RegulonDB

RegulonDB RegulonDB 11.1: Operon Form

metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp operon and associated TUs in Escherichia coli K-12 genome

Operon
Name:	metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp
This page displays every known transcription unit of this operon and their known regulation.

Transcription unit

Name:	pnp
Gene(s):	pnp Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[1] Regnier P., et al., 1986
Promoter
Name:	pnpp
+1:	3311326
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	158
Sequence:	gagtggccccttttttcaagctgacggcagcaattcactggaaactaatgtattgttgctAtgaatgatcttccgttgcag -35 -10 +1
Note(s):	The initiation efficiency at the pnp promoter is poor due to its poor homology to the consensus sequence in the -35 region. Regnier P,1986.
Evidence:	[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[2] Huerta AM., et al., 2003 [1] Regnier P., et al., 1986
Terminator(s)
Type:	rho-independent
Sequence:	cccggttaaaAGCCCCCCGCCGCAGCGGAGGGCaaatggcaac
Reference(s):	[3] Regnier P., et al., 1987

Transcription unit

Name:	rpsO
Gene(s):	rpsO Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[1] Regnier P., et al., 1986
Promoter
Name:	rpsOp
+1:	3311786
Distance from start of the gene:	102
Sequence:	aatacccggcgtaatgttaaccgtcttgcgataacaggtcgctacgagtagaatactgccGcttaacgtcgcgtaaattgt
Evidence:	[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[1] Regnier P., et al., 1986 [4] Salgado H, et al., 2012
Terminator(s)
Type:	rho-independent
Sequence:	gtcagcttgaAAAAAGGGGCCACTCAGGCCCCCTTTTctgaaactcg
Reference(s):	[1] Regnier P., et al., 1986

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	ppGpp	inhibition	rpsOp	nd		[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s):	[5] Traxler MF., et al., 2008

Transcription unit

Name:	rpsO-pnp
Gene(s):	pnp, rpsO Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s):	[1] Regnier P., et al., 1986
Promoter
Name:	rpsOp
+1:	3311786
Distance from start of the gene:	102
Sequence:	aatacccggcgtaatgttaaccgtcttgcgataacaggtcgctacgagtagaatactgccGcttaacgtcgcgtaaattgt
Evidence:	[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[1] Regnier P., et al., 1986 [4] Salgado H, et al., 2012
Terminator(s)
Type:	rho-independent
Sequence:	cccggttaaaAGCCCCCCGCCGCAGCGGAGGGCaaatggcaac
Reference(s):	[3] Regnier P., et al., 1987

Allosteric regulation of RNA-polymerase

	Regulator	Function	Promoter target of RNApol	Growth Conditions	Note	Evidence	Reference
	ppGpp	inhibition	rpsOp	nd		[EXP-IEP-GENE-EXPRESSION-ANALYSIS]	[5]

Evidence:	[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s):	[5] Traxler MF., et al., 2008

Transcription unit

Name:	infB
Gene(s):	infB Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[6] Brandi A., et al., 2019
Promoter
Name:	infBp
+1:	3316027
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	13
Sequence:	actgattatggctgcccgtaatatttgctggttcggtgacgaagcgtaataaactgtagcAggaaggaacagcatgacaga -35 -10 +1
Note(s):	The activity of the infBp promoter is increased under cold shock Brandi A,2019. This transcription initiation of this promoter was mapped in the strain MRE600; however, the full size of the transcript unit of infB was determined in strains derived from K-12. On the other hand, the other promoters transcribing infBp mapped in the same nucleotide in a strain derived from K-12 as in MRE600 Brandi A,2019.
Evidence:	[COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Brandi A., et al., 2019
Terminator(s)
Type:	rho-independent
Sequence:	ccataataaaTTCTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATTTCAGGTGGAagggctgttc
Reference(s):	[7] Feng CQ., et al., 2019 [8] Lesnik EA., et al., 2001

Transcription unit

Name:	nusA-infB
Gene(s):	infB, nusA Genome Browser M3D Gene expression COLOMBOS
Note(s):	This transcription unit was mapped in the strain MRE600; however, the full size of the transcript of the other transcription unit containing the infB gene was determined in a strain derived from K-12, suggesting that the transcription is similar in both strains Brandi A,2019.
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[6] Brandi A., et al., 2019
Promoter
Name:	nusAp
+1:	3317602
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	76
Sequence:	cgttatcaaagcggtagacggtgaaatgatcacagttaccgtcgaaggtaaagatgaagtGttcgcgctgagtaatatcca -35 -10 +1
Evidence:	[COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Brandi A., et al., 2019
Terminator(s)
Type:	rho-independent
Sequence:	ccataataaaTTCTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATTTCAGGTGGAagggctgttc
Reference(s):	[7] Feng CQ., et al., 2019 [8] Lesnik EA., et al., 2001

