appY:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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{|{{Prettytable}}
{|   id="F46a9b39052a2b"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''appY''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''appY''
Acid (poly)phosphatase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0556, b0564, JW0553''<ref name='LIB:Riley_2006'/>, JW0553''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11689.F46a9b39052a2b&page=11689&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0556, b0564, JW0553''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='128267'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9b390caaf5"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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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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MG1655
MG1655
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12.56 minutes&nbsp;
12.56 minutes&nbsp;
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MG1655: 582904..583653<br />{{GBrowseFigureByCoord|581904|584653|ecoli|MG1655}}
MG1655: 582904..583653<br /><gbrowseImage>
name=NC_000913:582904..583653
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10050 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10050 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:581904..584653 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|581904|584653|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:582904..583653&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|582904|583653|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10050 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10050 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 559033..559782<br /><gbrowseImage>
name=NC_012967:559033..559782
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|559033|559782|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|559033|559782|FASTA Dump}}
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[[BW2952]]
|
 
|
NC_012759: 485664..486413<br /><gbrowseImage>
name=NC_012759:485664..486413
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|485664|486413|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|485664|486413|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 582904..583653<br />{{GBrowseFigureByCoord|581904|584653|ecoli_W3110|W3110}}  
W3110: 582904..583653<br /><gbrowseImage>
name=NC_007779:582904..583653
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|581904|584653|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|582904|583653|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 522236..522985<br /><gbrowseImage>
name=NC_010473:522236..522985
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|520738|524483|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|520738|524483|FASTA Dump}}  
|-
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:581904..584653 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:582904..583653&plugin_action=Go FASTA Dump]
 
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DH10B: 635496..636245<br /><gbrowseImage>
name=NC_010473:635496..636245
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|633998|637743|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|633998|637743|FASTA Dump}}
 
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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|- {{table_heading_style}}
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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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&Delta;appY (Keio:JW0553)
&Delta;appY (Keio:JW0553)
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[[PMID:16738554]]<ref name=PMID:16738554/>
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=106960 CGSC8679]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106960 CGSC8679]<ref name='LIB:cgsc'/>  
|
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''&#916;appY773::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:100022|CGSC:100022]]
|
 
|- class="tableEdit_footer"
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0553
JW0553
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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


Status:Clone OK
Status:Clone OK
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Primer 2:CCGTCAATTGTTTTGTTTATTCC  
Primer 2:CCGTCAATTGTTTTGTTTATTCC  
|-
|-
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[[:Category:Kohara_Phage:23E10|23E10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=160 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12A1|12A1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=161 Genobase]
|
PMID:3038334
|-  
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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'/>
|
|
est. P1 cotransduction: 30% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 30% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:purE79::Tn10  
Synonyms: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'/>
|
|
est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms: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]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10050 EcoCyc:EG10050] 
EcoCyc:EG10050
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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]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0048 EchoBASE:EB0048] 
EcoGene:EG10050
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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=b0564 EcoliGenExpDB:b0564] 
RegulonDB:ECK120000046
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10050 EcoGene:EG10050]
[http://www.ncbi.nlm.nih.gov/gene?term=948797 GeneID:948797]
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z2104 ECOO157CYC:Z2104] 
EchoBASE:EB0048
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/31146 CGSC:31146] 
ASAP:ABE-0001929
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Gene List:DLP12 prophage]]
[[Category:app genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 19 September 2013

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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

appY

Mnemonic

Acid (poly)phosphatase

Synonyms

ECK0556, b0564, JW0553[1], JW0553

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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

12.56 minutes 

MG1655: 582904..583653
<gbrowseImage> name=NC_000913:582904..583653 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 559033..559782
<gbrowseImage> name=NC_012967:559033..559782 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 485664..486413
<gbrowseImage> name=NC_012759:485664..486413 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 582904..583653
<gbrowseImage> name=NC_007779:582904..583653 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 522236..522985
<gbrowseImage> name=NC_010473:522236..522985 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 635496..636245
<gbrowseImage> name=NC_010473:635496..636245 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

ΔappY (Keio:JW0553)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8679[3]

ΔappY773::kan

PMID:16738554[2]

CGSC:100022


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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

JW0553

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGATTATGTTTGCTCCGTAGT

Primer 2:CCGTCAATTGTTTTGTTTATTCC

23E10

Kohara Phage

Genobase

PMID:3038334[5]

12A1

Kohara Phage

Genobase

PMID:3038334[5]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 30% [6]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[3]

est. P1 cotransduction: 8% [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:EG10050

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10050

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000046

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948797

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0048

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001929

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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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).

Categories

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