setA:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0072, b0070, JW0069, yabM''<ref name='LIB:Riley_2006'/>
''ECK0072, b0070, JW0069, yabM''<ref name='LIB:Riley_2006'/>, yabM''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="D46a9a7cf92ad7"  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="D46a9a7cf92ad7"  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: 77621..78799<br /><gbrowseImage>
MG1655: 77621..78799<br /><gbrowseImage>
name=NC_000913:77621..78799
name=NC_000913:77621..78799
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11754 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11754 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|76621|79799|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|76621|79799|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|77621|78799|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|77621|78799|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11754 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11754 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|77620|NC_78798|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|77620|78798|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|77620|NC_78798|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|77620|78798|FASTA Dump}}  
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W3110: 77621..78799<br /><gbrowseImage>
W3110: 77621..78799<br /><gbrowseImage>
name=AC_000091:77621..78799
name=NC_007779:77621..78799
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|76621|79799|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|76621|79799|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|77621|78799|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|77621|78799|FASTA Dump}}  


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****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="H46a9a7d03aec3"  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="H46a9a7d03aec3"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="C46a9a7d07b505"  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="C46a9a7d07b505"  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;setA (Keio:JW0069)
''setA(del)'' (Keio:JW0069)
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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=106651 CGSC8370]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106651 CGSC8370]<ref name='LIB:cgsc'/>  
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''&#916;setA777::kan''
''setA777(del)::kan''
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****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="I4e04c3bede6b2"  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="I4e04c3bede6b2"  class=" tableEdit Genetic_interaction_table dataTable"   
|- {{table_heading_style}}
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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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****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="E46a9a7d123180"  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="E46a9a7d123180"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCAACGTCTTTAACCTTTGCGGT  
Primer 2:CCAACGTCTTTAACCTTTGCGGT  
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[[:Category:Kohara_Phage:8H11|8H11]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=108 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:6C1|6C1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=109 Genobase]
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PMID:3038334
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****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="X46a9a7d1abbff"  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="X46a9a7d1abbff"  class=" tableEdit Gene_accessions_table"   
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|- {{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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EcoCyc:EG11754
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[[EcoGene]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11754 EcoCyc:EG11754]
EcoGene:EG11754
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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]])
[[RegulonDB]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1704 EchoBASE:EB1704]
RegulonDB:ECK120001692
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0070 EcoliGenExpDB:b0070]
[http://www.ncbi.nlm.nih.gov/gene?term=944793 GeneID:944793]
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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=EG11754 EcoGene:EG11754]
EchoBASE:EB1704
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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=0000257&formSubmitReturn=1 ASAP:ABE-0000257]
ASAP:ABE-0000257
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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{|   id="S46a675042eb7a"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:36, 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

setA

Mnemonic

Sugar efflux transporter

Synonyms

ECK0072, b0070, JW0069, yabM[1], yabM

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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

1.67 minutes 

MG1655: 77621..78799
<gbrowseImage> name=NC_000913:77621..78799 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 80425..81603
<gbrowseImage> name=NC_012967:80425..81603 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 77620..78798
<gbrowseImage> name=NC_012759:77620..78798 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 77621..78799
<gbrowseImage> name=NC_007779:77621..78799 source=W3110 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

setA(del) (Keio:JW0069)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC8370[3]

setA777(del)::kan

PMID:16738554[2]

CGSC:102920


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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

JW0069

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCATCTGGATAATGACGATGGC

Primer 2:CCAACGTCTTTAACCTTTGCGGT

8H11

Kohara Phage

Genobase

PMID:3038334[5]

6C1

Kohara Phage

Genobase

PMID:3038334[5]

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[3]

est. P1 cotransduction: 14% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[3]

est. P1 cotransduction: 82% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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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:EG11754

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11754

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001692

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944793

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1704

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000257

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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