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rihC:On One Page

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Standard Name

rihC

Gene Synonym(s)

ECK0031, b0030, JW0028, yaaF[1]

Product Desc.

ribonucleoside hydrolase 3[2][3]

Ribonucleoside hydrolase[4]

Product Synonyms(s)

ribonucleoside hydrolase 3[1], YaaF[2][1], RihC[2][1], B0030[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rihC[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(rihC)    Textpresso(rihC)

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Notes

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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

rihC

Mnemonic

Ribonucleoside hydrolase

Synonyms

ECK0031, b0030, JW0028, yaaF[1]

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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.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

0.59 minutes 

MG1655: 27293..28207
gbrowse_img.php?coord=27293..28207&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 31365..32279
gbrowse_img.php?coord=31365..32279&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 27293..28207
gbrowse_img.php?coord=27293..28207&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 27293..28207
gbrowse_img.php?coord=27293..28207&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 27293..28207
gbrowse_img.php?coord=27293..28207&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

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

ΔrihC (Keio:JW0028)

deletion

deletion

PMID:16738554

Shigen
CGSC8348[5]

yaaF::Tn5KAN

PMID:12519969

ASAP

At position 349 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20001

yaaF::Tn5KAN

PMID:12519969

ASAP

At position 349 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB20002

ΔrihC743::kan

PMID:16738554

CGSC:102716


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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW0028

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGTTTACCTATCTTCCTCGA

Primer 2:CCCGACGCCAGAGCCAGCACCTC

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[5]

est. P1 cotransduction: 35% [6]
Synonyms:thr-34::Tn10

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 84% [6]
Synonyms:car-96::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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11082

EchoBASE (EcoliWiki Page)

EchoBASE:EB1074

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0030

EcoGene (EcoliWiki Page)

EcoGene:EG11082

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YAAF

ASAP (EcoliWikiPage)

ASAP:ABE-0000109


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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

RihC

Synonyms

ribonucleoside hydrolase 3[1], YaaF[2][1], RihC[2][1], B0030[2][1]

Product description

ribonucleoside hydrolase 3[2][3]

Ribonucleoside hydrolase[4]

EC number (for enzymes)
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Notes

Function

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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:0016798

hydrolase activity, acting on glycosyl bonds

GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326
HAMAP:MF_01432

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0016787

hydrolase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc [8]

complete

GO:0008152

metabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0326

P

Seeded from EcoCyc [8]

complete

GO:0006206

pyrimidine base metabolic process

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01432

P

Seeded from EcoCyc [8]

complete

GO:0006144

purine base metabolic process

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01432

P

Seeded from EcoCyc [8]

complete

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

required fields missing

GO:0009226

nucleotide-sugar biosynthetic process

P

Seeded from Riley et al 2006 [1].

required fields missing

GO:0015949

nucleobase, nucleoside and nucleotide interconversion

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence
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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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

Sequence

at EcoCyc 

MRLPIFLDTD PGIDDAVAIA AAIFAPELDL QLMTTVAGNV SVEKTTRNAL QLLHFWNAEI
PLAQGAAVPL VRAPRDAASV HGESGMAGYD FVEHNRKPLG IPAFLAIRDA LMRAPEPVTL
VAIGPLTNIA LLLSQCPECK PYIRRLVIMG GSAGRGNCTP NAEFNIAADP EAAACVFRSG
IEIVMCGLDV TNQAILTPDY LSTLPQLNRT GKMLHALFSH YRSGSMQSGL RMHDLCAIAW
LVRPDLFTLK PCFVAVETQG EFTSGTTVVD IDGCLGKPAN VQVALDLDVK GFQQWVAEVL ALAS
Length

304

Mol. Wt

32.56 kDa

pI

5.2 (calculated)

Extinction coefficient

22,460 - 23,460 (calc based on 4 Y, 3 W, and 8 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.

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

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11082-MONOMER

SwissModel (EcoliWiki Page)

SwissModel:P22564

UniProt (EcoliWiki Page)

UniProt:P22564

PFAM (EcoliWiki Page)

PFAM:PF01156

RefSeq (EcoliWiki Page)

RefSeq:NP_414571


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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

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

Transcription and Transcriptional Regulation

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

Transcription unit(s)

rihC

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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

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gbrowse_img.php?coord=27273..27313&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&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

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

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

TypeReferenceNotes

microarray

GEO Profiles:b0030 (EcoliWiki Page)

NCBI GEO profiles for rihC

microarray

GenExpDB:b0030 (EcoliWiki Page)

Summary of data for rihC 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 NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (27153..27357) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ01; Well:A1[9]

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Notes

Accessions Related to rihC Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11082

EchoBASE (EcoliWiki Page)

EchoBASE:EB1074

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0030

EcoGene (EcoliWiki Page)

EcoGene:EG11082


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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.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000012099 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000014129 (score: 1.000; bootstrap: 100%)
  • ENSANGP00000013256 (score: 0.206)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000034813 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G05620 (score: 1.000; bootstrap: 99%)
  • AT2G36310 (score: 0.300)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00025632 (score: 1.000; bootstrap: 100%)
  • WBGene00041901 (score: 0.151)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00017436 (score: 1.000; bootstrap: 100%)
  • WBGene00012834 (score: 0.181)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000000218 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-041010-52 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-041010-52 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0231227 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0030510 (score: 1.000; bootstrap: 100%)
  • FBgn0030511 (score: 0.198)
  • FBgn0032436 (score: 0.191)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA11456-PA (score: 1.000; bootstrap: 100%)
  • GA10803-PA (score: 0.222)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000001284 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q84MH2 (score: 1.000; bootstrap: 99%)
  • Q75GR9 (score: 1.000; bootstrap: 99%)
  • Q652Q8 (score: 1.000; bootstrap: 99%)
  • Q75GR8 (score: 0.671)
  • Q6ZJ05 (score: 0.668)
  • Q6PPF8 (score: 0.637)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDR400W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000131414 (score: 1.000; bootstrap: 100%)
  • NEWSINFRUP00000163815 (score: 0.541)
  • NEWSINFRUP00000128742 (score: 0.331)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00025772001 (score: 1.000; bootstrap: 100%)
  • GSTENP00027122001 (score: 0.181)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000032489 (score: 1.000; bootstrap: 96%)

From Inparanoid:20070104

Shigella flexneri

YAAF

From SHIGELLACYC

E. coli O157

YAAF

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF01156


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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 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 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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 5.2 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. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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