rnr:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

rnr

Gene Synonym(s)

ECK4175, b4179, JW5741, vacB, yjeC[1], yjeC

Product Desc.

EG11259- Exoribonuclease R; specifically required for SsrA-SmpB-dependent decay of non-stop aberrant mRNAs (Richards, 2006)[2]

Product Synonyms(s)

exoribonuclease R, RNase R[1], B4179[3][1], YjeC[3][1], Rnr[3][1], VacB[3][1] , ECK4175, JW5741, vacB, yjeC, b4179

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): nsrR-rnr-rlmB[3]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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rnr is transiently induced after a cold shock. rnr is orthologous with Shigella virulence gene vacB.[2]



Gene

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Nomenclature

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

Standard name

rnr

Mnemonic

RNase R

Synonyms

ECK4175, b4179, JW5741, vacB, yjeC[1], yjeC

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Notes

Location(s) and DNA Sequence

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<protect> 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

94.94 minutes 

MG1655: 4404677..4407118
<gbrowseImage> name=NC_000913:4404677..4407118 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4384809..4387250
<gbrowseImage> name=NC_012967:4384809..4387250 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4343412..4345853
<gbrowseImage> name=NC_012759:4343412..4345853 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4411334..4413775
<gbrowseImage> name=NC_007779:4411334..4413775 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4505039..4507480
<gbrowseImage> name=NC_010473:4505039..4507480 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

4404680

Edman degradation

PMID:11948193


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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

Δrnr (Keio:JW5741)

deletion

deletion

PMID:16738554

Shigen
CGSC11550[4]

Δrnr-729::kan

PMID:16738554

CGSC:102756


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Notes

Genetic Interactions

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<protect>

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

JW5741

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTCACAAGATCCTTTCCAGGA

Primer 2:CCtTCTGCCACTTTTTTCTTCGC

3A1

Kohara Phage

Genobase

PMID:3038334

6G4

Kohara Phage

Genobase

PMID:3038334

1G10

Kohara Phage

Genobase

PMID:3038334

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[4]

est. P1 cotransduction: 11% [5]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[4]

est. P1 cotransduction: 45% [5]

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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:EG11259

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11259

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001234

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948692

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1239

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013678

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

Rnr

Synonyms

exoribonuclease R, RNase R[1], B4179[3][1], YjeC[3][1], Rnr[3][1], VacB[3][1] , ECK4175, JW5741, vacB, yjeC, b4179

Product description

EG11259- Exoribonuclease R; specifically required for SsrA-SmpB-dependent decay of non-stop aberrant mRNAs (Richards, 2006)[2]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0005737

cytoplasm

PMID:16397293

C

Seeded from Riley et al 2006 [1].

Missing: evidence

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011129

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001900

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003029

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004476

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011805

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc (v14.0)

complete

GO:0004540

ribonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001900

F

Seeded from EcoCyc (v14.0)

complete

GO:0004540

ribonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004476

F

Seeded from EcoCyc (v14.0)

complete

GO:0009405

pathogenesis

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0843

P

Seeded from EcoCyc (v14.0)

complete

GO:0016070

RNA metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004476

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0004540

ribonuclease activity

PMID:9603904

IMP: Inferred from Mutant Phenotype

F

Table 2: extracts of rnr mutant cells have reduced poly(A) degrading activity

complete

GO:0016896

exoribonuclease activity, producing 5'-phosphomonoesters

PMID:11948193

IDA: Inferred from Direct Assay

F

Fig. 3 and Table 2

complete

GO:0004527

exonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0269

F

Seeded from EcoCyc (v14.0)

