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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	rnd
Gene Synonym(s)	ECK1802, b1804, JW1793^[1], JW1793
Product Desc.	RNase D, processes tRNA precursor^[2]^[3] Rnase D; processes tRNA precursors^[4]
Product Synonyms(s)	ribonuclease D^[1], B1804^[2]^[1], Rnd^[2]^[1] , ECK1802, JW1793, b1804
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
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	rnd
Mnemonic	RNase D
Synonyms	ECK1802, b1804, JW1793^[1], JW1793
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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	40.63 minutes	MG1655: 1886015..1884888 <gbrowseImage> name=NC_000913:1884888..1886015 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1866569..1865442 <gbrowseImage> name=NC_012967:1865442..1866569 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1776947..1778074 <gbrowseImage> name=NC_012759:1776947..1778074 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1889705..1888578 <gbrowseImage> name=NC_007779:1888578..1889705 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1976586..1975459 <gbrowseImage> name=NC_010473:1975459..1976586 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
Coding Start (SO:0000323)	MG1655	1884888	Edman degradation	PMID:3041371
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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
Δrnd (Keio:JW1793)	deletion	deletion	PMID:16738554	Shigen CGSC9502^[5]
rnd::Tn5KAN-2 (FB20454)	Insertion at nt 867 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20454	contains pKD46
rnd::Tn5KAN-2 (FB20455)	Insertion at nt 867 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20455	does not contain pKD46
Δrnd-729::kan			PMID:16738554	CGSC:102746
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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
JW1793	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATTACCAAATGATTACCAC Primer 2:CCtTGCGGATATTCCTGCAATAA
7F2	Kohara Phage	Genobase	PMID:3038334
6D1	Kohara Phage	Genobase	PMID:3038334
12B3	Kohara Phage	Genobase	PMID:3038334
zea-225::Tn10	Linked marker	CAG18465 = CGSC7388^[5]	est. P1 cotransduction: 59% ^[6] Synonyms:zdj-225::Tn10
eda-51::Tn10	Linked marker	CAG18486 = CGSC7392^[5]	est. P1 cotransduction: 13% ^[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:EG10858	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10858	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000849	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946328	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0851	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006003	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	Rnd
Synonyms	ribonuclease D^[1], B1804^[2]^[1], Rnd^[2]^[1] , ECK1802, JW1793, b1804
Product description	RNase D, processes tRNA precursor^[2]^[3] Rnase D; processes tRNA precursors^[4]
EC number (for enzymes)	3.1.26.3^[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:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002121	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002562	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012337	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:0004527	exonuclease activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0269	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004540	ribonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006292	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002121	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002562	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006292	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:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002562	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006292	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:0008408	3'-5' exonuclease activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002562	F	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:0033890	ribonuclease D activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.1.13.5	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	groL		PMID:16606699	Experiment(s):EBI-1140870
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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 MNYQMITTDD ALASLCEAVR AFPAIALDTE FVRTRTYYPQ LGLIQLFDGE HLALIDPLGI TDWSPLKAIL RDPSITKFLH AGSEDLEVFL NVFGELPQPL IDTQILAAFC GRPMSWGFAS MVEEYSGVTL DKSESRTDWL ARPLTERQCE YAAADVWYLL PITAKLMVET EASGWLPAAL DECRLMQMRR QEVVAPEDAW RDITNAWQLR TRQLACLQLL ADWRLRKARE RDLAVNFVVR EEHLWSVARY MPGSLGELDS LGLSGSEIRF HGKTLLALVE KAQTLPEDAL PQPMLNLMDM PGYRKAFKAI KSLITDVSET HKISAELLAS RRQINQLLNW HWKLKPQNNL PELISGWRGE LMAEALHNLL QEYPQ
Length	375
Mol. Wt	42.735 kDa
pI	5.1 (calculated)
Extinction coefficient	79,410 - 80,035 (calc based on 9 Y, 12 W, and 5 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	213..279	PF00570 HRDC domain	PMID:19920124
Domain	3..171	PF01612 3'-5' exonuclease	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=rnd 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:16129758	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946328	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006003	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P09155	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10858	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10858	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946328	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000849	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0851	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	Notes	Reference(s)
Protein	Ecoli K-12	5.04+/-0.059	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.020408163	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	785	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	89	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	304	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)
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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_000913:1885995..1886035 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:b1804 (EcoliWiki Page)	NCBI GEO profiles for rnd
microarray	GenExpDB:b1804 (EcoliWiki Page)	Summary of data for rnd 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 (1885940..1886092) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:D10^[7]
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Notes

Accessions Related to rnd Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10858	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0851	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1804
EcoGene	EcoGene:EG10858	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000849	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006003	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
Apis mellifera	ENSAPMP00000025523 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Arabidopsis thaliana	AT2G32415 (score: 1.000; bootstrap: 61%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000003354 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00026000 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00000796 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000024598 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000004852 (score: 1.000; bootstrap: 100%) ENSCINP00000018812 (score: 0.381)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0203581 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0038269 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA20243-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000004870 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000353563 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000025383 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000014003 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1355322 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000047115 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000014629 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YOR001W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC1F31 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000133183 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00028266001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000013853 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	RND	From SHIGELLACYC
E. coli O157	RND	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)	PF00570 HRDC domain
Pfam (EcoliWiki Page)	PF01612 3'-5' exonuclease
Superfamily (EcoliWiki Page)	SUPERFAMILY:47819
Superfamily (EcoliWiki Page)	SUPERFAMILY:47819
Superfamily (EcoliWiki Page)	SUPERFAMILY:53098
Panther (EcoliWiki Page)	PTHR12124:SF3
EcoCyc	EcoCyc:EG10858	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10858	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000849	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0851	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006003	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 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 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 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

rnd: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

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 rnd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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