glcD: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}}
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{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="V46a9eac9820c5" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''glcD''  
''glcD''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Glycolate
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2974, b2979, JW2946, gox, yghM''<ref name='LIB:Riley_2006'/>
''ECK2974, b2979, JW2946, gox, yghM''<ref name='LIB:Riley_2006'/>, yghM''


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*  
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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="P46a9eaca0da37"  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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67.34 minutes&nbsp;
67.34 minutes&nbsp;
|
|
MG1655: 3126043..3124544<br />{{GBrowseFigureByCoord|3123544|3127043|ecoli|MG1655}}
MG1655: 3126043..3124544<br /><gbrowseImage>
name=NC_000913:3124544..3126043
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7545 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7545 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3123544|3127043|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3123544|3127043|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3124544|3126043|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3124544|3126043|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7545 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7545 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 3054913..3053414<br /><gbrowseImage>
name=NC_012967:3053414..3054913
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|3053414|3054913|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3053414|3054913|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 3011692..3013191<br /><gbrowseImage>
name=NC_012759:3011692..3013191
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|3011692|3013191|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3011692|3013191|FASTA Dump}}
|-  
|-  
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&nbsp;
&nbsp;
|
|
W3110: 3126677..3125178<br />{{GBrowseFigureByCoord|3124178|3127677|ecoli_W3110|W3110}}
W3110: 3126677..3125178<br /><gbrowseImage>
name=NC_007779:3125178..3126677
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|3124178|3127677|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3124178|3127677|GBrowse(W3110)}}  
|
{{GBrowseFastaLink|W3110|NC_007779|3125178|3126677|FASTA Dump}}
|-
|
[[DH10B]]
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3125178|3126677|FASTA Dump}}


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DH10B: 3223788..3222289<br /><gbrowseImage>
name=NC_010473:3222289..3223788
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3219291|3226786|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3219291|3226786|FASTA Dump}}
 
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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;"   
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|- {{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}}
{|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="C46a9eacb12bf3"  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
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|
|
   
   
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009773 glcD::Tn5KAN-I-SceI] (FB20998)
|
Insertion at nt 1106 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20998]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009773 glcD::Tn5KAN-I-SceI] (FB20999)
|
Insertion at nt 1106 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20999]
|
does not contain [[pKD46]]
|-  
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16523.U4e04bc06d9976-->
<!--
******************************************************************************************
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U4e04bc06d9976"  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.16523.U4e04bc06d9976&page=16523&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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|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCGAAACGCTCCAGTTCAGGGAA  
Primer 2:CCGAAACGCTCCAGTTCAGGGAA  
|-
|
[[:Category:Kohara_Phage:1G7|1G7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=478 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12F3|12F3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=501 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:2F9|2F9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=502 Genobase]
|
PMID:3038334
|-  
|-  
|
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est. P1 cotransduction: 38% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 38% <ref name='LIB:Nichols_linked_Tn'/>  


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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="N46a9eacc6a699"  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=G7545 EcoCyc:G7545]
EcoCyc:G7545
|
|
''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=EB2820 EchoBASE:EB2820]
EcoGene:EG12997
|
|
''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=b2979 EcoliGenExpDB:b2979]
RegulonDB:ECK120004105
|
|
''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=C3709 ECOL199310CYC:C3709]
[http://www.ncbi.nlm.nih.gov/gene?term=947353 GeneID:947353]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12997 EcoGene:EG12997]
EchoBASE:EB2820
|
|
''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]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009773&formSubmitReturn=1 ASAP:ABE-0009773]
ASAP:ABE-0009773
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|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:glc genes]]
[[Category:glc genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:45, 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

glcD

Mnemonic

Glycolate

Synonyms

ECK2974, b2979, JW2946, gox, yghM[1], yghM

edit table


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

67.34 minutes 

MG1655: 3126043..3124544
<gbrowseImage> name=NC_000913:3124544..3126043 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3054913..3053414
<gbrowseImage> name=NC_012967:3053414..3054913 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3011692..3013191
<gbrowseImage> name=NC_012759:3011692..3013191 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3126677..3125178
<gbrowseImage> name=NC_007779:3125178..3126677 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3223788..3222289
<gbrowseImage> name=NC_010473:3222289..3223788 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


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
edit table


Notes

Alleles and Phenotypes

[back to top]


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

ΔglcD (Keio:JW2946)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10273[3]

glcD::Tn5KAN-I-SceI (FB20998)

Insertion at nt 1106 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20998

contains pKD46

glcD::Tn5KAN-I-SceI (FB20999)

Insertion at nt 1106 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20999

does not contain pKD46

ΔglcD753::kan

PMID:16738554[2]

CGSC:101134


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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

JW2946

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGCATCTTGTACGAAGAGCG

Primer 2:CCGAAACGCTCCAGTTCAGGGAA

1G7

Kohara Phage

Genobase

PMID:3038334[6]

12F3

Kohara Phage

Genobase

PMID:3038334[6]

2F9

Kohara Phage

Genobase

PMID:3038334[6]

nupG511::Tn10

Linked marker

CAG18472 = CGSC7433[3]

est. P1 cotransduction: 47% [7]

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[3]

est. P1 cotransduction: 38% [7]

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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:G7545

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12997

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004105

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947353

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2820

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009773

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. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  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 6.2 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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