RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: ompF
Synonym(s): OP00066
Gene(s): ompF   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was proved in an experiment with increasing concentrations of the antibiotic tetracycline that the ompC gene is induced in low concentrations (1.5 and 4 mg/L), but not in high ones (10 mg/L) Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007 This result might be attributed to the constant increase during the experiment of micF gene expression, whose sRNA product negatively regulates the expression of the ompF gene Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007.
MarA and Rob independently regulate expression of the outer membrane porin F gene, ompF, in response to salicylate, activating micF gene expression in response to salicylate Chubiz LM, Rao CV,2011. In addition, MarA can also repress OmpF expression through a MicF-independent pathway Chubiz LM, Rao CV,2011. On the other hand, reduction in ompC expression in a tolC mutant was due primarily to Rob Chubiz LM, Rao CV,2011.
The expression of the gene ompF is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
Under NlpE outer membrane lipoprotein overexpression, the transcription of the ompF gene is decreased by CpxR Raivio TL,2013
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ompF . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Reference(s): [1] Mizuno T., et al., 1983
Promoter
Name: ompFp
+1: 987092
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 110
Sequence: ctttatctttgtagcactttcacggtagcgaaacgttagtttgaatggaaagatgcctgcAgacacataaagacaccaaac
                               -35                    -10   +1                   
Note(s): Porin regulation by the CpxA-CpxR system and by the EnvZ-OmpR system converges at the porin promoters Batchelor E,2005.
The OmpR transcriptional factor cooperatively binds to the sites of the upstream regions from the ompFp promoter in a discontinuous galloping manner, as described by Yoshida T,2006
554 promoter regions from Escherichia coli were aligned in order to analyze their sequence similarities. Mitchell et al. (2003) Mitchell JE,2003 focused on conservation, patterns, similarities, and differences between promoters with or without an extended -10 5'-TG-3' element and other conserved elements. They experimentally showed that, for several naturally occurring extended -10 promoters, the 5'-TRTG-3' motif is an important determinant for promoter activity. Eleven promoters were selected for further experimental study. Of those, the seven most active (aroF > ompF > envA > purFp1 > purEF > purMN > gyrA) were investigated for the contribution of the extended -10 motif by changing the 5'-TG-3' motif. Promoters with poor matches to the -10 and -35 consensus hexamers are more dependent on the 5'-TG-3' motif, and this plays a similar role on different promoters. The dinucleotide at -17 and -16 in aroFp results in similar patterns of activity, suggesting that these bases play a similar role on different promoters Mitchell JE,2003.
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Inokuchi K., et al., 1984
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gattgctctgGAAGGTATAAAAAAAACAGGACCAAAGTCCTGTTTTTTCGGCATTTAACAAAGAGgtgtgctatt
Reference(s): [12] Feng CQ., et al., 2019
[13] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator ompFp 987134 987155 -52.5 tttgaaaccaAATCTTTATCTTTGTAGCACTTtcacggtagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [21]
proximal CRP-cyclic-AMP activator ompFp 987174 987195 -92.5 aagttccttaAATTTTACTTTTGGTTACATATtttttctttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [21]
remote CRP-cyclic-AMP activator ompFp 987203 987224 -121.5 gtctctatggAAATATGACGGTGTTCACAAAGttccttaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [21]
[CpxR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-phosphorylated repressor ompFp 987153 987169 -68.5 acatatttttTCTTTTTGAAACCAAATctttatcttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14], [15]
remote CpxR-phosphorylated repressor ompFp 987184 987185 -93.0 aattttacttTtggttacata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14], [15]
remote CpxR-phosphorylated repressor ompFp 987464 987465 -373.0 cctgttacggAatattacatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14], [15]
remote CpxR-phosphorylated repressor ompFp 987514 987530 -429.5 ttttctgtcaAGTTATCTGTTTGTTAAgtcaagcaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14], [15]
[EnvY,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd EnvY activator ompFp nd nd nd nd nd [EXP-IMP] W [33]
[Fur,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ activator ompFp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [21]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator ompFp 987194 987206 -108.0 cggtgttcacAAAGTTCCTTAAAttttactttt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
[IHF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF repressor ompFp 987148 987160 -62.0 ttctttttgaAACCAAATCTTTAtctttgtagc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
remote IHF repressor ompFp 987262 987274 -176.0 aatataaggaAATCATATAAATAgattaaaatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
[OmpR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OmpR-phosphorylated activator ompFp 987133 987152 -50.5 gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [16], [18], [19], [20], [23], [24], [25], [26], [27], [28], [29], [30]
proximal OmpR-phosphorylated activator ompFp 987153 987172 -70.5 gttacatattTTTTCTTTTTGAAACCAAATctttatcttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [17], [20], [23], [24], [25], [26], [27], [28], [29], [30], [31]
proximal OmpR-phosphorylated activator ompFp 987173 987192 -90.5 ttccttaaatTTTACTTTTGGTTACATATTttttcttttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [20], [23], [24], [25], [26], [27], [28], [29]
[OmpR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OmpR-phosphorylated repressor ompFp 987133 987152 -50.5 gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [16], [18], [19], [20], [23], [24], [25], [26], [27], [28], [29], [30]
proximal OmpR-phosphorylated repressor ompFp 987153 987172 -70.5 gttacatattTTTTCTTTTTGAAACCAAATctttatcttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [17], [20], [23], [24], [25], [26], [27], [28], [29], [30], [31]
remote OmpR-phosphorylated repressor ompFp 987453 987472 -370.5 cgatcatcctGTTACGGAATATTACATTGCaacatttacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [16], [17], [18], [19], [20]
[PhoB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd PhoB-phosphorylated activator ompFp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [32]
[RstA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-phosphorylated repressor ompFp 987176 987192 -92.0 ttccttaaatTTTACTTTTGGTTACATattttttctt nd [AS-NAS], [AS-NAS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [22]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA RybB ompF repressor 987018 987042 GCCACUGCCGUCAAUAAGUUCUGUC nd [EXP-IEP], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [5], [6]
small regulatory RNA MicF ompF repressor 986973 986998 GCUUCAUCAUUAUUUAUUACCCUCAU TRANSLATION-BLOCKING, MRNA-DEGRADATION [EXP-IDA], [EXP-IEP], [EXP-IMP], [EXP-IPI] [7], [8], [9], [10], [11]