complete

GO:0008997

ribonuclease R activity

PMID:11948193

IDA: Inferred from Direct Assay

F

Fig. 3 and Table 2

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

cca

PMID:15690043

Experiment(s):EBI-883997

Protein

infC

PMID:15690043

Experiment(s):EBI-883997

Protein

pgm

PMID:15690043

Experiment(s):EBI-883997

Protein

pssA

PMID:15690043

Experiment(s):EBI-883997

Protein

rplA

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rplB

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rplC

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rplF

PMID:15690043

Experiment(s):EBI-883997

Protein

rplI

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rplM

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rplN

PMID:15690043

Experiment(s):EBI-883997

Protein

rplO

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rpsA

PMID:15690043

Experiment(s):EBI-883997

Protein

rpsB

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rpsC

PMID:15690043

Experiment(s):EBI-883997

Protein

rpsD

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rpsE

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rpsF

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rpsG

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rpsM

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

rpsP

PMID:15690043

Experiment(s):EBI-883997, EBI-891136

Protein

intA

PMID:15690043

Experiment(s):EBI-883997

Protein

tgt

PMID:15690043

Experiment(s):EBI-883997

Protein

ycbY

PMID:15690043

Experiment(s):EBI-883997

Protein

yfiF

PMID:15690043

Experiment(s):EBI-883997, EBI-879491

Protein

ygiF

PMID:15690043

Experiment(s):EBI-883997

Protein

ihfA

PMID:15690043

Experiment(s):EBI-891136

Protein

hupA

PMID:15690043

Experiment(s):EBI-891136

Protein

rplP

PMID:15690043

Experiment(s):EBI-891136

Protein

rplT

PMID:15690043

Experiment(s):EBI-891136

Protein

rplU

PMID:15690043

Experiment(s):EBI-891136

Protein

rplV

PMID:15690043

Experiment(s):EBI-891136

Protein

rplW

PMID:15690043

Experiment(s):EBI-891136

Protein

rplX

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsH

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsI

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsK

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsN

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsO

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsR

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsT

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsU

PMID:15690043

Experiment(s):EBI-891136

Protein

rpsH

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsP

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):9.921698

Protein

rplP

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.670398

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.564045

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

ihfA

PMID:19402753

LCMS(ID Probability):99.0

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):11.502079

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplI

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):30.262063

Protein

rpsI

PMID:19402753

LCMS(ID Probability):99.0 MALDI(Z-score):6.592879

Protein

rpsR

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsO

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):3.597110

Protein

rpsK

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.388265

Protein

rplB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):38.617983

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):23.975877

Protein

rplO

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):21.852990

Protein

rpsU

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):3.411533

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):35.575045

Protein

rpsC

PMID:19402753

MALDI(Z-score):32.945078

Protein

rplT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):50.772162

Protein

infC

PMID:19402753

MALDI(Z-score):20.289543

Protein

rplF

PMID:19402753

LCMS(ID Probability):97.9 MALDI(Z-score):11.134401

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):29.084634

Protein

pssA

PMID:19402753

MALDI(Z-score):19.741475

Protein

yibL

PMID:19402753

LCMS(ID Probability):98.5

Protein

yfiF

PMID:19402753

MALDI(Z-score):26.783167

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MTKIFIRDDN GGTEMSQDPF QEREAEKYAN PIPSREFILE HLTKREKPAS RDELAVELHI
EGEEQLEGLR RRLRAMERDG QLVFTRRQCY ALPERLDLVK GTVIGHRDGY GFLRVEGRKD
DLYLSSEQMK TCIHGDQVLA QPLGADRKGR REARIVRVLV PKTSQIVGRY FTEAGVGFVV
PDDSRLSFDI LIPPDQIMGA RMGFVVVVEL TQRPTRRTKA VGKIVEVLGD NMGTGMAVDI
ALRTHEIPYI WPQAVEQQVA GLKEEVPEEA KAGRVDLRDL PLVTIDGEDA RDFDDAVYCE
KKRGGGWRLW VAIADVSYYV RPSTPLDREA RNRGTSVYFP SQVIPMLPEV LSNGLCSLNP
QVDRLCMVCE MTVSSKGRLT GYKFYEAVMS SHARLTYTKV WHILQGDQDL REQYAPLVKH
LEELHNLYKV LDKAREERGG ISFESEEAKF IFNAERRIER IEQTQRNDAH KLIEECMILA
NISAARFVEK AKEPALFRIH DKPSTEAITS FRSVLAELGL ELPGGNKPEP RDYAELLESV
ADRPDAEMLQ TMLLRSMKQA IYDPENRGHF GLALQSYAHF TSPIRRYPDL TLHRAIKYLL
AKEQGHQGNT TETGGYHYSM EEMLQLGQHC SMAERRADEA TRDVADWLKC DFMLDQVGNV
FKGVISSVTG FGFFVRLDDL FIDGLVHVSS LDNDYYRFDQ VGQRLMGESS GQTYRLGDRV
EVRVEAVNMD ERKIDFSLIS SERAPRNVGK TAREKAKKGD AGKKGGKRRQ VGKKVNFEPD
SAFRGEKKTK PKAAKKDARK AKKPSAKTQK IAAATKAKRA AKKKVAE
Length

