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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	rph
Gene Synonym(s)	ECK3633, b3643, JW3618, orfE^[1]^[2]
Product Desc.	RNase PH^[2]^[3]; Component of RNase PH^[3]
Product Synonyms(s)	B3643^[2], Rph^[2], OrfE^[2] , ECK3633, JW3618, b3643
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rph-pyrE^[2]
Regulation/Activity
Quick Links
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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	rph
Mnemonic
Synonyms	ECK3633, b3643, JW3618, orfE^[1]^[2]
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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	82.2 minutes	MG1655: 3814572..3813886 <gbrowseImage> name=NC_000913:3813886..3814572 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3754905..3754189 <gbrowseImage> name=NC_012967:3754189..3754905 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3702183..3702899 <gbrowseImage> name=NC_012759:3702183..3702899 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3823866..3824552 <gbrowseImage> name=NC_007779:3823866..3824552 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
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</protect>

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	3813886	Edman degradation	PMID:1885537
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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: Description	Reference	Availability	Comments
Δrph (Keio:JW3618)	deletion	deletion		PMID:16738554	Shigen CGSC10659^[4]
rph::Tn5KAN-I-SceI (FB21360)	Insertion at nt 84 in Plus orientation			PMID:15262929	E. coli Genome Project:FB21360	contains pKD46
rph::Tn5KAN-I-SceI (FB21361)	Insertion at nt 84 in Plus orientation			PMID:15262929	E. coli Genome Project:FB21361	does not contain pKD46
rphGIESIVATQKAALAN224ESNPL		GIESIVATQKAALAN224ESNPL	(in strain: K12 / MG1655 / ATCC 47076 and K12 / W3110 / ATCC 27325 / DSM 5911)			Strain variation; seeded from UniProt:P03842
rph-1				PMID:8501045	CGSC:37923
Δrph-749::kan				PMID:16738554	CGSC:102766
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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
JW3618	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCGTCCAGCAGGCCGTAGCAA Primer 2:CCtAATGGATTCGATTCCCCTCG
2A6	Kohara Phage	Genobase	PMID:3038334
4D2	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[4]	est. P1 cotransduction: % ^[5] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[4]	est. P1 cotransduction: 62% ^[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:EG10863	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10863	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000854	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948156	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0856	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011909	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	Rph
Synonyms	B3643^[2], Rph^[2], OrfE^[2] , ECK3633, JW3618, b3643
Product description	RNase PH^[2]^[3]; Component of RNase PH^[3]
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:0000049	tRNA binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00564	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000049	tRNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002381	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000175	3'-5'-exoribonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001247	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000175	3'-5'-exoribonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015847	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001247	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015847	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004549	tRNA-specific ribonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002381	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006396	RNA processing	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001247	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006396	RNA processing	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015847	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00564	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002381	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0819	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009022	tRNA nucleotidyltransferase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00564	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009022	tRNA nucleotidyltransferase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.7.7.56	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016740	transferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0808	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016779	nucleotidyltransferase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0548	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 PH	could be indirect
Protein	dnaJ		PMID:15690043	Experiment(s):EBI-886413
Protein	dnaK		PMID:15690043	Experiment(s):EBI-886413
Protein	mreB		PMID:15690043	Experiment(s):EBI-886413
Protein	narG		PMID:15690043	Experiment(s):EBI-886413
Protein	pstB		PMID:15690043	Experiment(s):EBI-886413
Protein	recA		PMID:15690043	Experiment(s):EBI-886413
Protein	hldD		PMID:15690043	Experiment(s):EBI-886413
Protein	tufA		PMID:15690043	Experiment(s):EBI-886413
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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 MRPAGRSNNQ VRPVTLTRNY TKHAEGSVLV EFGDTKVLCT ASIEEGVPRF LKGQGQGWIT AEYGMLPRST HTRNAREAAK GKQGGRTMEI QRLIARALRA AVDLKALGEF TITLDCDVLQ ADGGTRTASI TGACVALVDA LQKLVENGKL KTNPMKGMVA AVSVGIVNGE AVCDLEYVED SAAETDMNVV MTEDGRIIEV QGTAEGEPFT HEELLILLAL ARGESNPL
Length	228
Mol. Wt	24.424 kDa
pI	5.3 (calculated)
Extinction coefficient	9,970 - 10,470 (calc based on 3 Y, 1 W, and 4 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	References
Domain	10..142	PF01138 3' exoribonuclease family, domain 1	PMID:19920124
Domain	157..224	PF03725 3' exoribonuclease family, domain 2	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=rph taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

