hypC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|hypC}}{{Tab On|Gene|hypC}}{{Tab|Gene Product(s)|hypC}}{{Tab|Expression|hypC}}{{Tab|Evolution|hypC}}{{Tab|On One Page|hypC}}{{TabsBottom}}
{{Tab|Quickview|hypC}}{{Tab On|Gene|hypC}}{{Tab|Gene Product(s)|hypC}}{{Tab|Expression|hypC}}{{Tab|Evolution|hypC}}{{Tab|On One Page|hypC}}{{TabsBottom}}
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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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</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''hypC''  
''hypC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Hydrogenase pleiotropic
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2723, b2728, JW2698, hydB''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK2723, b2728, JW2698, hydB''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9e4d0bbd89"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!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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61.42 minutes&nbsp;
61.42 minutes&nbsp;
|
|
MG1655: 2849886..2850158<br />{{GBrowseFigureByCoord|2848886|2851158|ecoli|MG1655}}
MG1655: 2849886..2850158<br /><gbrowseImage>
name=NC_000913:2849886..2850158
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10485 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10485 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2848886..2851158 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2848886|2851158|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2849886..2850158&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2849886|2850158|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10485 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10485 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2746724..2746996<br /><gbrowseImage>
name=NC_012967:2746724..2746996
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2746724|2746996|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2746724|2746996|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2735698..2735970<br /><gbrowseImage>
name=NC_012759:2735698..2735970
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2735698|2735970|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2735698|2735970|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 2850520..2850792<br />{{GBrowseFigureByCoord|2849520|2851792|ecoli_W3110|W3110}}  
W3110: 2850520..2850792<br /><gbrowseImage>
name=NC_007779:2850520..2850792
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2849520|2851792|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2849520..2851792 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|2850520|2850792|FASTA Dump}}
|-  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2850520..2850792&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 2942428..2942700<br /><gbrowseImage>
name=NC_010473:2942428..2942700
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2941884|2943244|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2941884|2943244|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9e4d176cd0"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
2849889
|
Edman degradation
|
PMID:10783387<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9e4d1bd76e"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;hypC (Keio:JW2698)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108404 CGSC10123]<ref name='LIB:cgsc'/>
|
|-  
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''&#916;hypC732::kan''
|
|
&nbsp;
 
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&nbsp;
 
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&nbsp;
 
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&nbsp;
 
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&nbsp;
PMID:16738554
|
|
&nbsp;
[[cgscmutation:101506|CGSC:101506]]
|
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&nbsp;
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W4e04bd831c401"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9e4d2780f6"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
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JW2698
JW2698
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTTTTTCCTCGCCATACAACAG  
Primer 2:CCTTTTTCCTCGCCATACAACAG  
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[[:Category:Kohara_Phage:12F2|12F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=449 Genobase]
|
PMID:3038334
|-
|
[[srlD:Gene|srlD3131::Tn10]]
|
Linked marker
|
CAG18642 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40097 CGSC7423]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 40% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10
|-
|
[[cysI:Gene|cysI95::Tn10]]
|
Linked marker
|
CAG12173 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40099 CGSC7425]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 23% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:cysC95::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a9e4d31b728"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10485 EcoCyc:EG10485] 
EcoCyc:EG10485
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0480 EchoBASE:EB0480] 
EcoGene:EG10485
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2728 EcoliGenExpDB:b2728] 
RegulonDB:ECK120000478
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3288 ECOL199310CYC:C3288]
[http://www.ncbi.nlm.nih.gov/gene?term=947192 GeneID:947192]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10485 EcoGene:EG10485] 
EchoBASE:EB0480
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=HYPC ECOO157CYC:HYPC] 
ASAP:ABE-0008962
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16021.D46a9e4d31b728&page=16021&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33113 CGSC:33113] 
|
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{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
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===Notes===
===Notes===
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==Links==
==Links==
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==References==
==References==
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__NOTOC__
__NOTOC__
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:hyp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:44, 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

hypC

Mnemonic

Hydrogenase pleiotropic

Synonyms

ECK2723, b2728, JW2698, hydB[1][2]

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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

61.42 minutes 

MG1655: 2849886..2850158
<gbrowseImage> name=NC_000913:2849886..2850158 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2746724..2746996
<gbrowseImage> name=NC_012967:2746724..2746996 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2735698..2735970
<gbrowseImage> name=NC_012759:2735698..2735970 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2850520..2850792
<gbrowseImage> name=NC_007779:2850520..2850792 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2942428..2942700
<gbrowseImage> name=NC_010473:2942428..2942700 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

Coding Start (SO:0000323)

MG1655

2849889

Edman degradation

PMID:10783387[3]


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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

ΔhypC (Keio:JW2698)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC10123[5]

ΔhypC732::kan

PMID:16738554[4]

CGSC:101506


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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

JW2698

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCTGCATAGGCGTTCCCGGCCA

Primer 2:CCTTTTTCCTCGCCATACAACAG

12F2

Kohara Phage

Genobase

PMID:3038334[7]

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[5]

est. P1 cotransduction: 40% [8]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

cysI95::Tn10

Linked marker

CAG12173 = CGSC7425[5]

est. P1 cotransduction: 23% [8]
Synonyms:cysC95::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:EG10485

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10485

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000478

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947192

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0480

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008962

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Magalon, A & Bock, A (2000) Analysis of the HypC-hycE complex, a key intermediate in the assembly of the metal center of the Escherichia coli hydrogenase 3. J. Biol. Chem. 275 21114-20 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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
  7. ↑ 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
  8. ↑ 8.0 8.1 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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