hsdR:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Edited by wikibot
imported>Wikientrybot
No edit summary
Line 27: Line 27:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|{{Prettytable}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''hsdR''  
''hsdR''  
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4340, b4350, JW4313, Hs, hsp, hsr, rm''<ref name='LIB:Riley_2006'/>
''ECK4340, b4350, JW4313, Hs, hsp, hsr, rm''<ref name='LIB:Riley_2006'/>
|-
 
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.J46aa0d4642024&page=19251&pagename={{FULLPAGENAMEE}} edit table]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.J46aa0d4642024&page=19251&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.J46aa0d4642024-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.J46aa0d4642024-->
Line 59: Line 61:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' {{Prettytable}} id='150964'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
Line 80: Line 82:
{{GBrowseFastaLink|ecoli|NC_000913|4581272|4584838|FASTA Dump}}
{{GBrowseFastaLink|ecoli|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]  
|-
|-  
|
|
W3110
W3110
Line 91: Line 93:
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|4587929|4591495|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|4587929|4591495|FASTA Dump}}  
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.G46aa0d46c6c6b&page=19251&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.G46aa0d46c6c6b&page=19251&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.G46aa0d46c6c6b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.G46aa0d46c6c6b-->
Line 105: Line 108:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' {{Prettytable}} id='150965'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!|Feature type!!Location!!Description
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.Z46aa0d4790898&page=19251&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.Z46aa0d4790898&page=19251&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.Z46aa0d4790898-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.Z46aa0d4790898-->
Line 129: Line 133:
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}  
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}  
|- {{table_heading_style}}
|- {{table_heading_style}}
Line 144: Line 148:
|
|


|
|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
|
|
[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'/>  
Line 161: Line 164:
|
|
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
|
|[[PMID:9776741]]<ref name=PMID:9776741/>
[[PMID:9776741]]<ref name=PMID:9776741/>
|
|


Line 399: Line 401:
|
|


|
|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
|
|
[[cgscmutation:101416|CGSC:101416]]
[[cgscmutation:101416|CGSC:101416]]
Line 420: Line 421:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' {{Prettytable}} id='150967'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|-  
|
|
JW4313
JW4313
Line 434: Line 435:
|
|
[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]]<ref name=PMID:16769691/>


Status:Clone OK
Status:Clone OK
Line 442: Line 442:


Primer 2:CCGGCCAGCTCGTCCCAGATATA  
Primer 2:CCGGCCAGCTCGTCCCAGATATA  
|-
|-  
|
|
[[ytfN:Gene|zjf-920::Tn10]]
[[ytfN:Gene|zjf-920::Tn10]]
Line 450: Line 450:
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'/>
|
|
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  
|-
|-  
|
|
[[mdoB:Gene|mdoB202::Tn10]]
[[mdoB:Gene|mdoB202::Tn10]]
Line 461: Line 460:
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
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.P46aa0d48a62f1&page=19251&pagename={{FULLPAGENAMEE}} edit table] || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.P46aa0d48a62f1&page=19251&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.P46aa0d48a62f1-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.P46aa0d48a62f1-->
Line 481: Line 480:
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
|- {{table_heading_style}}
|- {{table_heading_style}}
Line 538: Line 537:
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0014264&formSubmitReturn=1 ASAP:ABE-0014264]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0014264&formSubmitReturn=1 ASAP:ABE-0014264]
|
|
   
   
Line 556: Line 555:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='100446'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Name!!URL!!Comments
!|Name!!URL!!Comments
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.Y46a7259173119&page=19251&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.19251.Y46a7259173119&page=19251&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.Y46a7259173119-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.19251.Y46a7259173119-->

Revision as of 19:04, 29 January 2009

{{#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 Alleles and Phenotypes Genetic Resources Accessions Links References Suggestions

Nomenclature

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

hsdR

Mnemonic
Synonyms

ECK4340, b4350, JW4313, Hs, hsp, hsr, rm[1]

edit table

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Notes

Location(s) and DNA Sequence

[back to top]


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
gbrowse_img.php?coord=4580272..4585838&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 4591495..4587929
gbrowse_img.php?coord=4586929..4592495&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

edit table

See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature type Location Description
edit table

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

[back to top]


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


edit table

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

[back to top]


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

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[3]

est. P1 cotransduction: % [6]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[3]

est. P1 cotransduction: 66% [6]
Synonyms:zjj-202::Tn10, zji-202::Tn10

edit table

See Help:Gene_resources for help entering information into the Genetic Resources table.

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10459

EchoBASE (EcoliWiki Page)

EchoBASE:EB0454

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4350

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C5425

EcoGene (EcoliWiki Page)

EcoGene:EG10459

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z5948

CGSC (EcoliWiki Page)

CGSC:620

ASAP (EcoliWikiPage)

ASAP:ABE-0014264


edit table

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Notes

Links

[back to top]


Name URL Comments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

References

[back to top]


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 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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=hsdR:Gene&oldid=665824"