</protect>

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:157783152	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948156	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011909	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P03842	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10863	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10863	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948156	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000854	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0856	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 MC4100	8.35E+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	E. coli K-12 MG1655	5342	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	1017	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	2005	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)
rph-pyrE
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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_000913:3814552..3814592 source=MG1655 flip=1 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:b3643 (EcoliWiki Page)	NCBI GEO profiles for rph
microarray	GenExpDB:b3643 (EcoliWiki Page)	Summary of data for rph 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 (3814079..3814331) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:G9^[6]
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Notes

Accessions Related to rph Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10863	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0856	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3643
EcoGene	EcoGene:EG10863	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000854	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011909	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	ENSANGP00000009222 (score: 1.000; bootstrap: 100%) ENSANGP00000017010 (score: 1.000; bootstrap: 100%) ENSANGP00000026025 (score: 0.101)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000019685 (score: 1.000; bootstrap: 100%) ENSAPMP00000000301 (score: 0.065)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G61620 (score: 1.000; bootstrap: 100%) AT4G27490 (score: 0.061)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000019451 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00025010 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00007201 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000002193 (score: 1.000; bootstrap: 100%) ENSCAFP00000007456 (score: 0.054)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1702 (score: 1.000; bootstrap: 55%) ZDB-CDNA-040425-2642 (score: 1.000; bootstrap: 55%) ZDB-CDNA-050522-362 (score: 0.134) ZDB-CDNA-050703-13 (score: 0.134) ZDB-GENE-050522-362 (score: 0.134)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0183823 (score: 1.000; bootstrap: 100%) DDB0185805 (score: 0.094) DDB0216807 (score: 0.086)	From Inparanoid:20070104
Homo sapiens	ENSP00000315476 (score: 1.000; bootstrap: 100%) ENSP00000288063 (score: 0.112) ENSP00000221233 (score: 0.067)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000009386 (score: 1.000; bootstrap: 100%) ENSMMUP00000018844 (score: 0.059)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000013076 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1923576 (score: 1.000; bootstrap: 100%) MGI:1919794 (score: 0.110) MGI:107889 (score: 0.072)	From Inparanoid:20070104
Oryza gramene	Q6K293 (score: 1.000; bootstrap: 100%) Q75LC8 (score: 0.080) Q69UI6 (score: 0.080)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000035368 (score: 1.000; bootstrap: 100%) ENSPTRP00000014169 (score: 0.112)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000016464 (score: 1.000; bootstrap: 100%) ENSRNOP00000025179 (score: 0.118) ENSRNOP00000028026 (score: 0.061)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000015321 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	RPH	From SHIGELLACYC
E. coli O157	RPH	From ECOO157CYC
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Do-It-Yourself Web Tools

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)	PF03725 3' exoribonuclease family, domain 2
Pfam (EcoliWiki Page)	PF01138 3' exoribonuclease family, domain 1
Superfamily (EcoliWiki Page)	SUPERFAMILY:54211
Superfamily (EcoliWiki Page)	SUPERFAMILY:55666
EcoCyc	EcoCyc:EG10863	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10863	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000854	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0856	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011909	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.

↑ ^1.0 ^1.1 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rph:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

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 rph Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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