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Name: | ygbF |
Gene(s): | cas2 Genome Browser M3D Gene expression COLOMBOS |
Evidence: | [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified |
Reference(s): | [1] Nonaka G., et al., 2006 |
Promoter | |
Name: | ygbFp |
+1: | 2878915 |
Sigma Factor: | Sigma32 Sigmulon |
Distance from start of the gene: | 62 |
Sequence: |
gcttatagaggacgtgcttgccgctggagaaatacaaccgccggccccacctgaagatgcAcagcctgttgccattccgct -35 -10 +1 |
Evidence: |
[COMP-AINF] [COMP-AINF-POSITIONAL-IDENTIFICATION] [COMP-AINF-SIMILAR-TO-CONSENSUS] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] |
Reference(s): |
[2] Huerta AM., et al., 2003 [1] Nonaka G., et al., 2006 |
Name: | casABCDE12 | ||||||||||
Gene(s): | cas2, cas1, casE, casD, casC, casB, casA Genome Browser M3D Gene expression COLOMBOS | ||||||||||
Note(s): | HNS binds in tandem at the casA-cas3 intergenic region, and it represses the transcription of the casA gene by inhibiting the RNA polymerase interaction with the casAp promoter. Analyses for footprinting show that HNS protects two long regions without defining the central positions of the binding sites of the protein HNS; for this reason, we only show the sequence of the hypersensitive site, TCGTTTTATT Dyszel JL,2010 HNS also represses the expression of the anti-Pcas divergent promoter, which is reported to produce an RNA with a length between 150 and 200 bp. There exists the possibility that this divergent promoter affects the transcription or translation of the ygcB gene. H-NS and LeuO are antagonistic regulators of casABCDE-cas12 Westra ER,2010. LeuO counteracts H-NS-dependent repression of casAp by reorganizing the DNA-protein contacts within the transcription initiation region Westra ER,2010. Repression of the CRP in the casABCDE-cas1-cas2 operon is H-NS independent Yang CD,2014 In fact, both compete for binding to the casAp promoter Yang CD,2014 The casABCDE-cas12 operon is repressed by the StpA protein when H-NS is absent Miti? D, Radov?i? M, Markulin D, Ivan?i?-Ba?e I,2020 |
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Evidence: | [COMP-AINF] Inferred computationally without human oversight [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined |
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Reference(s): | [3] Pul U., et al., 2010 | ||||||||||
Promoter | |||||||||||
Name: | casAp | ||||||||||
+1: | 2884319 | ||||||||||
Sigma Factor: | Sigma70 Sigmulon | ||||||||||
Distance from start of the gene: | 181 | ||||||||||
Sequence: |
tttctttaataataaaacgaataacttgcagatttgaaatgcatgcattattgtctttaaAcaattcaacacatcttaata -35 -10 +1 |
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Evidence: |
[COMP-AINF] [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] [EXP-IPI] |
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Reference(s): |
[2] Huerta AM., et al., 2003 [3] Pul U., et al., 2010 |
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 | repressor | casAp | 2884399 | 2884419 | -89.5 | gtatgaatatTTTATGTAATAAAATTCATGGtaattattat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [7] |
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 | H-NS | repressor | casAp | 2884358 | 2884372 | -46.0 | aagtttctttAATAATAAAACGAATaacttgcaga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [3], [4], [6], [8], [9] |
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 | LeuO | activator | casAp | 2884263 | 2884283 | 47.0 | ataggttaatTGTATTAAACCAATGAATATAtttttgcagt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] | W | [4], [6] |
proximal | LeuO | activator | casAp | 2884289 | 2884309 | 21.0 | acaattcaacACATCTTAATATATGTATAGGttaattgtat | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] | W | [4], [6] |
proximal | LeuO | activator | casAp | 2884389 | 2884409 | -80.0 | tttatgtaatAAAATTCATGGTAATTATTATaactaaaagt | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [IC], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] | W | [6] |
remote | LeuO | activator | casAp | 2884419 | 2884439 | -110.0 | tatgagatttTATATTCACAGTATGAATATTttatgtaata | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IEP-MICROARRAY], [IC], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [IC] | C | [4], [5], [6] |
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 | SlyA | activator | casAp | 2884233 | 2884244 | 81.5 | gtgaatgtgaTTATTGAATTAAttacgccgta | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] | W | [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 | ||||||||
proximal | StpA | activator | casAp | 2884358 | 2884372 | -46.0 | aagtttctttAATAATAAAACGAATaacttgcaga | nd | [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] | C | [3], [8] |
Name: | casDE-ygbTF |
Synonym(s): | ygcIH-ygbTF |
Gene(s): | cas2, cas1, casE, casD Genome Browser M3D Gene expression COLOMBOS |
Note(s): | ygcH, ygbT, and ygbF genes are transcribed together with three other genes located upstream of them. On the other hand, a σ32-dependent promoter was suggested to be located upstream of ygcI Wade JT,2006. Therefore, we inferred that the four genes (ygcIH-ygbTF) form a transcription unit transcribed from the σ32 promoter. |
Evidence: | [IC] Inferred by curator |
Promoter | |
Name: | casDp |
+1: | Unknown |
Sigma Factor: | Sigma32 Sigmulon |
Evidence: |
[EXP-IDA] [EXP-IEP] |
Reference(s): | [11] Wade JT., et al., 2006 |
Reference(s) |
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