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Name: | sra | ||||||||||
Gene(s): | sra Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | Global transcriptional regulators FIS, IHF, cAMP-CRP, and ppGpp directly or indirectly regulate positively the transcription of sra during the stationary phase, and the region between bp -455 and -325 from its ATG codon appears to be responsible for the action of these regulators, which do not interfere with sra expression in the exponential phase Izutsu K,2001. | ||||||||||
Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified | ||||||||||
Reference(s): | [1] Izutsu K., et al., 2001 | ||||||||||
Promoter | |||||||||||
Name: | srap | ||||||||||
+1: | 1556046 | ||||||||||
Sigma Factor: | Sigma38 Sigmulon | ||||||||||
Distance from start of the gene: | 83 | ||||||||||
Sequence: |
acgatcaattatgtggtcagtggccagcaccctacgctttaaggtgctatgcttgatcggCaacctaatttaggggtttag -35 -10 +1 |
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Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IEP] |
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Reference(s): |
[2] Huerta AM., et al., 2003 [1] Izutsu K., et al., 2001 [3] Lacour S., et al., 2004 |
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 | Fis | activator | srap | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [1] |
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 | IHF | activator | srap | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [1] |
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 | OmpR-phosphorylated | repressor | srap | nd | nd | nd | nd | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS] | W | [1] |
Allosteric regulation of RNA-polymerase |
Regulator | Function | Promoter target of RNApol | Growth Conditions | Note | Evidence | Reference | |
---|---|---|---|---|---|---|---|
ppGpp | activation | srap | nd |
[EXP-IEP] [EXP-IEP-GENE-EXPRESSION-ANALYSIS] |
[1] [4] |
Evidence: |
[EXP-IEP] Inferred from expression pattern [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis |
Reference(s): |
[1] Izutsu K., et al., 2001 [4] Traxler MF., et al., 2008 |
Name: | bdm-sra | ||||||||||
Gene(s): | sra, bdm Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | The expression of the gene bdm is increased when colicin (at 30 ng/ml) is added to the medium Kamen?ek S, ?gur-Bertok D,2013. | ||||||||||
Evidence: | [EXP-IMP-POLAR-MUTATION] Polar mutation | ||||||||||
Reference(s): | [5] Francez-Charlot A., et al., 2005 | ||||||||||
Promoter | |||||||||||
Name: | bdmp | ||||||||||
+1: | 1556340 | ||||||||||
Distance from start of the gene: | 60 | ||||||||||
Sequence: |
aaaatcatcaaccaggactaatcttaacaacgaagcggcaaatatttgccatgctgaatgTgctttataaatctgcgatcc |
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Evidence: | [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] | ||||||||||
Reference(s): | [5] Francez-Charlot A., et al., 2005 |
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 | RcsB-phosphorylated | activator | bdmp | 1556375 | 1556388 | -41.5 | aatcatcaacCAGGACTAATCTTAacaacgaagc | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [5] |
RNA cis-regulatory element | ![]() |
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Regulation, transcriptional elongation | |
Attenuator type: | Translational |
Strand: | reverse |
Structure type | Energy | LeftPos | RightPos | Sequence (RNA-strand) | |
---|---|---|---|---|---|
terminator | -7.4 | 1555970 | 1555997 | ggcgatgttgTCCTTAAAACTAGCTACAGGATTGAGGagttaaaatg |
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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