ybcY: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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''ybcY''  
''ybcY''  
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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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''ECK0554, b0562, JW0551''<ref name='LIB:Riley_2006'/>
''ECK0554, b0562, JW0551''<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|581375|581959|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|581375|581959|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6316 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6316 EcoCyc Sequence Dump]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|581375|581959|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|581375|581959|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=106958 CGSC8677]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106958 CGSC8677]<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:103702|CGSC:103702]]
[[cgscmutation:103702|CGSC:103702]]
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JW0551
JW0551
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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:CCTTTTTTTCCTGAAGCGGAAAA  
Primer 2:CCTTTTTTTCCTGAAGCGGAAAA  
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[[purK:Gene|purK79::Tn10]]
[[purK:Gene|purK79::Tn10]]
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CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 32% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 32% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:purE79::Tn10  
 
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[[dsbG:Gene|dsbG601::Tn10]]
[[dsbG:Gene|dsbG601::Tn10]]
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CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<ref name='LIB:cgsc'/>
CAG12149 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39387 CGSC7346]<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:zbd-601::Tn10, zbe-601::Tn10


Synonyms:zbd-601::Tn10, zbe-601::Tn10
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6316 EcoCyc:G6316]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6316 EcoCyc:G6316]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3405 EchoBASE:EB3405]
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3405 EchoBASE:EB3405]
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|-  
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0562 EcoliGenExpDB:b0562]
[http://chase.ou.edu/macro/searchlink.php?bnum=b0562 EcoliGenExpDB:b0562]
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|-
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
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[http://BioCyc.org/ECOL199310/new-image?object=C0651 ECOL199310CYC:C0651]
[http://BioCyc.org/ECOL199310/new-image?object=C0651 ECOL199310CYC:C0651]
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|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
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[http://ecogene.org/geneinfo.php?eg_id=EG13641 EcoGene:EG13641]
[http://ecogene.org/geneinfo.php?eg_id=EG13641 EcoGene:EG13641]
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|-
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
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[http://BioCyc.org/ECOO157/new-image?object=Z1925 ECOO157CYC:Z1925]
[http://BioCyc.org/ECOO157/new-image?object=Z1925 ECOO157CYC:Z1925]
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==References==
==References==
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__NOTOC__
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Revision as of 18:45, 21 January 2009

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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

ybcY

Mnemonic
Synonyms

ECK0554, b0562, JW0551[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

12.53 minutes 

MG1655: 581959..581375
gbrowse_img.php?coord=580375..582959&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 581959..581375
gbrowse_img.php?coord=580375..582959&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

ΔybcY (Keio:JW0551)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8677[3]

ΔybcY771::kan

PMID:16738554[2]

CGSC:103702


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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

JW0551

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGGAGTATCAAATCGGCTTGC

Primer 2:CCTTTTTTTCCTGAAGCGGAAAA

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 32% [5]nnSynonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[3]

est. P1 cotransduction: 7% [5]nnSynonyms:zbd-601::Tn10, zbe-601::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:G6316

EchoBASE (EcoliWiki Page)

EchoBASE:EB3405

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0562

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0651

EcoGene (EcoliWiki Page)

EcoGene:EG13641

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z1925


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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).


Categories

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