hsdR: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="J46aa0d4642024"  class=" tableEdit Gene_nomenclature_table" 
 
|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''hsdR''  
''hsdR''
|-
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
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Host specificity
|-
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK4340, b4350, JW4313, Hs, hsp, hsr, rm''<ref name='LIB:Riley_2006'/>
''ECK4340, b4350, JW4313, Hs, hsp, hsr, rm''<ref name='LIB:Riley_2006'/>
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='150964'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46aa0d46c6c6b"  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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98.74 minutes&nbsp;
98.74 minutes&nbsp;
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MG1655: 4584838..4581272<br />{{GBrowseFigureByCoord|4580272|4585838|ecoli|MG1655}}
MG1655: 4584838..4581272<br /><gbrowseImage>
name=NC_000913:4581272..4584838
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10459 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10459 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4580272..4585838 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4580272|4585838|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4581272..4584838&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4581272|4584838|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10459 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10459 EcoCyc Sequence Dump]  
|-
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[[REL606]]
|
 
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NC_012967: 4564736..4561224<br /><gbrowseImage>
name=NC_012967:4561224..4564736
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4561224|4564736|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|4561224|4564736|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 4519756..4523322<br /><gbrowseImage>
name=NC_012759:4519756..4523322
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4519756|4523322|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|4519756|4523322|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 4591495..4587929<br />{{GBrowseFigureByCoord|4586929|4592495|ecoli_W3110|W3110}}
W3110: 4591495..4587929<br /><gbrowseImage>
name=NC_007779:4587929..4591495
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4586929..4592495 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|4586929|4592495|GBrowse(W3110)}}
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4587929..4591495&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|4587929|4591495|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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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="D46aa0d47dca5e"  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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[[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=109364 CGSC11083]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109364 CGSC11083]<ref name='LIB:cgsc'/>  
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deletion
deletion
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|
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Lacks DNA specifying six DEAD-box motifs that are critical for helicase activity
Lacks DNA specifying six DEAD-box motifs that are critical for helicase activity
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[[PMID:9776741]]<ref name=PMID:9776741/>
PMID: 9776741
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[[cgscmutation:9513|CGSC:9513]]
[[cgscmutation:9513|CGSC:9513]]
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''hsdR11''
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[[cgscmutation:10099|CGSC:10099]]
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''hsdR27''
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[[cgscmutation:10718|CGSC:10718]]
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''hsdR18''
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[[cgscmutation:12161|CGSC:12161]]
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''hsdR519''
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[[cgscmutation:14514|CGSC:14514]]
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''hsdR13''
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[[cgscmutation:14535|CGSC:14535]]
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''hsdR29''
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[[cgscmutation:28917|CGSC:28917]]
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|-
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''&#916;hsdR748::kan''
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PMID:16738554
|
[[cgscmutation:101416|CGSC:101416]]
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|
   
   


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<protect><!--Alleles_notes--></protect>
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===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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JW4313
JW4313
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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:CCGGCCAGCTCGTCCCAGATATA  
Primer 2:CCGGCCAGCTCGTCCCAGATATA  
|-
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[[:Category:Kohara_Phage:12G5|12G5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=669 Genobase]
|
PMID:3038334
|-
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[[:Category:Kohara_Phage:10H12|10H12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=670 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7C1|7C1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=671 Genobase]
|
PMID:3038334
|-  
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[[ytfN:Gene|zjf-920::Tn10]]
[[ytfN:Gene|zjf-920::Tn10]]
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CAG12019 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40608 CGSC7484]<ref name='LIB:cgsc'/>
CAG12019 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40608 CGSC7484]<ref name='LIB:cgsc'/>
|
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zjh-901::Tn10, zjg-920::Tn10  
Synonyms:zjh-901::Tn10, zjg-920::Tn10  
|-
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[[mdoB:Gene|mdoB202::Tn10]]
[[mdoB:Gene|mdoB202::Tn10]]
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CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zjj-202::Tn10, zji-202::Tn10


Synonyms:zjj-202::Tn10, zji-202::Tn10
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===Notes===
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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=EG10459 EcoCyc:EG10459] 
EcoCyc:EG10459
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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=EB0454 EchoBASE:EB0454] 
EcoGene:EG10459
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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=b4350 EcoliGenExpDB:b4350] 
RegulonDB:ECK120000452
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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]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C5425 ECOL199310CYC:C5425]
[http://www.ncbi.nlm.nih.gov/gene?term=948878 GeneID:948878]
|
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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=EG10459 EcoGene:EG10459] 
EchoBASE:EB0454
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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=Z5948 ECOO157CYC:Z5948] 
ASAP:ABE-0014264
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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]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/620 CGSC:620] 
|
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===Notes===
===Notes===
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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:hsd genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:52, 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

hsdR

Mnemonic

Host specificity

Synonyms

ECK4340, b4350, JW4313, Hs, hsp, hsr, rm[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

98.74 minutes 

MG1655: 4584838..4581272
<gbrowseImage> name=NC_000913:4581272..4584838 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4564736..4561224
<gbrowseImage> name=NC_012967:4561224..4564736 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4519756..4523322
<gbrowseImage> name=NC_012759:4519756..4523322 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4591495..4587929
<gbrowseImage> name=NC_007779:4587929..4591495 source=W3110 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

ΔhsdR (Keio:JW4313)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11083[3]

hsdRΔ4

deletion

deletion

Lacks DNA specifying six DEAD-box motifs that are critical for helicase activity

PMID:9776741[4]

hsdR514

CGSC:4539

hsdR2

CGSC:4558

hsdR4

CGSC:4756

hsdR17

CGSC:5437

hsdR19

CGSC:8723

hsdR0

CGSC:9056

ΔhsdR24

CGSC:9513

hsdR11

CGSC:10099

hsdR27

CGSC:10718

hsdR18

CGSC:12161

hsdR519

CGSC:14514

hsdR13

CGSC:14535

hsdR29

CGSC:28917

ΔhsdR748::kan

PMID:16738554[2]

CGSC:101416


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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

JW4313

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTATGGGCgTTAAATATTTGGACAGGCCCG

Primer 2:CCGGCCAGCTCGTCCCAGATATA

12G5

Kohara Phage

Genobase

PMID:3038334[6]

10H12

Kohara Phage

Genobase

PMID:3038334[6]

7C1

Kohara Phage

Genobase

PMID:3038334[6]

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[3]

est. P1 cotransduction: % [7]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[3]

est. P1 cotransduction: 66% [7]
Synonyms:zjj-202::Tn10, zji-202::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:EG10459

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10459

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000452

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948878

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0454

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014264

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. ↑ Davies, GP et al. (1998) EcoKI with an amino acid substitution in any one of seven DEAD-box motifs has impaired ATPase and endonuclease activities. Nucleic Acids Res. 26 4828-36 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 6.2 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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