hyaE: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="Q46a9bcea440e8"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''hyaE''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''hyaE''
Hydrogenase 1
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0967, b0976, JW0958''<ref name='LIB:Riley_2006'/>, JW0958''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12511.Q46a9bcea440e8&page=12511&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0967, b0976, JW0958''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='130733'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46a9bceabc607"  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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22.32 minutes&nbsp;
22.32 minutes&nbsp;
|
|
MG1655: 1035577..1035975<br />{{GBrowseFigureByCoord|1034577|1036975|ecoli|MG1655}}
MG1655: 1035577..1035975<br /><gbrowseImage>
name=NC_000913:1035577..1035975
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10472 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10472 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1034577..1036975 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1034577|1036975|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1035577..1035975&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1035577|1035975|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10472 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10472 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1053445..1053843<br /><gbrowseImage>
name=NC_012967:1053445..1053843
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1053445|1053843|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1053445|1053843|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 938545..938943<br /><gbrowseImage>
name=NC_012759:938545..938943
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|938545|938943|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|938545|938943|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1036776..1037174<br />{{GBrowseFigureByCoord|1035776|1038174|ecoli_W3110|W3110}}
W3110: 1036776..1037174<br /><gbrowseImage>
name=NC_007779:1036776..1037174
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1035776..1038174 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|1035776|1038174|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1036776..1037174&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|1036776|1037174|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 1089505..1089903<br /><gbrowseImage>
name=NC_010473:1089505..1089903
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|1088709|1090699|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1088709|1090699|FASTA Dump}}
 
|- class="tableEdit_footer"
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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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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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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;hyaE (Keio:JW0958)
&Delta;hyaE (Keio:JW0958)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107235 CGSC8954]<ref name='LIB:cgsc'/>
|
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0003294 hyaE::Tn5KAN-2] (FB20078)
|
Insertion at nt 126 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20078]
|
does not contain [[pKD46]]
|-
|
''&#916;hyaE790::kan''
|
 
|
 
|
 
|
 
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
PMID:16738554
|
[[cgscmutation:101452|CGSC:101452]]
|
|
   
   
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<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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JW0958
JW0958
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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:CCTGAGGCACGCTCCTGCTGCGG  
Primer 2:CCTGAGGCACGCTCCTGCTGCGG  
|-
|-
|
[[:Category:Kohara_Phage:4H9|4H9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=224 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:4H11|4H11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=225 Genobase]
|
PMID:3038334
|-  
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[[ycbS:Gene|zcb-3059::Tn10]]
[[ycbS:Gene|zcb-3059::Tn10]]
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|
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est. P1 cotransduction: 26% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 26% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[yccE:Gene|zcc-282::Tn10]]
[[yccE:Gene|zcc-282::Tn10]]
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|
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est. P1 cotransduction: 36% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 36% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10472 EcoCyc:EG10472]
[[EcoCyc]]
|
|
EcoCyc:EG10472
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
|-  
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0467 EchoBASE:EB0467]
|
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0976 EcoliGenExpDB:b0976] 
EcoGene:EG10472
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C1117 ECOL199310CYC:C1117] 
RegulonDB:ECK120000465
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[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=EG10472 EcoGene:EG10472]
[http://www.ncbi.nlm.nih.gov/gene?term=945573 GeneID:945573]
|
|
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=HYAE ECOO157CYC:HYAE] 
EchoBASE:EB0467
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/31794 CGSC:31794] 
ASAP:ABE-0003294
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===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:hya genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:31, 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

hyaE

Mnemonic

Hydrogenase 1

Synonyms

ECK0967, b0976, JW0958[1], JW0958

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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

22.32 minutes 

MG1655: 1035577..1035975
<gbrowseImage> name=NC_000913:1035577..1035975 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1053445..1053843
<gbrowseImage> name=NC_012967:1053445..1053843 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 938545..938943
<gbrowseImage> name=NC_012759:938545..938943 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1036776..1037174
<gbrowseImage> name=NC_007779:1036776..1037174 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1089505..1089903
<gbrowseImage> name=NC_010473:1089505..1089903 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

ΔhyaE (Keio:JW0958)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8954[3]

hyaE::Tn5KAN-2 (FB20078)

Insertion at nt 126 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20078

does not contain pKD46

ΔhyaE790::kan

PMID:16738554[2]

CGSC:101452


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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

JW0958

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGCAACGACACGCCATTTGA

Primer 2:CCTGAGGCACGCTCCTGCTGCGG

4H9

Kohara Phage

Genobase

PMID:3038334[6]

4H11

Kohara Phage

Genobase

PMID:3038334[6]

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[3]

est. P1 cotransduction: 26% [7]

zcc-282::Tn10

Linked marker

CAG18466 = CGSC7359[3]

est. P1 cotransduction: 36% [7]

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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:EG10472

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10472

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000465

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945573

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0467

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003294

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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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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