cdd: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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''cdd''  
''cdd''  
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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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''ECK2136, b2143, JW2131''<ref name='LIB:Riley_2006'/>
''ECK2136, b2143, JW2131''<ref name='LIB:Riley_2006'/>
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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|2229866|2230750|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|2229866|2230750|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10137 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10137 EcoCyc Sequence Dump]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2235178|2236062|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2235178|2236062|FASTA Dump}}  
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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=108008 CGSC9727]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108008 CGSC9727]<ref name='LIB:cgsc'/>  
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|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
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[[cgscmutation:100270|CGSC:100270]]
[[cgscmutation:100270|CGSC:100270]]
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JW2131
JW2131
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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:CCAGCGAGAAGCACTCGGTCGAT  
Primer 2:CCAGCGAGAAGCACTCGGTCGAT  
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[[gatY:Gene|zbd-3104::Tn10]]
[[gatY:Gene|zbd-3104::Tn10]]
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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'/>
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est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zbc-3105::Tn10, zbd-3105::Tn10  
 
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Synonyms:zbc-3105::Tn10, zbd-3105::Tn10  
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[[napA:Gene|napA722::Tn10]]
[[napA:Gene|napA722::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'/>
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est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zeg-722, zei-722::Tn10


Synonyms:zeg-722, zei-722::Tn10
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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=0007086&formSubmitReturn=1 ASAP:ABE-0007086]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0007086&formSubmitReturn=1 ASAP:ABE-0007086]
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<noinclude><protect>
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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
 
<references/>
<references/>
__NOTOC__
__NOTOC__

Revision as of 21:18, 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

cdd

Mnemonic
Synonyms

ECK2136, b2143, JW2131[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

48.06 minutes 

MG1655: 2229866..2230750
gbrowse_img.php?coord=2228866..2231750&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 2235178..2236062
gbrowse_img.php?coord=2234178..2237062&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

Δcdd (Keio:JW2131)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9727[3]

cdd-5

CGSC:7316

cdd-7

CGSC:7784

cdd-1

CGSC:9218

cdd-6

CGSC:12001

cdd-50

CGSC:23043

Δcdd-770::kan

PMID:16738554[2]

CGSC:100270


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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

JW2131

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCATCCACGTTTTCAAACCGC

Primer 2:CCAGCGAGAAGCACTCGGTCGAT

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[3]

est. P1 cotransduction: 7% [5]nnSynonyms:zbc-3105::Tn10, zbd-3105::Tn10

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[3]

est. P1 cotransduction: 1% [5]nnSynonyms: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 (EcoliWiki Page)

EcoCyc:EG10137

EchoBASE (EcoliWiki Page)

EchoBASE:EB0135

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2143

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2675

EcoGene (EcoliWiki Page)

EcoGene:EG10137

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CDD

CGSC (EcoliWiki Page)

CGSC:932

ASAP (EcoliWikiPage)

ASAP:ABE-0007086


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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 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 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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