mcbA:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ybiM}}{{Tab On|Gene|ybiM}}{{Tab|Gene Product(s)|ybiM}}{{Tab|Expression|ybiM}}{{Tab|Evolution|ybiM}}{{Tab|On One Page|ybiM}}{{TabsBottom}}
{{Tab|Quickview|mcbA}}{{Tab On|Gene|mcbA}}{{Tab|Gene Product(s)|mcbA}}{{Tab|Expression|mcbA}}{{Tab|Evolution|mcbA}}{{Tab|On One Page|mcbA}}{{TabsBottom}}
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|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|{{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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==Nomenclature==
==Nomenclature==
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{|  id="C46a9b91c2a668"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ybiM''  
''mcbA''
|-
!align=left {{table_heading_style}} |Mnemonic
||
MqsR-controlled Colanic acid and Biofilm
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0795, b0806, JW5106'', ybiM<ref name='LIB:Riley_2006'/>, JW5106, ybiM''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12167.C46a9b91c2a668&page=12167&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0795, b0806, JW5106''<ref name='LIB:Riley_2006'/>
|-
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{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9b91ca2c4f"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
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18.13 minutes&nbsp;
18.13 minutes&nbsp;
|
|
MG1655: 841279..841019<br />{{GBrowseFigureByCoord|840019|842279|ecoli|MG1655}}
MG1655: 841279..841019<br /><gbrowseImage>
name=NC_000913:841019..841279
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6415 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6415 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:840019..842279 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|840019|842279|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:841019..841279&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|841019|841279|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6415 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6415 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 842478..842218<br />{{GBrowseFigureByCoord|841218|843478|ecoli_W3110|W3110}}  
W3110: 842478..842218<br /><gbrowseImage>
name=NC_007779:842218..842478
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|841218|843478|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|842218|842478|FASTA Dump}}  
|-
|
[[BW2952]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:841218..843478 GBrowse(W3110)]
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:842218..842478&plugin_action=Go FASTA Dump]
NC_012759: 743987..744247<br /><gbrowseImage>
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name=NC_012759:743987..744247
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source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|743987|744247|GBrowse(BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|743987|744247|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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|- {{table_heading_style}}
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;ybiM (Keio:JW5106)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04bee7e2880"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!|Resource!!Resource Type!!Source!!Notes/Reference
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|
JW5106
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAAAAAGTGCCTCACACTACT
 
Primer 2:CCTTTGTAGATGGTTGCAGTACC
|-
|
zbh-29::Tn10
|
Linked marker
|
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 49% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbi-29::Tn10
|-
|
zca-1230::Tn10
|
Linked marker
|
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbj-1230::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{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]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6415 EcoCyc:G6415] 
EcoCyc:G6415
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3102 EchoBASE:EB3102] 
EcoGene:EG13318
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0806 EcoliGenExpDB:b0806] 
RegulonDB:ECK120003015
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0891 ECOL199310CYC:C0891]
[http://www.ncbi.nlm.nih.gov/gene?term=947523 GeneID:947523]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13318 EcoGene:EG13318] 
EchoBASE:EB3102
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YBIM ECOO157CYC:YBIM] 
ASAP:ABE-0002753
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ybi genes]][[Category:Gene_List:REL606]]
[[Category:mcb genes]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 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

mcbA

Mnemonic

MqsR-controlled Colanic acid and Biofilm

Synonyms

ECK0795, b0806, JW5106, ybiM[1], JW5106, ybiM

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Notes

Location(s) and DNA Sequence

[back to top]


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

18.13 minutes 

MG1655: 841279..841019
<gbrowseImage> name=NC_000913:841019..841279 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 842478..842218
<gbrowseImage> name=NC_007779:842218..842478 source=W3110 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 743987..744247
<gbrowseImage> name=NC_012759:743987..744247 source=BW2952 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

ΔybiM (Keio:JW5106)

deletion

deletion

PMID:16738554[2]

Shigen


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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

JW5106

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCAAAAAGTGCCTCACACTACT

Primer 2:CCTTTGTAGATGGTTGCAGTACC

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[4]

est. P1 cotransduction: 49% [5]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[4]

est. P1 cotransduction: % [5]
Synonyms:zbj-1230::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:G6415

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13318

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003015

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947523

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3102

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002753

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. ↑ 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  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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