RegulonDB RegulonDB 10.9: Gene Form
   

spf gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

polA yihA spf CRP spfp spfp TSS_4538 TSS_4538 TSS_4537 TSS_4537 TSS_4536 TSS_4536 TSS_4535 TSS_4535 TSS_4534 TSS_4534

Gene      
Name: spf    Texpresso search in the literature
Synonym(s): ECK3856, EG30098, b3864
Genome position(nucleotides): 4049899 --> 4050009 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
41.44
External database links:  
ASAP:
ABE-0012621
CGSC:
157
ECHOBASE:
EB4261
ECOLIHUB:
spf
OU-MICROARRAY:
b3864
COLOMBOS: spf


Product      
Name: small regulatory RNA Spot 42
Synonym(s): IS197, Spf, Spf RNA
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.6 - antisense RNA
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
GO:0003729 - mRNA binding
biological_process GO:0045974 - regulation of translation, ncRNA-mediated
GO:0070928 - regulation of mRNA stability, ncRNA-mediated
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
[IPI] Inferred from physical interaction
Reference(s): [1] Chen S., et al., 2002
[2] Joyce CM., et al., 1982
[3] Komine Y., et al., 1991
[4] Mihailovic MK., et al., 2018
[5] Moller T., et al., 2002
[6] Wang X., et al., 2015
[7] Windbichler N., et al., 2008
[8] Wright PR., et al., 2013
External database links:  
ECOCYC:
SPF-RNA
ECOLIWIKI:
b3864


Operon      
Name: spf         
Operon arrangement:
Transcription unit        Promoter
spf


Transcriptional Regulation      
Display Regulation             
Repressed by: CRP


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 TSS_4534 4047199 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4535 4048629 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4536 4048749 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4537 4049298 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4538 4049325 forward nd [RS-EPT-CBR] [9]


Evidence    

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



Reference(s)    

 [1] Chen S., Lesnik EA., Hall TA., Sampath R., Griffey RH., Ecker DJ., Blyn LB., 2002, A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome., Biosystems 65(2-3):157-77

 [2] Joyce CM., Grindley ND., 1982, Identification of two genes immediately downstream from the polA gene of Escherichia coli., J Bacteriol 152(3):1211-9

 [3] Komine Y., Inokuchi H., 1991, Physical map locations of the genes that encode small stable RNAs in Escherichia coli., J Bacteriol 173(17):5252

 [4] Mihailovic MK., Vazquez-Anderson J., Li Y., Fry V., Vimalathas P., Herrera D., Lease RA., Powell WB., Contreras LM., 2018, High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites., Nat Commun 9(1):4084

 [5] Moller T., Franch T., Udesen C., Gerdes K., Valentin-Hansen P., 2002, Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon., Genes Dev 16(13):1696-706

 [6] Wang X., Ji SC., Jeon HJ., Lee Y., Lim HM., 2015, Two-level inhibition of galK expression by Spot 42: Degradation of mRNA mK2 and enhanced transcription termination before the galK gene., Proc Natl Acad Sci U S A 112(24):7581-6

 [7] Windbichler N., von Pelchrzim F., Mayer O., Csaszar E., Schroeder R., 2008, Isolation of small RNA-binding proteins from E. coli: evidence for frequent interaction of RNAs with RNA polymerase., RNA Biol 5(1):30-40

 [8] Wright PR., Richter AS., Papenfort K., Mann M., Vogel J., Hess WR., Backofen R., Georg J., 2013, Comparative genomics boosts target prediction for bacterial small RNAs., Proc Natl Acad Sci U S A 110(37):E3487-96

 [9] 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.


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