Transcription unit

Name:	rimP-nusA-infB
Synonym(s):	yhbC-nusA-infB
Gene(s):	infB, nusA, rimP Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[9] Regnier P., et al., 1990 [10] Regnier P., et al., 1989
Promoter
Name:	rimPp
+1:	3318175
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	169
Sequence:	ttcaaatccggcccccgcaaccactttcccttagagtcctttttcaaatatactgtgaagActtcggccttcgtagtggga -35 -10 +1
Note(s):	The activity of the rimPp promoter is increased under cold shock Brandi A,2019. Zaslaver et al. demonstrated in 2006, by means of a library of fluorescent transcription fusions, that this promoter can be transcribed in vitro Zaslaver A,2006.
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP]
Reference(s):	[6] Brandi A., et al., 2019 [2] Huerta AM., et al., 2003 [11] Maciag A., et al., 2011 [10] Regnier P., et al., 1989 [12] Zaslaver A., et al., 2006
Terminator(s)
Type:	rho-independent
Sequence:	ccataataaaTTCTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATTTCAGGTGGAagggctgttc
Reference(s):	[7] Feng CQ., et al., 2019 [8] Lesnik EA., et al., 2001

Transcription unit

Name:	metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
Gene(s):	pnp, rpsO, truB, rbfA, infB, nusA, rimP, metY Genome Browser M3D Gene expression COLOMBOS
Note(s):	Sometimes the transcription initiated upstream of the metY gene reads through into the rpsO-pnp genes Sands JF,1988.
Evidence:	[EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s):	[13] Nakamura Y., et al., 1985 [14] Sands JF., et al., 1988
Promoter
Name:	metYp1
+1:	3318297
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	8
Sequence:	cggtacaccaaatcccagcagtatttgcattttttacccaaaacgagtagaatttgccacGtttcaggcgcggggtggagc -35 -10 +1
Note(s):	Of all the promoters transcribing to the nusA-infB operon, the metYp1 promoter is the most cold stress-responsive promoter Brandi A,2019.
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Brandi A., et al., 2019 [2] Huerta AM., et al., 2003 [15] Ishii S., et al., 1984 [16] Nagase T., et al., 1988
Terminator(s)
Type:	rho-independent
Sequence:	cccggttaaaAGCCCCCCGCCGCAGCGGAGGGCaaatggcaac
Reference(s):	[3] Regnier P., et al., 1987

TF binding sites (TFBSs)

[Fis,+] 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)
proximal	Fis	activator	metYp1	3318365	3318379	-75.0	actataatgcCTGCAGATTTTACGTcccgtctcgg	nd	[COMP-HINF], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	nd	[17]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
Fis	activator	metYp1	3318365	3318379	-75.0	actataatgcCTGCAGATTTTACGTcccgtctcgg	nd	[17]

Transcription unit

Name:	metY-yhbC-nusA-infB
Synonym(s):	metY
Gene(s):	infB, nusA, rimP, metY Genome Browser M3D Gene expression COLOMBOS
Note(s):	This transcription unit is processed by RNase III in a hairpin structure downstream of the metY gene Regnier P,1989.
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[10] Regnier P., et al., 1989
Promoter
Name:	metYp1
+1:	3318297
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	8
Sequence:	cggtacaccaaatcccagcagtatttgcattttttacccaaaacgagtagaatttgccacGtttcaggcgcggggtggagc -35 -10 +1
Note(s):	Of all the promoters transcribing to the nusA-infB operon, the metYp1 promoter is the most cold stress-responsive promoter Brandi A,2019.
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Brandi A., et al., 2019 [2] Huerta AM., et al., 2003 [15] Ishii S., et al., 1984 [16] Nagase T., et al., 1988
Terminator(s)
Type:	rho-independent
Sequence:	ccataataaaTTCTCCTGACAAAAAAGGGGCTGTTAGCCCCTTTTTAAAATTAATTTCAGGTGGAagggctgttc
Reference(s):	[7] Feng CQ., et al., 2019 [8] Lesnik EA., et al., 2001

TF binding sites (TFBSs)