827

Mol. Wt

93.689 kDa

pI

8.8 (calculated)

Extinction coefficient

64,750 - 65,875 (calc based on 25 Y, 5 W, and 9 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

260..588

PF00773 RNB domain

PMID:19920124

Domain

640..725

PF00575 S1 RNA binding domain

PMID:19920124

Domain

87..144

PF08206 Ribonuclease B OB domain

PMID:19920124

Domain

156..213

PF08206 Ribonuclease B OB domain

PMID:19920124

Domain

22..85

PF08461 Ribonuclease R winged-helix domain

PMID:19920124

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rnr taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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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

NCBI (Protein) (EcoliWiki Page)

GI:90111698

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948692

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013678

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P21499

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11259

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11259

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948692

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001234

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1239

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

2.83E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

90.493+/-1.462

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.16048+/-0.01542

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by FISH

PMID:20671182

Protein

E. coli K-12 MG1655

1121

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

605

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

1051

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

nsrR-rnr-rlmB

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Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:4404657..4404697 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b4179 (EcoliWiki Page)

NCBI GEO profiles for rnr

microarray

GenExpDB:b4179 (EcoliWiki Page)

Summary of data for rnr from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
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Notes

Accessions Related to rnr Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11259

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1239

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4179

EcoGene

EcoGene:EG11259

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001234

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013678

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Anopheles gambiae

  • ENSANGP00000003705 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT2G17510 (score: 1.000; bootstrap: 100%)
  • AT1G77680 (score: 0.079)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000000481 (score: 1.000; bootstrap: 100%)
  • ENSBTAP00000026500 (score: 0.091)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00018612 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000007481 (score: 1.000; bootstrap: 96%)
  • ENSCAFP00000025455 (score: 0.189)
  • ENSCAFP00000016451 (score: 0.097)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000008123 (score: 1.000; bootstrap: 100%)
  • ENSCINP00000012409 (score: 0.109)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0189843 (score: 1.000; bootstrap: 100%)
  • DDB0192046 (score: 0.111)
  • DDB0206173 (score: 0.055)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0039183 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000012350 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000304580 (score: 1.000; bootstrap: 100%)
  • ENSP00000321583 (score: 0.185)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000001070 (score: 1.000; bootstrap: 100%)
  • ENSMMUP00000004924 (score: 0.132)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000000245 (score: 1.000; bootstrap: 100%)
  • ENSMODP00000012199 (score: 0.208)

From Inparanoid:20070104

Mus musculus

  • MGI:2442555 (score: 1.000; bootstrap: 100%)
  • MGI:2143272 (score: 0.118)

From Inparanoid:20070104

Oryza gramene

  • Q6Z6A3 (score: 1.000; bootstrap: 100%)
  • Q9SNK4 (score: 0.110)
  • Q8H885 (score: 0.095)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000010072 (score: 1.000; bootstrap: 95%)
  • ENSPTRP00000012297 (score: 0.072)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000029411 (score: 1.000; bootstrap: 100%)
  • ENSRNOP00000014071 (score: 0.224)
  • ENSRNOP00000025779 (score: 0.130)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YOL021C (score: 1.000; bootstrap: 95%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC26H80 (score: 1.000; bootstrap: 100%)
  • SPAC2C47c (score: 0.107)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000166614 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000153486 (score: 0.116)
  • NEWSINFRUP00000140976 (score: 0.095)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00008353001 (score: 1.000; bootstrap: 98%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000027001 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000034647 (score: 0.176)
  • ENSXETP00000049254 (score: 0.106)

From Inparanoid:20070104

Shigella flexneri

VACB

From SHIGELLACYC

E. coli O157

VACB

From ECOO157CYC

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Notes

Families

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

Database Accession Notes

Superfamily (EcoliWiki Page)

SUPERFAMILY:50249

Panther (EcoliWiki Page)

PTHR23355:SF9

Pfam (EcoliWiki Page)

PF00773 RNB domain

Pfam (EcoliWiki Page)

PF00575 S1 RNA binding domain

Pfam (EcoliWiki Page)

PF08206 Ribonuclease B OB domain

Pfam (EcoliWiki Page)

PF08206 Ribonuclease B OB domain

Pfam (EcoliWiki Page)

PF08461 Ribonuclease R winged-helix domain

EcoCyc

EcoCyc:EG11259

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11259

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001234

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1239

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013678

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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