rrfD:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|rrfD}}{{Tab On|Gene|rrfD}}{{Tab|Gene Product(s)|rrfD}}{{Tab|Expression|rrfD}}{{Tab|Evolution|rrfD}}{{Tab|On One Page|rrfD}}{{TabsBottom}}
{{Tab|Quickview|rrfD}}{{Tab On|Gene|rrfD}}{{Tab|Gene Product(s)|rrfD}}{{Tab|Expression|rrfD}}{{Tab|Evolution|rrfD}}{{Tab|On One Page|rrfD}}{{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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==Nomenclature==
==Nomenclature==
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{|  id="N46a9f1d72be99"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''rrfD''  
''rrfD''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Ribosomal RNA, 5S
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3261, b3274, JWR0075, G7978, rrvD''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3261, b3274, JWR0075, G7978, rrvD''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
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{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===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="M46a9f1d7b00b4"  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
|-
|-  
|
|
MG1655
MG1655
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73.75 minutes&nbsp;
73.75 minutes&nbsp;
|
|
MG1655: 3421809..3421690<br />{{GBrowseFigureByCoord|3420690|3422809|ecoli|MG1655}}
MG1655: 3421809..3421690<br /><gbrowseImage>
name=NC_000913:3421690..3421809
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG30073 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG30073 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3420690..3422809 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3420690|3422809|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3421690..3421809&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3421690|3421809|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG30073 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG30073 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3351560..3351679<br /><gbrowseImage>
name=NC_012967:3351560..3351679
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3351560|3351679|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3351560|3351679|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3308838..3308957<br /><gbrowseImage>
name=NC_012759:3308838..3308957
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3308838|3308957|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3308838|3308957|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3423642..3423523<br />{{GBrowseFigureByCoord|3422523|3424642|ecoli_W3110|W3110}}  
W3110: 3423642..3423523<br /><gbrowseImage>
name=NC_007779:3423523..3423642
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3422523|3424642|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3423523|3423642|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 3519554..3519435<br /><gbrowseImage>
name=NC_010473:3519435..3519554
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3422523..3424642 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3519197|3519792|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3423523..3423642&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3519197|3519792|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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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="X46a9f1d8b8500"  class=" tableEdit Gene_allele_table dataTable" 
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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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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!|Resource!!Resource Type!!Source!!Notes/Reference
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|
 
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:
 
Primer 1:
 
Primer 2:
|-
|
[[:Category:Kohara_Phage:6G9|6G9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=530 Genobase]
|
PMID:3038334
|-
|
[[acrF:Gene|acrF3083::Tn10]]
|
Linked marker
|
CAG12075 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40247 CGSC7447]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 79% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10
|-
|
[[smg:Gene|smg-3082::Tn10]]
|
Linked marker
|
CAG12071 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40240 CGSC7444]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 79% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:EG30073
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG30073
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG30073 EcoCyc:EG30073] 
RegulonDB:ECK120002515
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4236 EchoBASE:EB4236]
[http://www.ncbi.nlm.nih.gov/gene?term=947769 GeneID:947769]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3274 EcoliGenExpDB:b3274] 
EchoBASE:EB4236
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[ASAP]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG30073 EcoGene:EG30073] 
ASAP:ABE-0010744
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:rrf genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:46, 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

[back to top]


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

Standard name

rrfD

Mnemonic

Ribosomal RNA, 5S

Synonyms

ECK3261, b3274, JWR0075, G7978, rrvD[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

73.75 minutes 

MG1655: 3421809..3421690
<gbrowseImage> name=NC_000913:3421690..3421809 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3351560..3351679
<gbrowseImage> name=NC_012967:3351560..3351679 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3308838..3308957
<gbrowseImage> name=NC_012759:3308838..3308957 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3423642..3423523
<gbrowseImage> name=NC_007779:3423523..3423642 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3519554..3519435
<gbrowseImage> name=NC_010473:3519435..3519554 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
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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

Plasmid clone

Shigen

PMID:16769691[3]

Status:

Primer 1:

Primer 2:

6G9

Kohara Phage

Genobase

PMID:3038334[4]

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[5]

est. P1 cotransduction: 79% [6]
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 79% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::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:EG30073

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG30073

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002515

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947769

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4236

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010744

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. ↑ 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
  4. ↑ 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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).

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