[Fis,+] 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)
proximal	Fis	activator	metYp1	3318365	3318379	-75.0	actataatgcCTGCAGATTTTACGTcccgtctcgg	nd	[COMP-HINF], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	nd	[17]

Transcription factor	Function	Promoter	Binding Sites	Evidence (Confirmed, Strong, Weak)	Reference(s)
Fis	activator	metYp1	3318365	3318379	-75.0	actataatgcCTGCAGATTTTACGTcccgtctcgg	nd	[17]

Transcription unit

Name:	metY
Gene(s):	metY Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[15] Ishii S., et al., 1984 [16] Nagase T., et al., 1988
Promoter
Name:	metYp1
+1:	3318297
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	8
Sequence:	cggtacaccaaatcccagcagtatttgcattttttacccaaaacgagtagaatttgccacGtttcaggcgcggggtggagc -35 -10 +1
Note(s):	Of all the promoters transcribing to the nusA-infB operon, the metYp1 promoter is the most cold stress-responsive promoter Brandi A,2019.
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s):	[6] Brandi A., et al., 2019 [2] Huerta AM., et al., 2003 [15] Ishii S., et al., 1984 [16] Nagase T., et al., 1988
Terminator(s)
Type:	rho-independent
Sequence:	taacaaaaaaCCCCGATAAATCGGGGctttatataa
Reference(s):	[15] Ishii S., et al., 1984 [18] Peters JM., et al., 2009 [19] Zuker M. 2003
Type:	rho-independent
Sequence:	cataaaaaaaGGGCCTAAAGCCCagttattctg
Reference(s):	[15] Ishii S., et al., 1984

TF binding sites (TFBSs)

[Fis,+] 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)
proximal	Fis	activator	metYp1	3318365	3318379	-75.0	actataatgcCTGCAGATTTTACGTcccgtctcgg	nd	[COMP-HINF], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS]	nd	[17]

Transcription unit

Name:	metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
Gene(s):	pnp, rpsO, truB, rbfA, infB, nusA, rimP, metY Genome Browser M3D Gene expression COLOMBOS
Note(s):	Sometimes the transcription initiated upstream of the metY gene reads through into the rpsO-pnp genes Sands JF,1988. It has been sugested that a DNA loop is formed when ArgR binds to the three Arg boxes. The binding of each of two regulators (CRP and ArgR) to the regulatory region of metY interferes with the binding of the other, but ArgR binding overrides CRP binding. ArgR repress the metY operon only when CRP is present.
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IMP-POLAR-MUTATION] Polar mutation
Reference(s):	[13] Nakamura Y., et al., 1985 [14] Sands JF., et al., 1988
Promoter
Name:	metYp2
+1:	3318375
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	86
Sequence:	cattcacatgattagcaataaacgttgacaaaatgtggcgtggatcactataatgcctgcAgattttacgtcccgtctcgg -35 -10 +1
Note(s):	The activity of the metYp2 promoter is increased under cold shock Brandi A,2019.
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[6] Brandi A., et al., 2019 [20] Granston AE., et al., 1990 [2] Huerta AM., et al., 2003 [4] Salgado H, et al., 2012
Terminator(s)
Type:	rho-independent
Sequence:	cccggttaaaAGCCCCCCGCCGCAGCGGAGGGCaaatggcaac
Reference(s):	[3] Regnier P., et al., 1987

TF binding sites (TFBSs)

[ArgR,-] 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)
proximal	ArgR-L-arginine	repressor	metYp2	3318428	3318445	-61.5	atgaaagtgaACTGGATATTCATTCACAtgattagcaa	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[21], [22]
remote	ArgR-L-arginine	repressor	metYp2	3318547	3318564	-180.5	atgcaaaataAATGAGTTTTCATTTAATcatcttttat	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[21], [22]
remote	ArgR-L-arginine	repressor	metYp2	3318568	3318585	-201.5	ttccgctctcACTGAATTTTTATGCAAAataaatgagt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[21], [22]

[CRP,-] 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)
proximal	CRP-cyclic-AMP	repressor	metYp2	3318384	3318405	-19.5	aacgttgacaAAATGTGGCGTGGATCACTATAatgcctgcag	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[22]

