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Expression|

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Standard Name	truC
Gene Synonym(s)	yqcB, ECK2785, b2791, JW2762^[1]^[2], JW2762
Product Desc.	tRNA pseudouridine 65 synthase^[2]^[3] tRNA U65 pseudouridine synthase; modification found in tRNA(Ile1)^[4]
Product Synonyms(s)	tRNA pseudouridine synthase^[1], B2791^[2]^[1], TruC^[2]^[1], YqcB^[2]^[1] , ECK2785, JW2762, yqcB, b2791
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yqcA^[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	truC
Mnemonic	tRNA uridine
Synonyms	yqcB, ECK2785, b2791, JW2762^[1]^[2], JW2762
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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	62.96 minutes	MG1655: 2921806..2921024 <gbrowseImage> name=NC_000913:2921024..2921806 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2811931..2812713 <gbrowseImage> name=NC_012967:2811931..2812713 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2808172..2808954 <gbrowseImage> name=NC_012759:2808172..2808954 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2922440..2921658 <gbrowseImage> name=NC_007779:2921658..2922440 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3015684..3014902 <gbrowseImage> name=NC_010473:3014902..3015684 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	AA change(s)	Phenotype: Description	Reference	Availability	Comments
truCD54T	D54T	Loss of activity			seeded from UniProt:P0AA41
ΔtruC789::kan			PMID:16738554	CGSC:106362
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
10B5	Kohara Phage	Genobase	PMID:3038334
8C5	Kohara Phage	Genobase	PMID:3038334
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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:G7449	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13171	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004012	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947242	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2963	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009147	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	TruC
Synonyms	tRNA pseudouridine synthase^[1], B2791^[2]^[1], TruC^[2]^[1], YqcB^[2]^[1] , ECK2785, JW2762, yqcB, b2791
Product description	tRNA pseudouridine 65 synthase^[2]^[3] tRNA U65 pseudouridine synthase; modification found in tRNA(Ile1)^[4]
EC number (for enzymes)	4.2.1.70^[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:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006145	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006399	tRNA metabolic process	PMID:11720289	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006224	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009451	RNA modification	PMID:11720289	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020103	F	Seeded from EcoCyc (v14.0)	complete
	GO:0031119	tRNA pseudouridine synthesis	PMID:11720289	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006145	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009982	pseudouridine synthase activity	PMID:11720289	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006224	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008033	tRNA processing	PMID:11720289	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0009982	pseudouridine synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020103	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
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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 MLEILYQDEW LVAVNKPSGW LVHRSWLDRD EKVVVMQTVR DQIGQHVFTA HRLDRPTSGV LLMGLSSEAG RLLAQQFEQH QIQKRYHAIV RGWLMEEAVL DYPLVEELDK IADKFAREDK GPQPAVTHYR GLATVEMPVA TGRYPTTRYG LVELEPKTGR KHQLRRHLAH LRHPIIGDSK HGDLRQNRSG AEHFGLQRLM LHASQLSLTH PFTGEPLTIH AGLDDTWMQA LSQFGWRGLL PENERVEFSA PSGQDGEISS
Length	260
Mol. Wt	29.665 kDa
pI	7.1 (calculated)
Extinction coefficient	41,940 (calc based on 6 Y, 6 W, and 0 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	10..170	PF00849 RNA pseudouridylate synthase		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=truC 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:16130698	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947242	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009147	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AA41	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7449	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13171	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947242	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004012	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2963	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	3.82E+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	553	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	57	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	142	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)
yqcA
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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_000913:2921786..2921826 source=MG1655 flip=1 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:b2791 (EcoliWiki Page)	NCBI GEO profiles for truC
microarray	GenExpDB:b2791 (EcoliWiki Page)	Summary of data for truC 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
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Notes

Accessions Related to truC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7449	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2963	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2791
EcoGene	EcoGene:EG13171	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004012	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009147	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
Arabidopsis thaliana	AT1G56345 (score: 1.000; bootstrap: 56%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00038743 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040801-238 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040801-252 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000007605 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YQCB	From SHIGELLACYC
E. coli O157	Z4107	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
Panther (EcoliWiki Page)	PTHR10436:SF39
Superfamily (EcoliWiki Page)	SUPERFAMILY:55120
Pfam (EcoliWiki Page)	PF00849 RNA pseudouridylate synthase
EcoCyc	EcoCyc:G7449	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13171	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004012	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2963	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009147	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 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 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.

truC: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 truC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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