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Standard Name	rihC
Gene Synonym(s)	ECK0031, b0030, JW0028, yaaF^[1], yaaF
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] , ECK0031, JW0028, yaaF, b0030
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rihC^[2]
Regulation/Activity
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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], yaaF
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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	0.59 minutes	MG1655: 27293..28207 <gbrowseImage> name=NC_000913:27293..28207 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 31365..32279 <gbrowseImage> name=NC_012967:31365..32279 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 27293..28207 <gbrowseImage> name=NC_012759:27293..28207 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 27293..28207 <gbrowseImage> name=NC_007779:27293..28207 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 27293..28207 <gbrowseImage> name=NC_010473:27293..28207 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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)	Reference	Availability	Comments
rihC(del) (Keio:JW0028)	deletion	deletion	PMID:16738554	Shigen CGSC8348^[5]
yaaF::Tn5KAN-I-SceI (FB20001)	Insertion at nt 349 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20001	does not contain pKD46
yaaF::Tn5KAN-I-SceI (FB20002)	Insertion at nt 349 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20002	contains pKD46
rihC743(del)::kan			PMID:16738554	CGSC:102716
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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
JW0028	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTTTACCTATCTTCCTCGA Primer 2:CCCGACGCCAGAGCCAGCACCTC
22B12	Kohara Phage	Genobase	PMID:3038334
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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11082	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11082	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001070	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944796	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1074	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000109	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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] , ECK0031, JW0028, yaaF, b0030
Product description	ribonucleoside hydrolase 3^[2]^[3] Ribonucleoside hydrolase^[4]
EC number (for enzymes)	3.2.2.-^[1]
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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				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0009226	nucleotide-sugar biosynthetic process				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0006144	purine base metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01432	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006206	pyrimidine base metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01432	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0326	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:0016798	hydrolase activity, acting on glycosyl bonds	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01432	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016798	hydrolase activity, acting on glycosyl bonds	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0326	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		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
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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 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.

Type	Residues	Description	Notes	References
Domain	2..304	PF01156 Inosine-uridine preferring nucleoside hydrolase		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=rihC 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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Resource type	Source	Notes/Reference
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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:16128024	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000109	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P22564	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11082	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11082	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944796	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944796	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001070	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1074	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	Reference(s)
Protein	E. coli K-12 MG1655	612	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	85	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	270	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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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

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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_000913:27273..27313 source=MG1655 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: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 Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (27153..27357) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:A1^[7]
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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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11082	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1074	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0030
EcoGene	EcoGene:EG11082	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001070	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000109	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	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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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)	PF01156 Inosine-uridine preferring nucleoside hydrolase
Superfamily (EcoliWiki Page)	SUPERFAMILY:53590
EcoCyc	EcoCyc:EG11082	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11082	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001070	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1074	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000109	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^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)
↑ ^2.0 ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rihC:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

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Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to rihC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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