malF: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="Y46aa0543b0c08"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''malF''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''malF''
Maltose
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4025, b4033, JW3993''<ref name='LIB:Riley_2006'/>, JW3993, malJ''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18625.Y46aa0543b0c08&page=18625&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK4025, b4033, JW3993''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='149085'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46aa05443f453"  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
Line 72: Line 76:
91.42 minutes, 91.42 minutes&nbsp;
91.42 minutes, 91.42 minutes&nbsp;
|
|
MG1655: 4243098..4241554<br />{{GBrowseFigureByCoord|4240554|4244098|ecoli|MG1655}}
MG1655: 4243098..4241554<br /><gbrowseImage>
name=NC_000913:4241554..4243098
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10555 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10555 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4240554..4244098 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4240554|4244098|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4241554..4243098&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4241554|4243098|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10555 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10555 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4224007..4222463<br /><gbrowseImage>
name=NC_012967:4222463..4224007
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4222463|4224007|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4222463|4224007|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 4180399..4181943<br /><gbrowseImage>
name=NC_012759:4180399..4181943
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4180399|4181943|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4180399|4181943|FASTA Dump}}
|-  
|
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4248665..4247121<br />{{GBrowseFigureByCoord|4246121|4249665|ecoli_W3110|W3110}}  
W3110: 4248665..4247121<br /><gbrowseImage>
name=NC_007779:4247121..4248665
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4246121|4249665|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|4247121|4248665|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 4342794..4341250<br /><gbrowseImage>
name=NC_010473:4341250..4342794
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4246121..4249665 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|4338162|4345882|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4247121..4248665&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|4338162|4345882|FASTA Dump}}
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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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;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="D46aa0545516e9"  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;malF (Keio:JW3993)
''malF(del)'' (Keio:JW3993)
|
|
deletion
deletion
Line 145: Line 209:


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109155 CGSC10874]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=109155 CGSC10874]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
|
malFP420A
|
|
P420A
|
|
No effect
|
|
|
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916]
|-
|
malFG380C,S
|
|
G380C,S
|
|
No growth on maltose
|
|
|
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916]
|-
|
malFE401A,C,K,L
|
|
E401A,C,K,L
|
|
Reduction of transport rate
|
|
|
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916]
|-
|
malFS403C,D,K,L
|
|
S403C,D,K,L
|
|
Reduction of transport rate
|
|
|
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916]
|-
|
malFG407A,P
|
|
G407A,P
|
|
No effect
|
|
|
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916]
|-
|
malFL334W
|
|
L334W
|
|
Ability to transport lactose in a saturable manner
|
|
|
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916]
|-
|
malFL372W
|
|
L372W
|
|
Growth on maltose but not on media containing either maltoheptaose or maltoheptaose plus maltose
|
|
|
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916]
|-
|
malFN376K,H
|
|
N376K,H
|
|
No growth on maltose
|
|
|
seeded from [http://www.uniprot.org/uniprot/P02916 UniProt:P02916]
|-  
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|
|
[[PMID:2540407]]<ref name=PMID:2540407/>
PMID:2540407
|
|
[[cgscmutation:40369|CGSC:40369]]
[[cgscmutation:40369|CGSC:40369]]
Line 247: Line 449:


|
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[[PMID:2540407]]<ref name=PMID:2540407/>
PMID:2540407
|
|
[[cgscmutation:40372|CGSC:40372]]
[[cgscmutation:40372|CGSC:40372]]
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|-  
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|
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''&#916;malF729::kan''
''malF729(del)::kan''
|
|


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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:101732|CGSC:101732]]
[[cgscmutation:101732|CGSC:101732]]
|
|
   
   
|-
|
''malF(del)''
|
deletion
|
deletion
|
Resistant to
|
Thio(5)maltose increase resistance.
|
PMID:6998971
|
|
Selection for mutant maltose transport system


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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===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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JW3993
JW3993
Line 299: Line 540:
[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
Line 306: Line 547:


Primer 2:CCATCAAACTTCATTCGCGTGGC  
Primer 2:CCATCAAACTTCATTCGCGTGGC  
|-
|-
|
[[:Category:Kohara_Phage:7A4|7A4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=633 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1F8|1F8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=634 Genobase]
|
PMID:3038334
|-  
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[[thiC:Gene|thiC39::Tn10]]
[[thiC:Gene|thiC39::Tn10]]
Line 314: Line 573:
CAG18500 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40361 CGSC7472]<ref name='LIB:cgsc'/>
CAG18500 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40361 CGSC7472]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:thi-39::Tn10  
Synonyms:thi-39::Tn10  
|-
|-  
|
|
[[yjcS:Gene|zje-2241::Tn10]]
[[yjcS:Gene|zje-2241::Tn10]]
Line 326: Line 584:
|
|
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10555 EcoCyc:EG10555] 
EcoCyc:EG10555
|
|
''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=EB0550 EchoBASE:EB0550] 
EcoGene:EG10555
|
|
''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=b4033 EcoliGenExpDB:b4033] 
RegulonDB:ECK120000548
|
|
''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=C5003 ECOL199310CYC:C5003]
[http://www.ncbi.nlm.nih.gov/gene?term=948532 GeneID:948532]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10555 EcoGene:EG10555] 
EchoBASE:EB0550
|
|
''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=MALF ECOO157CYC:MALF] 
ASAP:ABE-0013195
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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===Categories===
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[[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:mal genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:51, 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

malF

Mnemonic

Maltose

Synonyms

ECK4025, b4033, JW3993[1], JW3993, malJ

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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

91.42 minutes, 91.42 minutes 

MG1655: 4243098..4241554
<gbrowseImage> name=NC_000913:4241554..4243098 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4224007..4222463
<gbrowseImage> name=NC_012967:4222463..4224007 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4180399..4181943
<gbrowseImage> name=NC_012759:4180399..4181943 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4248665..4247121
<gbrowseImage> name=NC_007779:4247121..4248665 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4342794..4341250
<gbrowseImage> name=NC_010473:4341250..4342794 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

malF(del) (Keio:JW3993)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC10874[3]

malFP420A

P420A

No effect

seeded from UniProt:P02916

malFG380C,S

G380C,S

No growth on maltose

seeded from UniProt:P02916

malFE401A,C,K,L

E401A,C,K,L

Reduction of transport rate

seeded from UniProt:P02916

malFS403C,D,K,L

S403C,D,K,L

Reduction of transport rate

seeded from UniProt:P02916

malFG407A,P

G407A,P

No effect

seeded from UniProt:P02916

malFL334W

L334W

Ability to transport lactose in a saturable manner

seeded from UniProt:P02916

malFL372W

L372W

Growth on maltose but not on media containing either maltoheptaose or maltoheptaose plus maltose

seeded from UniProt:P02916

malFN376K,H

N376K,H

No growth on maltose

seeded from UniProt:P02916

malF3089::Tn10

Insertion at 4,242,342 bp in MG1655 (NC_000913)

adapted from Nichols et al.[4]

CAG12164 = CGSC7476[3]

Synonyms:

malF64(Oc)

CGSC:7076

ochre (UAA) mutation

malF55::Tn10

CGSC:9952

malF59::Tn5

CGSC:9960

malF3089::Tn10

PMID:2540407[5]

CGSC:40369

malF3180::Tn10kan

PMID:2540407[5]

CGSC:40372

malF729(del)::kan

PMID:16738554[2]

CGSC:101732

malF(del)

deletion

deletion

Resistant to

Thio(5)maltose increase resistance.

PMID:6998971[6]

Selection for mutant maltose transport system

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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

JW3993

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGATGTCATTAAAAAGAAACA

Primer 2:CCATCAAACTTCATTCGCGTGGC

7A4

Kohara Phage

Genobase

PMID:3038334[8]

1F8

Kohara Phage

Genobase

PMID:3038334[8]

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[3]

est. P1 cotransduction: 12% [4]
Synonyms:thi-39::Tn10

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[3]

est. P1 cotransduction: 3% [4]

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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:EG10555

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10555

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000548

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948532

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0550

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013195

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 3.3 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 4.2 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).
  5. ↑ 5.0 5.1 Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 PubMed
  6. ↑ Ferenci, T (1980) Methyl-alpha-maltoside and 5-thiomaltose: analogs transported by the Escherichia coli maltose transport system. J. Bacteriol. 144 7-11 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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

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