RegulonDB

RegulonDB RegulonDB 11.1: Operon Form

tcyP operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	tcyP
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	tcyP
Gene(s):	tcyP Genome Browser M3D Gene expression COLOMBOS
Note(s):	tcyP expression is activated in sulfate-containing medium and repressed in cysteine-containing medium Chonoles Imlay KR,2015
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[1] Chonoles Imlay KR., et al., 2015
Promoter
Name:	tcyPp
+1:	1810882
Distance from start of the gene:	52
Sequence:	tggaataagcaattccatttgaatataagagccagctcacagttctgttaatcttgcgccAacactatgactgctacgcag
Evidence:	[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[1] Chonoles Imlay KR., et al., 2015 [2] Salgado H, et al., 2012

TF binding sites (TFBSs)

[CysB,+] Phrase

Type	Transcription factor	Function	Promoter	Binding Sites				Growth Conditions	Evidence	Confidence level (C: Confirmed, S: Strong, W: Weak)	Reference(s)
Type	Transcription factor	Function	Promoter	LeftPos	RightPos	Central Rel-Pos	Sequence	Growth Conditions	Evidence		Reference(s)
nd	CysB	activator	tcyPp	nd	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	W	[1]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
CysB	activator	tcyPp	nd	nd	nd	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[1]

RNA cis-regulatory element

Regulation, transcriptional elongation
Attenuator type:	Translational
Strand:	forward

	Structure type	Energy	LeftPos	RightPos	Sequence (RNA-strand)
	terminator	-6.4	1810887	1810907	cgccaacactATGACTGCTACGCAGTGATAgaaataataa

Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"

Evidence
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

Reference(s)
[1] Chonoles Imlay KR., Korshunov S., Imlay JA., 2015, Physiological Roles and Adverse Effects of the Two Cystine Importers of Escherichia coli., J Bacteriol 197(23):3629-44
[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] Chonoles Imlay KR., Korshunov S., Imlay JA., 2015, Physiological Roles and Adverse Effects of the Two Cystine Importers of Escherichia coli., J Bacteriol 197(23):3629-44

[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