Transcription unit

Name:	metY
Gene(s):	metY Genome Browser M3D Gene expression COLOMBOS
Evidence:	[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s):	[15] Ishii S., et al., 1984
Promoter
Name:	metYp2
+1:	3318375
Sigma Factor:	Sigma70 Sigmulon
Distance from start of the gene:	86
Sequence:	cattcacatgattagcaataaacgttgacaaaatgtggcgtggatcactataatgcctgcAgattttacgtcccgtctcgg -35 -10 +1
Note(s):	The activity of the metYp2 promoter is increased under cold shock Brandi A,2019.
Evidence:	[COMP-AINF] [COMP-HINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR]
Reference(s):	[6] Brandi A., et al., 2019 [20] Granston AE., et al., 1990 [2] Huerta AM., et al., 2003 [4] Salgado H, et al., 2012
Terminator(s)
Type:	rho-independent
Sequence:	taacaaaaaaCCCCGATAAATCGGGGctttatataa
Reference(s):	[15] Ishii S., et al., 1984 [18] Peters JM., et al., 2009 [19] Zuker M. 2003
Type:	rho-independent
Sequence:	cataaaaaaaGGGCCTAAAGCCCagttattctg
Reference(s):	[15] Ishii S., et al., 1984

TF binding sites (TFBSs)

[ArgR,-] 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)
proximal	ArgR-L-arginine	repressor	metYp2	3318428	3318445	-61.5	atgaaagtgaACTGGATATTCATTCACAtgattagcaa	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[21], [22]
remote	ArgR-L-arginine	repressor	metYp2	3318547	3318564	-180.5	atgcaaaataAATGAGTTTTCATTTAATcatcttttat	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[21], [22]
remote	ArgR-L-arginine	repressor	metYp2	3318568	3318585	-201.5	ttccgctctcACTGAATTTTTATGCAAAataaatgagt	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]	W	[21], [22]

[CRP,-] 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)
proximal	CRP-cyclic-AMP	repressor	metYp2	3318384	3318405	-19.5	aacgttgacaAAATGTGGCGTGGATCACTATAatgcctgcag	nd	[EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION]	C	[22]

RNA cis-regulatory element

Regulation, transcriptional elongation
Attenuator type:	Transcriptional
Strand:	reverse

Structure type	Energy	LeftPos	RightPos	Sequence (RNA-strand)
terminator	-11.9	3313193	3313217	taattttaaaAAGGGGCTAACAGCCCCTTTTTTGtcaggagaat
terminator	-14.6	3311370	3311394	tttcagaaaaGGGGGCCTGAGTGGCCCCTTTTTTcaagctgacg
terminator	-12.9	3318063	3318090	cagttatataAAGCCCCGATTTATCGGGGTTTTTTGTtatctgacta
anti-terminator	-8.4	3313210	3313245	caacgtgaacAGCCCTTCCACCTGAAATTAATTTTAAAAAGGGGCtaacagcccc
anti-terminator	-11.7	3311392	3311433	tcatcgagcgCCTGGGTCTGCGTCGCTAATTCTTGCGAGTTTCAGAAAAGGgggcctgagt
anti-terminator	-3.3	3318085	3318105	tgcggttataGGGTTCAGTTATATAAAGCCccgatttatc
anti-anti-terminator	-23.2	3313243	3313303	cgtttacgctGCATCCGGCATGGATTGCCTGATGTGACGCTGGCGCGTCTTATCAGGTCAACGTGAACAGcccttccacc
anti-anti-terminator	-16.8	3311417	3311460	gtaaagacgtAGCACGTTACACCCAGCTCATCGAGCGCCTGGGTCTGCGTCGCtaattcttgc
anti-anti-terminator	-12.6	3318098	3318139	aaaaatccttCTGGAAAGTGCTCCAGACCGCAGTTGCGGTTATAGGGTTCAgttatataaa

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"

REGULATION, RNA cis-regulatory element:
Rfam type:	Cis-reg; leader
Strand:	reverse

	Description	Rfam score	Left Pos	Right Pos	Sequence (RNA-strand)
	Ribosomal S15 leader	115.6	3311628	3311742	uaacguacacUGGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCAaacgacaccg

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

Evidence
[COMP-AINF] Inferred computationally without human oversight
[COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[COMP-HINF] Inferred by a human based on computational evidence
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping
[EXP-IEP] Inferred from expression pattern
[EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
[COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences
[COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.
[EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IMP-SITE-MUTATION] Site mutation

Reference(s)
[1] Regnier P., Portier C., 1986, Initiation, attenuation and RNase III processing of transcripts from the Escherichia coli operon encoding ribosomal protein S15 and polynucleotide phosphorylase., J Mol Biol 187(1):23-32
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RegulonDB