RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

truC gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	truC
Synonym(s):	ECK2785, G7449, b2791, yqcB
Genome position(nucleotides):	2923002 <-- 2923784 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.02
External database links:

ASAP:	ABE-0009147
ECHOBASE:	EB2963
OU-MICROARRAY:	b2791
PortEco:	truC
STRING:	511145.b2791
COLOMBOS:	truC

Product

Name:

tRNA pseudouridine⁶⁵ synthase

Synonym(s):

TruC, YqcB

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

29.666

Isoelectric point:

7.102

Motif(s):

Type	Positions	Sequence
	11 -> 170	LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAGRLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYRGLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAH
	54 -> 54	D

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0106029 - tRNA pseudouridine synthase activity GO:0016853 - isomerase activity GO:0003723 - RNA binding GO:0009982 - pseudouridine synthase activity
	biological_process	GO:0006399 - tRNA metabolic process GO:0009451 - RNA modification GO:0001522 - pseudouridine synthesis GO:0031119 - tRNA pseudouridine synthesis GO:0008033 - tRNA processing

Note(s):

Note(s): ...[more].

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

PRODB:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

yqcC-truC-yqcA

Operon arrangement:

Transcription unit	Promoter

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	yqcAp5	2923050	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.756. P-value: 8.784e-5 Read more >	[ICWHO]	[1]
promoter	TSS_3089	2923556	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3090	2924137	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3091	2924349	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3092	2924385	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3093	2924391	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3094	2924394	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3095	2924415	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3096 (cluster)	2924424	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924423 to 2924424, where the highest frequency is at position 2922446. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3097	2924436	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3098 (cluster)	2924452	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924451 to 2924452, where the highest frequency is at position 2922474. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3099	2924464	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3100	2924466	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3101	2924468	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3102 (cluster)	2924473	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924472 to 2924473, where the highest frequency is at position 2922494. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3103 (cluster)	2924477	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924476 to 2924477, where the highest frequency is at position 2922498. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
promoter	TSS_3104	2924484	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3105	2924496	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3106	2924507	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3107	2924509	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_3108 (cluster)	2924522	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2924521 to 2924522, where the highest frequency is at position 2922544. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]

Evidence
[ICWHO] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

[2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

RegulonDB