rnc: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

rnc

Gene Synonym(s)

ECK2565, b2567, JW2551, ranA[1], ranA

Product Desc.

RNase III, ds RNA[2]; RNase III[3];

Component of RNase III[3]

RNase III; cleaves double-stranded RNA[4]

Product Synonyms(s)

RNase III[1], B2567[2][1], RanA[2][1], Rnc[2][1] , ECK2565, JW2551, ranA, b2567

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rnc-era-recO-pdxJ-acpS[2], rnc-era[2]

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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rnc is a non-essential gene (Takiff, 1989; Yu, 2000) and the failure to obtain a viable insertion (Baba, 2006) may be due to a polar effect on the downstream essential era gene.[4]



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

rnc

Mnemonic

RNase C

Synonyms

ECK2565, b2567, JW2551, ranA[1], ranA

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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

58.22 minutes 

MG1655: 2702085..2701405
<gbrowseImage> name=NC_000913:2701405..2702085 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2624875..2625555
<gbrowseImage> name=NC_012967:2624875..2625555 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2587210..2587890
<gbrowseImage> name=NC_012759:2587210..2587890 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2702719..2702039
<gbrowseImage> name=NC_007779:2702039..2702719 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2793850..2793170
<gbrowseImage> name=NC_010473:2793170..2793850 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

2701405

Edman degradation

PMID:2105934


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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

rnc::Tn5KAN-I-SceI (FB20853)

Insertion at nt 562 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20853

contains pKD46

rnc::Tn5KAN-I-SceI (FB20854)

Insertion at nt 562 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20854

does not contain pKD46

rncG44D

G44D

In rnc-105; loss of activity

seeded from UniProt:P0A7Y0

rnc-105

CGSC:6351

rnc-40::ΔTn10

Auxotrophies

Presence of A40 insertion mutation causes transcription of era gene derives only from the mini-Tn10 and is Tetracycline dependent. In absence of Tet this insertion prevents era expression. Table 2.

PMID:1537799

Strain History W3110

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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

JW2551

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAACCCCATCGTAATTAATCG

Primer 2:CCTTCCAGCTCCAGTTTTTTCAA

7G4

Kohara Phage

Genobase

PMID:3038334

4A12

Kohara Phage

Genobase

PMID:3038334

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 20% [6]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 76% [6]

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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:EG10857

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10857

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000848

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947033

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0850

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008448

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

Rnc

Synonyms

RNase III[1], B2567[2][1], RanA[2][1], Rnc[2][1] , ECK2565, JW2551, ranA, b2567

Product description

RNase III, ds RNA[2]; RNase III[3];

Component of RNase III[3]

RNase III; cleaves double-stranded RNA[4]

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:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000999

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011907

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014720

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:0003725

double-stranded RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001159

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:0004519

endonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc (v14.0)

complete

GO:0004525

ribonuclease III activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00104

F

Seeded from EcoCyc (v14.0)

complete

GO:0004525

ribonuclease III activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000999

F

Seeded from EcoCyc (v14.0)

complete

GO:0004525

ribonuclease III activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011907

F

Seeded from EcoCyc (v14.0)

complete

GO:0004525

ribonuclease III activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.26.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001159

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014720

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00104

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006364

rRNA processing

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00104

P

Seeded from EcoCyc (v14.0)

complete

GO:0006396

RNA processing

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000999

P

Seeded from EcoCyc (v14.0)

complete

GO:0006397

mRNA processing

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00104

P

Seeded from EcoCyc (v14.0)

complete

GO:0016075

rRNA catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011907

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

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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

Subunits of RNase III

could be indirect

Protein

rnb

PMID:19402753

MALDI(Z-score):29.133723

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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 

MNPIVINRLQ RKLGYTFNHQ ELLQQALTHR SASSKHNERL EFLGDSILSY VIANALYHRF
PRVDEGDMSR MRATLVRGNT LAELAREFEL GECLRLGPGE LKSGGFRRES ILADTVEALI
GGVFLDSDIQ TVEKLILNWY QTRLDEISPG DKQKDPKTRL QEYLQGRHLP LPTYLVVQVR
GEAHDQEFTI HCQVSGLSEP VVGTGSSRRK AEQAAAEQAL KKLELE
Length

226

Mol. Wt

25.55 kDa

pI

6.8 (calculated)

Extinction coefficient

14,440 - 14,690 (calc based on 6 Y, 1 W, and 2 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

156..223

PF00035 Double-stranded RNA binding motif

PMID:19920124

Domain

38..128

PF00636 RNase3 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=rnc 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:16130492

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947033

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008448

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A7Y0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10857

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10857

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947033

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000848

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0850

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

3.82E+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

69.417+/-0.613

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.183088235

Molecules/cell

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

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

3393

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

676

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

1435

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)

rnc-era-recO-pdxJ-acpS

rnc-era

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Figure courtesy of RegulonDB

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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_000913:2702065..2702105 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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:b2567 (EcoliWiki Page)

NCBI GEO profiles for rnc

microarray

GenExpDB:b2567 (EcoliWiki Page)

Summary of data for rnc 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 rnc Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10857

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0850

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2567

EcoGene

EcoGene:EG10857

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000848

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008448

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

  • ENSANGP00000028563 (score: 1.000; bootstrap: 78%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000015797 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT3G20420 (score: 1.000; bootstrap: 100%)
  • AT5G45150 (score: 0.282)
  • AT1G01040 (score: 0.144)
  • AT3G43920 (score: 0.088)
  • AT4G15417 (score: 0.075)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000023346 (score: 1.000; bootstrap: 87%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00026581 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00009163 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000027962 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000003015 (score: 1.000; bootstrap: 93%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-030131-3445 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0034246 (score: 1.000; bootstrap: 63%)
  • FBgn0039016 (score: 0.109)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA19635-PA (score: 1.000; bootstrap: 53%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000021035 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000339845 (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000015994 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000005919 (score: 1.000; bootstrap: 88%)

From Inparanoid:20070104

Mus musculus

  • MGI:1261425 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Oryza gramene

  • Q69KJ0 (score: 1.000; bootstrap: 100%)
  • Q8LMR2 (score: 0.208)
  • Q6ATG6 (score: 0.152)
  • Q5N870 (score: 0.144)
  • Q75IB2 (score: 0.112)
  • Q69LX2 (score: 0.112)
  • Q7XQ14 (score: 0.105)
  • Q8W367 (score: 0.096)
  • Q7XD96 (score: 0.096)
  • Q5JK90 (score: 0.054)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000028748 (score: 1.000; bootstrap: 87%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000050633 (score: 1.000; bootstrap: 90%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YMR239C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC1191c (score: 1.000; bootstrap: 69%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000159261 (score: 1.000; bootstrap: 73%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00016527001 (score: 1.000; bootstrap: 85%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000036421 (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Shigella flexneri

RNC

From SHIGELLACYC

E. coli O157

RNC

From ECOO157CYC

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Do-It-Yourself Web Tools

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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

Pfam (EcoliWiki Page)

PF00636 RNase3 domain

Pfam (EcoliWiki Page)

PF00035 Double-stranded RNA binding motif

Superfamily (EcoliWiki Page)

SUPERFAMILY:54768

Panther (EcoliWiki Page)

PTHR11207:SF0

Superfamily (EcoliWiki Page)

SUPERFAMILY:69065

EcoCyc

EcoCyc:EG10857

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10857

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000848

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0850

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008448

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  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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