063 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

allB(del) (Keio:JW0500)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC8645[3]

allB724(del)::kan

PMID:16738554[2]

CGSC:99972


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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

JW0500

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTCTTTTGATTTAATCATTAA

Primer 2:CCCTGCTGATGTTTAAGGATAAA

9E5

Kohara Phage

Genobase

PMID:3038334[5]

6E7

Kohara Phage

Genobase

PMID:3038334[5]

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 21% [6]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 62% [6]
Synonyms:purE79::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:G6281

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13619

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002889

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945134

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3384

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001768

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).

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