ubiD:Gene: Difference between revisions

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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''ubiD''  
''ubiD''  
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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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''ECK3835, b3843, JW3819, yigC, yigY''<ref name='LIB:Riley_2006'/>
''ECK3835, b3843, JW3819, yigC, yigY''<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|4023011|4024504|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|4023011|4024504|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11396 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11396 EcoCyc Sequence Dump]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3610200|3611693|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3610200|3611693|FASTA Dump}}  
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===Notes===
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JW3819
JW3819
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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:CCGGCGCTTTTACCGTTGTTAAA  
Primer 2:CCGGCGCTTTTACCGTTGTTAAA  
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metEo-3079::Tn10
metEo-3079::Tn10
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CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 60% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 60% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.  
 
|-  
Synonyms:metE3079::Tn10  
 
 
The Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.  
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[[fadA:Gene|fad-751::Tn10]]
[[fadA:Gene|fad-751::Tn10]]
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CAG18496 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40344 CGSC7465]<ref name='LIB:cgsc'/>
CAG18496 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40344 CGSC7465]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:fadAB101::Tn10


Synonyms:fadAB101::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=0012557&formSubmitReturn=1 ASAP:ABE-0012557]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012557&formSubmitReturn=1 ASAP:ABE-0012557]
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
 
<references/>
<references/>
__NOTOC__
__NOTOC__

Revision as of 21:36, 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

ubiD

Mnemonic
Synonyms

ECK3835, b3843, JW3819, yigC, yigY[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

86.71 minutes 

MG1655: 4023011..4024504
gbrowse_img.php?coord=4022011..4025504&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3611693..3610200
gbrowse_img.php?coord=3609200..3612693&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

ubiD410

CGSC:9931


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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

JW3819

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCGACGCCATGAAATATAACGA

Primer 2:CCGGCGCTTTTACCGTTGTTAAA

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[3]

est. P1 cotransduction: 60% [4]nnSynonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

fad-751::Tn10

Linked marker

CAG18496 = CGSC7465[3]

est. P1 cotransduction: 87% [4]nnSynonyms:fadAB101::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:EG11396

EchoBASE (EcoliWiki Page)

EchoBASE:EB1369

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3843

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4790

EcoGene (EcoliWiki Page)

EcoGene:EG11396

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YIGC

ASAP (EcoliWikiPage)

ASAP:ABE-0012557


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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. ↑ 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
  3. ↑ 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 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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