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| Operon |  |
|---|---|
| Name: | cyaR |
| This page displays every known transcription unit of this operon and their known regulation. | |
| Name: | cyaR | |||||||||
| Gene(s): | cyaR Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | A stem-loop of the ρ-independent terminator for the cyaR gene was predicted by Johansen et al. (2008). However, the terminator is inside of the cyaR gene Johansen J,2008 CRP controls cyaR expression under conditions in which cAMP levels are high De Lay N,2009 |
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| Evidence: | [BTEI] Boundaries of transcription experimentally identified [ICWHO] Inferred computationally without human oversight [LTED] Length of transcript experimentally determined |
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| Reference(s): |
[1] Johansen J., et al., 2008 [2] Wassarman KM., et al., 2001 |
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| Promoter | ||||||||||
| Name: | cyaRp3 | |||||||||
| +1: | 2167114 | |||||||||
| Sigma Factor: | Sigma38 Sigmulon | |||||||||
| Distance from start of the gene: | 0 | |||||||||
| Sequence: |
tggaaaattcttagaaaccgatcacatacagctgcatttattaaggttatcatccgtttcGctgaaaaacataacccataa -35 -10 +1 |
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| Note(s): | cyaRp could be transcribed from EσE, since cyaR expression is up-regulated in response to an increase in the activity of σE. Furthermore, a small group of σE-regulated factors is also regulated by σ70. Another issue is the fact that the -10 and -35 boxes of cyaR match with the ecfFp2 boxes, which are under control of σE. In addition, cyaRp contains in the upstream region an AU-rich region which may have a role in recognition of the alternative RNA polymerases Johansen J,2008 |
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| Evidence: |
[AIPP] [HTTIM] [ICWHO] [IDA] [IEP] [IHBCE] [RS-EPT-CBR] [TIM] |
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| Reference(s): |
[3] De Lay N., et al., 2009 [4] Huerta AM., et al., 2003 [1] Johansen J., et al., 2008 [5] Maciag A., et al., 2011 [6] Salgado H, et al., 2012 |
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| Terminator(s) | ||||||||||
| Type: | rho-independent | |||||||||
| Sequence: | gaaccacctcCTTAGCCTGTGTAATCTCCCTTACACGGGCTTATTTTTTacgcgtaata | |||||||||
| Reference(s): | [3] De Lay N., et al., 2009 | |||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | CRP-cyclic-AMP | activator | cyaRp3 | 2167061 | 2167082 | -42.5 | ggatggaaaaTTCTTAGAAACCGATCACATACagctgcattt | nd | [GEA], [AIBSCS], [BPP], [SM] | [1], [3] |
| Name: | cyaR | |||||||||
| Gene(s): | cyaR Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | A stem-loop of the ρ-independent terminator for the cyaR gene was predicted by Johansen et al. (2008). However, the terminator is inside of the cyaR gene Johansen J,2008 CRP controls cyaR expression under conditions in which cAMP levels are high De Lay N,2009 |
|||||||||
| Evidence: | [BTEI] Boundaries of transcription experimentally identified [ICWHO] Inferred computationally without human oversight [LTED] Length of transcript experimentally determined |
|||||||||
| Reference(s): |
[1] Johansen J., et al., 2008 [2] Wassarman KM., et al., 2001 |
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| Promoter | ||||||||||
| Name: | cyaRp2 | |||||||||
| +1: | 2167114 | |||||||||
| Sigma Factor: | Sigma24 Sigmulon | |||||||||
| Distance from start of the gene: | 0 | |||||||||
| Sequence: |
tggaaaattcttagaaaccgatcacatacagctgcatttattaaggttatcatccgtttcGctgaaaaacataacccataa -35 -10 +1 |
|||||||||
