ybcY:Gene: Difference between revisions

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!align=left {{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'/>, JW0551''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="L46a9b385da55b"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9b385da55b"  class=" tableEdit Gene_location_table"   
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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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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6316 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6316 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|580375|582959|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|580375|582959|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|581375|581959|FASTA Dump}}
{{GBrowseFastaLink|MG1655|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: 581959..581375<br /><gbrowseImage>
W3110: 581959..581375<br /><gbrowseImage>
name=AC_000091:581375..581959
name=NC_007779:581375..581959
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|580375|582959|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|580375|582959|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|581375|581959|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|581375|581959|FASTA Dump}}  
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DH10B: 521361..520707<br /><gbrowseImage>
DH10B: 521361..520707<br /><gbrowseImage>
name=NC_010473:520707..521361
name=NC_010473:520707..521361
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|519399|522669|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|519399|522669|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|519399|522669|FASTA Dump}}  
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DH10B: 634621..633967<br /><gbrowseImage>
DH10B: 634621..633967<br /><gbrowseImage>
name=NC_010473:633967..634621
name=NC_010473:633967..634621
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|632659|635929|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|632659|635929|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|632659|635929|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|632659|635929|FASTA Dump}}  


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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="X46a9b38682a41"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9b38682a41"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="F46a9b386c2b78"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="F46a9b386c2b78"  class=" tableEdit Gene_allele_table dataTable"   
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!|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
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{|   id="A4e04c6696b5a7"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04c6696b5a7"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="R46a9b3876ac63"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9b3876ac63"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTTTTTTTCCTGAAGCGGAAAA  
Primer 2:CCTTTTTTTCCTGAAGCGGAAAA  
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[[:Category:Kohara_Phage:23E10|23E10]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=160 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:12A1|12A1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=161 Genobase]
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PMID:3038334
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{|   id="Y46a9b387f3518"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a9b387f3518"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6316 EcoCyc:G6316]
EcoCyc:G6316
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3405 EchoBASE:EB3405]
EcoGene:EG13641
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0562 EcoliGenExpDB:b0562]
RegulonDB:ECK120002924
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C0651 ECOL199310CYC:C0651]
[http://www.ncbi.nlm.nih.gov/gene?term=945170 GeneID:945170]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG13641 EcoGene:EG13641]
EchoBASE:EB3405
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=Z1925 ECOO157CYC:Z1925]
ASAP:ABE-0001919
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:33, 19 September 2013

{{#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 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

ybcY

Mnemonic
Synonyms

ECK0554, b0562, JW0551[1], JW0551

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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
<gbrowseImage> name=NC_000913:581375..581959 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 581959..581375
<gbrowseImage> name=NC_007779:581375..581959 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 521361..520707
<gbrowseImage> name=NC_010473:520707..521361 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 634621..633967
<gbrowseImage> name=NC_010473:633967..634621 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

ΔybcY (Keio:JW0551)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8677[3]

ΔybcY771::kan

PMID:16738554[2]

CGSC:103702


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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

JW0551

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGGAGTATCAAATCGGCTTGC

Primer 2:CCTTTTTTTCCTGAAGCGGAAAA

23E10

Kohara Phage

Genobase

PMID:3038334[5]

12A1

Kohara Phage

Genobase

PMID:3038334[5]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 32% [6]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[3]

est. P1 cotransduction: 7% [6]
Synonyms: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

EcoCyc:G6316

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13641

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002924

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945170

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3405

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001919

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 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 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
  6. ↑ 6.0 6.1 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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