fruB:Gene: Difference between revisions

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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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*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="X46a9d7a46f3c0" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''fruB''  
''fruB''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Fructose
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2162, b2169, JW2156, fruF, G415''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK2162, b2169, JW2156, fruF, G415''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, fpr''


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*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9d7a4ec53b"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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48.72 minutes&nbsp;
48.72 minutes&nbsp;
|
|
MG1655: 2261517..2260387<br />{{GBrowseFigureByCoord|2259387|2262517|ecoli|MG1655}}
MG1655: 2261517..2260387<br /><gbrowseImage>
name=NC_000913:2260387..2261517
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7990 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7990 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2259387|2262517|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2259387|2262517|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2260387|2261517|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2260387|2261517|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7990 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7990 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 2214683..2213553<br /><gbrowseImage>
name=NC_012967:2213553..2214683
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|2213553|2214683|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2213553|2214683|FASTA Dump}}
|-  
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&nbsp;
&nbsp;
|
|
W3110: 2266829..2265699<br />{{GBrowseFigureByCoord|2264699|2267829|ecoli_W3110|W3110}}
W3110: 2266829..2265699<br /><gbrowseImage>
name=NC_007779:2265699..2266829
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2264699|2267829|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2264699|2267829|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2265699|2266829|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2265699|2266829|FASTA Dump}}  


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*  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9d7a5a3032"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="P46a9d7a5e7d46"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{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
|-  
|-  
|
|
&Delta;fruB (Keio:JW2156)
''fruB(del)'' (Keio:JW2156)
|
|
deletion
deletion
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|
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|[[PMID:16738554]]<ref name=PMID:16738554/>
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108030 CGSC9749]<ref name='LIB:cgsc'/>  
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108030 CGSC9749]<ref name='LIB:cgsc'/>  
|
|
   
   
|-  
|-  
|
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''&#916;fruB725::kan''
''fruB725(del)''::kan
|
|


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|[[PMID:16738554]]<ref name=PMID:16738554/>
|
PMID:16738554
|
|
[[cgscmutation:101020|CGSC:101020]]
[[cgscmutation:101020|CGSC:101020]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14899.X4e04bb7ce1760-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X4e04bb7ce1760"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.14899.X4e04bb7ce1760&page=14899&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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*  
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****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46a9d7a69d4cd"  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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|
|
[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:CCTGCGCCCTCCCCAAGACCAGC  
Primer 2:CCTGCGCCCTCCCCAAGACCAGC  
|-
|
[[:Category:Kohara_Phage:4F2|4F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=368 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12C12|12C12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=369 Genobase]
|
PMID:3038334
|-  
|-  
|
|
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CAG12021 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39386 CGSC7344]<ref name='LIB:cgsc'/>
CAG12021 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39386 CGSC7344]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zbc-3105::Tn10, zbd-3105::Tn10  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10  
|-  
|-  
|
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CAG12098 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40003 CGSC7400]<ref name='LIB:cgsc'/>
CAG12098 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40003 CGSC7400]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 17% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zeg-722, zei-722::Tn10  
est. P1 cotransduction: 17% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zeg-722, zei-722::Tn10  


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*  
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9d7a743663"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7990 EcoCyc:G7990]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0005 EchoBASE:EB0005]
EcoCyc:G7990
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2169 EcoliGenExpDB:b2169]
EcoGene:EG10005
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2704 ECOL199310CYC:C2704]
RegulonDB:ECK120004449
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10005 EcoGene:EG10005]
[http://www.ncbi.nlm.nih.gov/gene?term=946677 GeneID:946677]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=FRUB ECOO157CYC:FRUB]
EchoBASE:EB0005
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007180&formSubmitReturn=1 ASAP:ABE-0007180]
ASAP:ABE-0007180
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{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:fru genes]]
[[Category:fru genes]][[Category:Gene_List:REL606]]

Latest revision as of 20:41, 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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

fruB

Mnemonic

Fructose

Synonyms

ECK2162, b2169, JW2156, fruF, G415[1][2], fpr

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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

48.72 minutes 

MG1655: 2261517..2260387
<gbrowseImage> name=NC_000913:2260387..2261517 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2214683..2213553
<gbrowseImage> name=NC_012967:2213553..2214683 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2266829..2265699
<gbrowseImage> name=NC_007779:2265699..2266829 source=W3110 preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

[back to top]


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

fruB(del) (Keio:JW2156)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9749[4]

fruB725(del)::kan

PMID:16738554[3]

CGSC:101020


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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

JW2156

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTCCAGTTATCCGTACAGGA

Primer 2:CCTGCGCCCTCCCCAAGACCAGC

4F2

Kohara Phage

Genobase

PMID:3038334[6]

12C12

Kohara Phage

Genobase

PMID:3038334[6]

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[4]

est. P1 cotransduction: % [7]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[4]

est. P1 cotransduction: 17% [7]
Synonyms:zeg-722, zei-722::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:G7990

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10005

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004449

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946677

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0005

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007180

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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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