| Note(s): | cyaRp could be transcribed from EσE, since cyaR expression is up-regulated in response to an increase in the activity of σE. Furthermore, a small group of σE-regulated factors is also regulated by σ70. Another issue is the fact that the -10 and -35 boxes of cyaR match with the ecfFp2 boxes, which are under control of σE. In addition, cyaRp contains in the upstream region an AU-rich region which may have a role in recognition of the alternative RNA polymerases Johansen J,2008 |
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| Evidence: |
[AIPP] [HTTIM] [ICWHO] [IDA] [IEP] [IHBCE] [RS-EPT-CBR] [TIM] |
|||||||||
| Reference(s): |
[3] De Lay N., et al., 2009 [4] Huerta AM., et al., 2003 [1] Johansen J., et al., 2008 [5] Maciag A., et al., 2011 [6] Salgado H, et al., 2012 |
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| Terminator(s) | ||||||||||
| Type: | rho-independent | |||||||||
| Sequence: | gaaccacctcCTTAGCCTGTGTAATCTCCCTTACACGGGCTTATTTTTTacgcgtaata | |||||||||
| Reference(s): | [3] De Lay N., et al., 2009 | |||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | CRP-cyclic-AMP | activator | cyaRp2 | 2167061 | 2167082 | -42.5 | ggatggaaaaTTCTTAGAAACCGATCACATACagctgcattt | nd | [GEA], [AIBSCS], [BPP], [SM] | [1], [3] |
| Name: | cyaR | |||||||||
| Gene(s): | cyaR Genome Browser M3D Gene expression COLOMBOS | |||||||||
| Note(s): | A stem-loop of the ρ-independent terminator for the cyaR gene was predicted by Johansen et al. (2008). However, the terminator is inside of the cyaR gene Johansen J,2008 CRP controls cyaR expression under conditions in which cAMP levels are high De Lay N,2009 |
|||||||||
| Evidence: | [BTEI] Boundaries of transcription experimentally identified [ICWHO] Inferred computationally without human oversight [LTED] Length of transcript experimentally determined |
|||||||||
| Reference(s): |
[1] Johansen J., et al., 2008 [2] Wassarman KM., et al., 2001 |
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| Promoter | ||||||||||
| Name: | cyaRp | |||||||||
| +1: | 2167114 | |||||||||
| Sigma Factor: | Sigma70 Sigmulon | |||||||||
| Distance from start of the gene: | 0 | |||||||||
| Sequence: |
tggaaaattcttagaaaccgatcacatacagctgcatttattaaggttatcatccgtttcGctgaaaaacataacccataa -35 -10 +1 |
|||||||||
| Note(s): | cyaRp could be transcribed from EσE, since cyaR expression is up-regulated in response to an increase in the activity of σE. Furthermore, a small group of σE-regulated factors is also regulated by σ70. Another issue is the fact that the -10 and -35 boxes of cyaR match with the ecfFp2 boxes, which are under control of σE. In addition, cyaRp contains in the upstream region an AU-rich region which may have a role in recognition of the alternative RNA polymerases Johansen J,2008 |
|||||||||
| Evidence: |
[AIPP] [HTTIM] [ICWHO] [IDA] [IEP] [IHBCE] [RS-EPT-CBR] [TIM] |
|||||||||
| Reference(s): |
[3] De Lay N., et al., 2009 [4] Huerta AM., et al., 2003 [1] Johansen J., et al., 2008 [5] Maciag A., et al., 2011 [6] Salgado H, et al., 2012 |
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| Terminator(s) | ||||||||||
| Type: | rho-independent | |||||||||
| Sequence: | gaaccacctcCTTAGCCTGTGTAATCTCCCTTACACGGGCTTATTTTTTacgcgtaata | |||||||||
| Reference(s): | [3] De Lay N., et al., 2009 | |||||||||
| Type | Transcription factor | Function | Promoter | Binding Sites | Growth Conditions | Evidence (Confirmed, Strong, Weak) | Reference(s) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| LeftPos | RightPos | Central Rel-Pos | Sequence | |||||||
| proximal | CRP-cyclic-AMP | activator | cyaRp | 2167061 | 2167082 | -42.5 | ggatggaaaaTTCTTAGAAACCGATCACATACagctgcattt | nd | [GEA], [AIBSCS], [BPP], [SM] | [1], [3] |
| Reference(s) |
|
|---|---|
[AIPP] Automated inference of promoter position