malF:Gene: Difference between revisions

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{|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}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''malF''  
''malF''  
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK4025, b4033, JW3993''<ref name='LIB:Riley_2006'/>
''ECK4025, b4033, JW3993''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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{{GBrowseFastaLink|ecoli|NC_000913|4241554|4243098|FASTA Dump}}
{{GBrowseFastaLink|ecoli|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]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|4247121|4248665|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|4247121|4248665|FASTA Dump}}  
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===Notes===
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|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
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[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]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109155 CGSC10874]<ref name='LIB:cgsc'/>  
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|[[PMID:2540407]]<ref name=PMID:2540407/>
[[PMID:2540407]]<ref name=PMID:2540407/>
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[[cgscmutation:40369|CGSC:40369]]
[[cgscmutation:40369|CGSC:40369]]
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|[[PMID:2540407]]<ref name=PMID:2540407/>
[[PMID:2540407]]<ref name=PMID:2540407/>
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[[cgscmutation:40372|CGSC:40372]]
[[cgscmutation:40372|CGSC:40372]]
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|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
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[[cgscmutation:101732|CGSC:101732]]
[[cgscmutation:101732|CGSC:101732]]
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===Notes===
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JW3993
JW3993
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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]]<ref name=PMID:16769691/>


Status:Clone OK
Status:Clone OK
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Primer 2:CCATCAAACTTCATTCGCGTGGC  
Primer 2:CCATCAAACTTCATTCGCGTGGC  
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[[thiC:Gene|thiC39::Tn10]]
[[thiC:Gene|thiC39::Tn10]]
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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'/>
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est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:thi-39::Tn10  
 
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[[yjcS:Gene|zje-2241::Tn10]]
[[yjcS:Gene|zje-2241::Tn10]]
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est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/>  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0013195&formSubmitReturn=1 ASAP:ABE-0013195]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0013195&formSubmitReturn=1 ASAP:ABE-0013195]
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<noinclude><protect>
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==References==
==References==
{{BacktoTop}}
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<references/>
<references/>
__NOTOC__
__NOTOC__

Revision as of 21:38, 21 January 2009

{{#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 Alleles and Phenotypes 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
Synonyms

ECK4025, b4033, JW3993[1]

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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
gbrowse_img.php?coord=4240554..4244098&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 4248665..4247121
gbrowse_img.php?coord=4246121..4249665&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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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 Location Description
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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

ΔmalF (Keio:JW3993)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10874[3]

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

ΔmalF729::kan

PMID:16738554[2]

CGSC:101732


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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[6]

Status:Clone OK

Primer 1:GCCGATGTCATTAAAAAGAAACA

Primer 2:CCATCAAACTTCATTCGCGTGGC

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[3]

est. P1 cotransduction: 12% [4]nnSynonyms: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 (EcoliWiki Page)

EcoCyc:EG10555

EchoBASE (EcoliWiki Page)

EchoBASE:EB0550

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4033

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C5003

EcoGene (EcoliWiki Page)

EcoGene:EG10555

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:MALF

CGSC (EcoliWiki Page)

CGSC:531

ASAP (EcoliWikiPage)

ASAP:ABE-0013195


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Notes

Links

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Name URL Comments
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References

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  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. ↑ 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


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