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Name: | soxS | ||||||||||
Synonym(s): | OP00296 | ||||||||||
Gene(s): | soxS Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The expression of the soxS gene is induced quickly under oxidative stress Lu C,2003 In addition, it was proved in an experiment with increasing concentrations of the antibiotic tetracycline that the soxS gene is induced in low concentrations (1.5 and 4 mg/L) but not in high ones (10 mg/L); this suggests that the product of this gene plays a role under this condition Viveiros M, Dupont M, Rodrigues L, Couto I, Davin-Regli A, Martins M, Pagès JM, Amaral L,2007 soxS is also induced in the presence of menadione, salicylic acid, and norfloxacin in a MarR-dependent way Reyes-Fernández EZ, Schuldiner S,2020. Under nitrogen-rich growth conditions, the expression of the soxS gene was increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur Kumar R,2011 Overexpression of MarA and Rob represses the soxSp promoter Chubiz LM, Glekas GD, Rao CV,2012 SoxS represses the soxSp promoter in response to paraquat Chubiz LM, Glekas GD, Rao CV,2012 Decanoate represses the soxSp promoter independently of Rob Chubiz LM, Glekas GD, Rao CV,2012 The expression of the gene soxS is increased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013 The transcription of the gene soxS is enhanced under high oxygen saturation (300%) in the absence of the superoxide dismutase proteins SodA and SodB Baez A,2013 |
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Evidence: | [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined | ||||||||||
Reference(s): |
[1] Fozo EM., et al., 2008 [2] Nunoshiba T., et al., 1993 [3] Wu J., et al., 1991 |
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Promoter | |||||||||||
Name: | soxSp | ||||||||||
+1: | 4277423 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 40 | ||||||||||
Sequence: |
taatttcttttccataaatcgctttacctcaagttaacttgaggaattatactccccaacAgatgaattaacgaactgaac -35 -10 +1 |
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Note(s): | The soxS promoter is induced by the presence of salicylate Jain K, Saini S,2016 | ||||||||||
Evidence: |
[COMP-AINF] [COMP-HINF-POSITIONAL-IDENTIFICATION] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [RS-EPT-CBR] |
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Reference(s): |
[4] Huerta AM., et al., 2003 [5] Salgado H, et al., 2012 [3] Wu J., et al., 1991 |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | AcrR | repressor | soxSp | 4277444 | 4277454 | -25.5 | cgctttacctCAAGTTAACTTgaggaattat | nd | [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | S | [10] |
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 | FNR | repressor | soxSp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [11] |
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+ | repressor | soxSp | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [11] |
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 | SoxR | activator | soxSp | 4277409 | 4277426 | 6.0 | tatactccccAACAGATGAATTAACGAActgaacactg | nd | [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL] | S | [9] |
proximal | SoxR | activator | soxSp | 4277440 | 4277457 | -25.5 | aatcgctttaCCTCAAGTTAACTTGAGGaattatactc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [7], [8], [9] |
Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence | Confidence level (C: Confirmed, S: Strong, W: Weak) | Reference(s) | |||
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LeftPos | RightPos | Central Rel-Pos | Sequence | ||||||||
proximal | SoxS | repressor | soxSp | 4277411 | 4277430 | 3.0 | gaattatactCCCCAACAGATGAATTAACGaactgaacac | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-RNA-SEQ], [COMP-HINF], [EXP-CHIP-EXO-MANUAL], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | C | [2], [9] |
sRNA | TU Regulated | Function | Binding Sites | Regulatory Mechanism | Evidence (Confirmed, Strong, Weak) | Reference(s) | ||
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PosLeft | PosRight | Target sequence (mRNA) | ||||||
small regulatory RNA MgrR | soxS | repressor | 4277340 | 4277355 | UCAAUCCAUGCGAUAA | nd | [EXP-IMP], [EXP-IMP-SITE-MUTATION] | [6] |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Transcriptional |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
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terminator | -9.5 | 4277473 | 4277518 | gcgtttcgccACTTCGCCGGGGGTTAGCAGCGCTTTAATGCGGGGTAATTTCTTTtccataaatc | |
anti-terminator | -8.4 | 4277505 | 4277539 | cgccgataccGCCACACCGCTGCGTTTCGCCACTTCGCCGGGGGttagcagcgc | |
anti-anti-terminator | -14.16 | 4277522 | 4277558 | tactttcataGAAATGCAGCGCCGATACCGCCACACCGCTGCGTTTcgccacttcg |
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" |
Reference(s) |
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