Transcription unit          
Name: ompF
Synonym(s): OP00066
Gene(s): ompF   Genome Browser M3D Gene expression COLOMBOS
Note(s): It was proved in an experiment with increasing concentrations of the antibiotic tetracycline that the ompC gene is induced in low concentrations (1.5 and 4 mg/L), but not in high ones (10 mg/L) Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007 This result might be attributed to the constant increase during the experiment of micF gene expression, whose sRNA product negatively regulates the expression of the ompF gene Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007.
MarA and Rob independently regulate expression of the outer membrane porin F gene, ompF, in response to salicylate, activating micF gene expression in response to salicylate Chubiz LM, Rao CV,2011. In addition, MarA can also repress OmpF expression through a MicF-independent pathway Chubiz LM, Rao CV,2011. On the other hand, reduction in ompC expression in a tolC mutant was due primarily to Rob Chubiz LM, Rao CV,2011.
The expression of the gene ompF is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The increased expression under aerobiosis appears to be caused by the transcription factor PhoB Marzan LW,2013
Under NlpE outer membrane lipoprotein overexpression, the transcription of the ompF gene is decreased by CpxR Raivio TL,2013
A potential RNA G-quadruplex structure, formed by guanine-rich sequences located in the coding sequence region of the gene, was identified for ompF . This structure could regulate the expression of the gene, as observed for hemL gene expression Shao X, Zhang W, Umar MI, Wong HY, Seng Z, Xie Y, Zhang Y, Yang L, Kwok CK, Deng X,2020.
Reference(s): [1] Mizuno T., et al., 1983
Promoter
Name: ompFp2
+1: 987092
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 110
Sequence: ctttatctttgtagcactttcacggtagcgaaacgttagtttgaatggaaagatgcctgcAgacacataaagacaccaaac
Note(s): Porin regulation by the CpxA-CpxR system and by the EnvZ-OmpR system converges at the porin promoters Batchelor E,2005.
The OmpR transcriptional factor cooperatively binds to the sites of the upstream regions from the ompFp promoter in a discontinuous galloping manner, as described by Yoshida T,2006
554 promoter regions from Escherichia coli were aligned in order to analyze their sequence similarities. Mitchell et al. (2003) Mitchell JE,2003 focused on conservation, patterns, similarities, and differences between promoters with or without an extended -10 5'-TG-3' element and other conserved elements. They experimentally showed that, for several naturally occurring extended -10 promoters, the 5'-TRTG-3' motif is an important determinant for promoter activity. Eleven promoters were selected for further experimental study. Of those, the seven most active (aroF > ompF > envA > purFp1 > purEF > purMN > gyrA) were investigated for the contribution of the extended -10 motif by changing the 5'-TG-3' motif. Promoters with poor matches to the -10 and -35 consensus hexamers are more dependent on the 5'-TG-3' motif, and this plays a similar role on different promoters. The dinucleotide at -17 and -16 in aroFp results in similar patterns of activity, suggesting that these bases play a similar role on different promoters Mitchell JE,2003.
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[RS-EPT-CBR]
Reference(s): [3] Inokuchi K., et al., 1984
[34] Lelong C., et al., 2007
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: gattgctctgGAAGGTATAAAAAAAACAGGACCAAAGTCCTGTTTTTTCGGCATTTAACAAAGAGgtgtgctatt
Reference(s): [12] Feng CQ., et al., 2019
[13] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator ompFp2 987134 987155 -52.5 tttgaaaccaAATCTTTATCTTTGTAGCACTTtcacggtagc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [21]
proximal CRP-cyclic-AMP activator ompFp2 987174 987195 -92.5 aagttccttaAATTTTACTTTTGGTTACATATtttttctttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [21]
remote CRP-cyclic-AMP activator ompFp2 987203 987224 -121.5 gtctctatggAAATATGACGGTGTTCACAAAGttccttaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [21]
