bglF: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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{|{{Prettytable}}
{|   id="N46a9fd39f03e8"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''bglF''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''bglF''
beta-Glucoside
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3715, b3722, JW3700, bglC, blgB, bglS''<ref name='LIB:Riley_2006'/>, bglS''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18005.N46a9fd39f03e8&page=18005&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3715, b3722, JW3700, bglC, blgB, bglS''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='147219'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9fd3a7ebc0"  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
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MG1655
MG1655
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84.1 minutes&nbsp;
84.1 minutes&nbsp;
|
|
MG1655: 3903620..3901743<br />{{GBrowseFigureByCoord|3900743|3904620|ecoli|MG1655}}
MG1655: 3903620..3901743<br /><gbrowseImage>
name=NC_000913:3901743..3903620
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10115 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10115 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3900743..3904620 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3900743|3904620|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3901743..3903620&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3901743|3903620|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10115 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10115 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 3865965..3864088<br /><gbrowseImage>
name=NC_012967:3864088..3865965
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3864088|3865965|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3864088|3865965|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3790076..3791953<br /><gbrowseImage>
name=NC_012759:3790076..3791953
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3790076|3791953|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3790076|3791953|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 3731084..3732961<br />{{GBrowseFigureByCoord|3730084|3733961|ecoli_W3110|W3110}}  
W3110: 3731084..3732961<br /><gbrowseImage>
name=NC_007779:3731084..3732961
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3730084|3733961|GBrowse(W3110)}}  
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3730084..3733961 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|3731084|3732961|FASTA Dump}}
|-  
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3731084..3732961&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 4001204..3999327<br /><gbrowseImage>
name=NC_010473:3999327..4001204
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3995573|4004958|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3995573|4004958|FASTA Dump}}
 
|- class="tableEdit_footer"
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
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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;bglF (Keio:JW3700)
&Delta;bglF (Keio:JW3700)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108985 CGSC10704]<ref name='LIB:cgsc'/>
|
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|
''&#916;bglF753::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100188|CGSC:100188]]
|
 
|- class="tableEdit_footer"
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.18005.U4e04b83361b59-->
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW3700
JW3700
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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]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCGCGAATGATGGATAACAGCGG  
Primer 2:CCGCGAATGATGGATAACAGCGG  
|-
|-
|
[[:Category:Kohara_Phage:7A1|7A1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=561 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5E3|5E3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=562 Genobase]
|
PMID:3038334
|-  
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zid-501::Tn10
zid-501::Tn10
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est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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[[rbsA:Gene|rbsD296::Tn10]]
[[rbsA:Gene|rbsD296::Tn10]]
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CAG18501 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40333 CGSC7460]<ref name='LIB:cgsc'/>
CAG18501 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40333 CGSC7460]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 34% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 34% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zie-296::Tn10


Synonyms:zie-296::Tn10
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===Notes===
===Notes===
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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=EG10115 EcoCyc:EG10115] 
EcoCyc:EG10115
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0113 EchoBASE:EB0113] 
EcoGene:EG10115
|
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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]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3722 EcoliGenExpDB:b3722] 
RegulonDB:ECK120000111
|
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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=C4644 ECOL199310CYC:C4644]
[http://www.ncbi.nlm.nih.gov/gene?term=948236 GeneID:948236]
|
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10115 EcoGene:EG10115] 
EchoBASE:EB0113
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/18502 CGSC:18502] 
ASAP:ABE-0012171
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{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:bgl genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:49, 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

bglF

Mnemonic

beta-Glucoside

Synonyms

ECK3715, b3722, JW3700, bglC, blgB, bglS[1], bglS

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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

84.1 minutes 

MG1655: 3903620..3901743
<gbrowseImage> name=NC_000913:3901743..3903620 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3865965..3864088
<gbrowseImage> name=NC_012967:3864088..3865965 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3790076..3791953
<gbrowseImage> name=NC_012759:3790076..3791953 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3731084..3732961
<gbrowseImage> name=NC_007779:3731084..3732961 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4001204..3999327
<gbrowseImage> name=NC_010473:3999327..4001204 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

ΔbglF (Keio:JW3700)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10704[3]

ΔbglF753::kan

PMID:16738554[2]

CGSC:100188


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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

JW3700

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCACGGAGTTAGCCAGAAAAAT

Primer 2:CCGCGAATGATGGATAACAGCGG

7A1

Kohara Phage

Genobase

PMID:3038334[5]

5E3

Kohara Phage

Genobase

PMID:3038334[5]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[3]

est. P1 cotransduction: 35% [6]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[3]

est. P1 cotransduction: 34% [6]
Synonyms:zie-296::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:EG10115

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10115

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000111

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948236

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0113

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012171

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. ↑ 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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