RegulonDB RegulonDB 10.9: Operon Form
   

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




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


Transcription unit       
Name: hupB
Gene(s): hupB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [1] Claret L., et al., 1996
[2] Kohno K., et al., 1990
Promoter
Name: hupBp4
+1: 461305
Distance from start of the gene: 146
Sequence: acctcgcgcaaaatgcactaataaaaacagggctggcaggctaattcgggcttgccagccTttttttgtctcgctaagtta
Note(s): This promoter is much weaker than hupBp2 and hupBp3.
Evidence: [TIM]
Reference(s): [1] Claret L., et al., 1996
Terminator(s)
Type: rho-independent
Sequence: ctaagcgttgTCCCCAGTGGGGAtgtgacgaag
Reference(s): [2] Kohno K., et al., 1990
Type: rho-independent
Sequence: gaagttcaagGGCGCATCTACTGATGTGCCttttttattt
Reference(s): [2] Kohno K., et al., 1990


Transcription unit          
Name: hupB
Gene(s): hupB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [2] Kohno K., et al., 1990
Promoter
Name: hupBp3
+1: 461332
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 119
Sequence: cagggctggcaggctaattcgggcttgccagcctttttttgtctcgctaagttagatggcGgatcgggcttgcccttatta
                         -35                    -10         +1                   
Evidence: [ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Claret L., et al., 1996
[3] Huerta AM., et al., 2003
[2] Kohno K., et al., 1990
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: ctaagcgttgTCCCCAGTGGGGAtgtgacgaag
Reference(s): [2] Kohno K., et al., 1990
Type: rho-independent
Sequence: gaagttcaagGGCGCATCTACTGATGTGCCttttttattt
Reference(s): [2] Kohno K., et al., 1990
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator hupBp3 461238 461259 -83.5 gtgactgcaaAATAGTGACCTCGCGCAAAATGCactaataaaa nd [BPP], [GEA] [1]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis1 repressor hupBp3 461180 461194 -145.0 gcgcattgagGAAGTTCTGACTCTGGcgctgcaaaa nd [BPP], [GEA] [1]
remote Fis2 repressor hupBp3 461203 461217 -122.0 tggcgctgcaAAATGAACCGTCTGGTatgcaggttg nd [BPP], [GEA] nd
proximal Fis3 repressor hupBp3 461235 461249 -89.5 gttgtgactgCAAAATAGTGACCTCGcgcaaaatgc nd [BPP], [GEA] nd
remote Fis4 repressor hupBp3 461465 461479 141.0 ataaatctcaATTGATCGACAAGATTgctgcagggg nd [BPP], [GEA] [1]
Note(s): 1FIS represses the hupBp3 promoter only when CRP is absent.
2FIS represses the hupBp3 promoter only when CRP is absent.
3FIS represses the hupBp3 promoter only when CRP is absent.
4FIS represses the hupBp3 promoter only when CRP is absent.1FIS represses the hupBp3 promoter only when CRP is absent.
2FIS represses the hupBp3 promoter only when CRP is absent.
3FIS represses the hupBp3 promoter only when CRP is absent.
5FIS represses the hupBp3 promoter only when CRP is absent.


Transcription unit          
Name: hupB
Gene(s): hupB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [2] Kohno K., et al., 1990
Promoter
Name: hupBp2
+1: 461395
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 56
Sequence: tcgggcttgcccttattaaggggtgttgtaaggggatggctggcctgatataactgctgcGcgttcgtaccttgaaggatt
                          -35                    -10        +1                   
Evidence: [ICWHO]
[RS-EPT-CBR]
[TIM]
Reference(s): [1] Claret L., et al., 1996
[3] Huerta AM., et al., 2003
[2] Kohno K., et al., 1990
[4] Salgado H, et al., 2012
Terminator(s)
Type: rho-independent
Sequence: ctaagcgttgTCCCCAGTGGGGAtgtgacgaag
Reference(s): [2] Kohno K., et al., 1990
Type: rho-independent
Sequence: gaagttcaagGGCGCATCTACTGATGTGCCttttttattt
Reference(s): [2] Kohno K., et al., 1990
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Fis repressor hupBp2 461180 461194 -208.0 gcgcattgagGAAGTTCTGACTCTGGcgctgcaaaa nd [BPP], [GEA] [1]
remote Fis repressor hupBp2 461203 461217 -185.0 tggcgctgcaAAATGAACCGTCTGGTatgcaggttg nd [BPP], [GEA] [1]
remote Fis repressor hupBp2 461235 461249 -152.5 gttgtgactgCAAAATAGTGACCTCGcgcaaaatgc nd [BPP], [GEA] [1]
remote Fis repressor hupBp2 461465 461479 78.0 ataaatctcaATTGATCGACAAGATTgctgcagggg nd [BPP], [GEA] [1]


Transcription unit       
Name: hupB
Gene(s): hupB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
Reference(s): [2] Kohno K., et al., 1990
Promoter
Name: hupBp1
+1: 461442
Distance from start of the gene: 9
Sequence: atataactgctgcgcgttcgtaccttgaaggattcaagtgcgatataaattataaagaggAagagaagagtgaataaatct
Evidence: [TIM]
Reference(s): [1] Claret L., et al., 1996
[2] Kohno K., et al., 1990
Terminator(s)
Type: rho-independent
Sequence: ctaagcgttgTCCCCAGTGGGGAtgtgacgaag
Reference(s): [2] Kohno K., et al., 1990
Type: rho-independent
Sequence: gaagttcaagGGCGCATCTACTGATGTGCCttttttattt
Reference(s): [2] Kohno K., et al., 1990


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
Evidence: [ICA] Inferred by computational analysis
Reference(s): [5] Merino E, et al., 2005
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -25.3 461273 461313 aataaaaacaGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCTTTTTTTGTctcgctaagt
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"





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