[CpxR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-phosphorylated repressor ompFp2 987153 987169 -68.5 acatatttttTCTTTTTGAAACCAAATctttatcttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14], [15]
remote CpxR-phosphorylated repressor ompFp2 987184 987185 -93.0 aattttacttTtggttacata nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14], [15]
remote CpxR-phosphorylated repressor ompFp2 987464 987465 -373.0 cctgttacggAatattacatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14], [15]
remote CpxR-phosphorylated repressor ompFp2 987514 987530 -429.5 ttttctgtcaAGTTATCTGTTTGTTAAgtcaagcaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [14], [15]
[EnvY,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd EnvY activator ompFp2 nd nd nd nd nd [EXP-IMP] W [33]
[Fur,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd Fur-Fe2+ activator ompFp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [21]
[IHF,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote IHF activator ompFp2 987194 987206 -108.0 cggtgttcacAAAGTTCCTTAAAttttactttt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
[IHF,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal IHF repressor ompFp2 987148 987160 -62.0 ttctttttgaAACCAAATCTTTAtctttgtagc nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
remote IHF repressor ompFp2 987262 987274 -176.0 aatataaggaAATCATATAAATAgattaaaatt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] nd nd
[OmpR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OmpR-phosphorylated activator ompFp2 987133 987152 -50.5 gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [16], [18], [19], [20], [23], [24], [25], [26], [27], [28], [29], [30]
proximal OmpR-phosphorylated activator ompFp2 987153 987172 -70.5 gttacatattTTTTCTTTTTGAAACCAAATctttatcttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [17], [20], [23], [24], [25], [26], [27], [28], [29], [30], [31]
proximal OmpR-phosphorylated activator ompFp2 987173 987192 -90.5 ttccttaaatTTTACTTTTGGTTACATATTttttcttttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [20], [23], [24], [25], [26], [27], [28], [29]
[OmpR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal OmpR-phosphorylated repressor ompFp2 987133 987152 -50.5 gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [16], [18], [19], [20], [23], [24], [25], [26], [27], [28], [29], [30]
proximal OmpR-phosphorylated repressor ompFp2 987153 987172 -70.5 gttacatattTTTTCTTTTTGAAACCAAATctttatcttt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [17], [20], [23], [24], [25], [26], [27], [28], [29], [30], [31]
remote OmpR-phosphorylated repressor ompFp2 987453 987472 -370.5 cgatcatcctGTTACGGAATATTACATTGCaacatttacg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [16], [17], [18], [19], [20]
[PhoB,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd PhoB-phosphorylated activator ompFp2 nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [32]
[RstA,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal RstA-phosphorylated repressor ompFp2 987176 987192 -92.0 ttccttaaatTTTACTTTTGGTTACATattttttctt nd [AS-NAS], [AS-NAS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [22]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA RybB ompF repressor 987018 987042 GCCACUGCCGUCAAUAAGUUCUGUC nd [EXP-IEP], [EXP-IMP-SITE-MUTATION], [EXP-IPI] [5], [6]
small regulatory RNA MicF ompF repressor 986973 986998 GCUUCAUCAUUAUUUAUUACCCUCAU TRANSLATION-BLOCKING [EXP-IDA], [EXP-IEP], [EXP-IPI] [7], [9], [10], [11]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [EXP-IMP] Inferred from mutant phenotype

 [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-CELLULAR-EXTRACTS] Binding of cellular extracts

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [AS-NAS] Non-traceable author statement

 [EXP-IEP] Inferred from expression pattern

 [EXP-IPI] Inferred from physical interaction

 [EXP-IDA] Inferred from direct assay


Reference(s)    

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RegulonDB