RegulonDB RegulonDB 10.8: Gene Form
   

cspF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cspB cspF ynfS Cis-reg; thermoregulator cspFp8 cspFp8 TSS_1864 TSS_1864 cspFp6 cspFp6 cspBp cspBp cspFp7 cspFp7

Gene      
Name: cspF    Texpresso search in the literature
Synonym(s): ECK1552, EG12205, b1558
Genome position(nucleotides): 1641855 --> 1642067 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.36
External database links:  
ASAP:
ABE-0005205
ECHOBASE:
EB2121
OU-MICROARRAY:
b1558
PortEco:
cspF
STRING:
511145.b1558
COLOMBOS: cspF


Product      
Name: Qin prophage; cold shock protein CspF
Synonym(s): CspF
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 7.563
Isoelectric point: 10.028
Motif(s):
 
Type Positions Sequence
7 -> 67 GIVKTFDGKSGKGLITPSDGRIDVQLHVSALNLRDAEEITTGLRVEFCRINGLRGPSAANV
5 -> 69 MTGIVKTFDGKSGKGLITPSDGRIDVQLHVSALNLRDAEEITTGLRVEFCRINGLRGPSAANVYL

 

Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0003677 - DNA binding
GO:0003723 - RNA binding
GO:0001072 - transcription antitermination factor activity, RNA binding
biological_process GO:0031564 - transcription antitermination
GO:0010468 - regulation of gene expression
GO:0060567 - negative regulation of DNA-templated transcription, termination
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
EG12205-MONOMER
ECOLIWIKI:
b1558
INTERPRO:
IPR019844
INTERPRO:
IPR012156
INTERPRO:
IPR012340
INTERPRO:
IPR002059
INTERPRO:
IPR011129
MODBASE:
P0A976
PFAM:
PF00313
PRIDE:
P0A976
PROSITE:
PS00352
PROSITE:
PS51857
REFSEQ:
NP_416076
SMART:
SM00357
SMR:
P0A976
SWISSMODEL:
P0A976
UNIPROT:
P0A976


Operon      
Name: cspF         
Operon arrangement:
Transcription unit        Promoter
cspF
 


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter cspFp7 1641690 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter cspBp 1641715 reverse nd [AIPP], [RS-EPT-CBR] [2], [3]
  promoter cspFp6 1641765 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_1864 1641831 forward nd [RS-EPT-CBR] [2]
  promoter cspFp8 1641846 forward Similarity to the consensus
Read more >
[ICWHO] [1]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [AIPP] Automated inference of promoter position

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [3] Wang N., Yamanaka K., Inouye M., 1999, CspI, the ninth member of the CspA family of Escherichia coli, is induced upon cold shock., J Bacteriol 181(5):1603-9


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