EcoliHub logo

Try the new EcoliHub and let us know what you'd like to see.

rnc:On One Page

From EcoliWiki

Jump to: navigation, search
Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]



See Help:Quickview for help with entering information in the Quickview table.

Standard Name

rnc

Gene Synonym(s)

ECK2565, b2567, JW2551, ranA[1]

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]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

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

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(rnc)    Textpresso(rnc)

edit table

See Help:Quickview for help with entering information in the Quickview table.

Notes

[back to top]


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

[back to top]


Nomenclature

[back to top]


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]

edit 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.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

58.22 minutes 

MG1655: 2702085..2701405
gbrowse_img.php?coord=2701405..2702085&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 2624875..2625555
gbrowse_img.php?coord=2624875..2625555&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 2702719..2702039
gbrowse_img.php?coord=2702039..2702719&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 2793850..2793170
gbrowse_img.php?coord=2793170..2793850&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 2587210..2587890
gbrowse_img.php?coord=2587210..2587890&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

edit table

Notes

Sequence Features

[back to top]


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

Feature typeLocationDescription
edit table

Notes

Alleles and Phenotypes

[back to top]


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

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

rnc::Tn5KAN

PMID:12519969

ASAP

At position 562 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20853

rnc::Tn5KAN

PMID:12519969

ASAP

At position 562 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20854

rncG44D

G44D

In rnc-105; loss of activity

seeded from UniProt:P0A7Y0

rnc-105

CGSC:6351


edit table

Notes

Genetic Resources

[back to top]


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

ResourceResource TypeSourceNotes/Reference

JW2551

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAACCCCATCGTAATTAATCG

Primer 2:CCTTCCAGCTCCAGTTTTTTCAA

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]

edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10857

EchoBASE (EcoliWiki Page)

EchoBASE:EB0850

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2567

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3091

EcoGene (EcoliWiki Page)

EcoGene:EG10857

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:RNC

CGSC (EcoliWiki Page)

CGSC:271

ASAP (EcoliWikiPage)

ASAP:ABE-0008448


edit table

Notes

Links

[back to top]



Product(s)

[back to top]



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]

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)
edit table

Notes

Function

[back to top]


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

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0005515

protein binding

PMID:15690043

IPI: Inferred from Physical Interaction

UniProtKB:P30850

F

Seeded from EcoCyc [7]

complete

GO:0016787

hydrolase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc [7]

complete

GO:0016075

rRNA catabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011907

P

Seeded from EcoCyc [7]

complete

GO:0006397

mRNA processing

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00104

P

Seeded from EcoCyc [7]

complete

GO:0006396

RNA processing

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000999

P

Seeded from EcoCyc [7]

complete

GO:0006364

rRNA processing

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00104

P

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [8]

complete

GO:0005622

intracellular

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001159
InterPro:IPR014720

C

Seeded from EcoCyc [7]

complete

GO:0004525

ribonuclease III activity

GO_REF:0000002
GO_REF:0000002
GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR000999
InterPro:IPR011907
EC:3.1.26.3
HAMAP:MF_00104

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0004518

nuclease activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc [7]

complete

GO:0004519

endonuclease activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0255

F

Seeded from EcoCyc [7]

complete

GO:0003725

double-stranded RNA binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001159

F

Seeded from EcoCyc [7]

complete

GO:0003723

RNA binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR000999
InterPro:IPR011907
InterPro:IPR014720
SP_KW:KW-0694

F

Seeded from EcoCyc [7]

complete

GO:0006401

RNA catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

edit table

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

Partner TypePartnerNotesReferencesEvidence

Protein

Subunits of RNase III

could be indirect


edit table

Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
edit table

Notes

Structure and Physical Properties

[back to top]


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

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)

edit table


Domains/Motifs/Modification Sites

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

TypeResiduesDescriptionNotesReferences
edit table


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

Structures
Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource typeSourceNotes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10857-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0A7Y0

PFAM (EcoliWiki Page)

PFAM:PF00636

RefSeq (EcoliWiki Page)

RefSeq:NP_417062


edit table

Notes

Links

[back to top]




Expression

[back to top]



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

[back to top]


See Help:Cellular levels

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


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

edit table
Figure courtesy of RegulonDB

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

[back to top]


gbrowse_img.php?coord=2702065..2702105&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

[back to top]


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

Allele NameMutationPhenotypeReference
edit table


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

TypeReferenceNotes

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

edit table


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

Resource NameResource TypeDescriptionSourceNotes
edit table

Notes

Accessions Related to rnc Expression

[back to top]


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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10857

EchoBASE (EcoliWiki Page)

EchoBASE:EB0850

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2567

EcoGene (EcoliWiki Page)

EcoGene:EG10857


edit table

Notes

Links

[back to top]



Evolution

[back to top]



Homologs in Other Organisms

[back to top]


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

OrganismHomologs (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

edit table


Do-It-Yourself Web Tools

Notes

Families

[back to top]


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

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00636


edit table

Notes

Links

[back to top]



References

[back to top]


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 3.4 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).
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ 8.0 8.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

[back to top]


Retrieved from "http://ecoliwiki.net/colipedia/index.php/rnc:On_One_Page"
Personal tools