RegulonDB RegulonDB 10.8: Gene Form
   

rbn gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

elaD rbn elaA OxyR elaDp8 elaDp8 elaAp4 elaAp4 elaAp3 elaAp3 TSS_2528 TSS_2528 rbnp4 rbnp4 TSS_2527 TSS_2527 TSS_2526 TSS_2526 TSS_2525 TSS_2525

Gene      
Name: rbn    Texpresso search in the literature
Synonym(s): ECK2262, G7175, b2268, ecoZ, elaC, rnz, zipD
Genome position(nucleotides): 2381608 --> 2382525 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.76
External database links:  
ASAP:
ABE-0007496
ECHOBASE:
EB4008
OU-MICROARRAY:
b2268
PortEco:
rbn
STRING:
511145.b2268
COLOMBOS: rbn


Product      
Name: ribonuclease BN
Synonym(s): EcoZ, ElaC, Rbn, Rnz, ZipD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 32.93
Isoelectric point: 6.071
Motif(s):
 
Type Positions Sequence
36 -> 154 LFDCGEGTQHQLLHTAFNPGKLDKIFISHLHGDHLFGLPGLLCSRSMSGIIQPLTIYGPQGIREFVETALRISGSWTDYPLEIVEIGAGEILDDGLRKVTAYPLEHPLECYGYRIEEHD
154 -> 154 D
203 -> 270 PGKALAIFGDTGPCDAALDLAKGVDVMVHEATLDITMEAKANSRGHSSTRQAATLAREAGVGKLIITH
217 -> 217 D

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.1 - RNA
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0004527 - exonuclease activity
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0004532 - exoribonuclease activity
GO:0016896 - exoribonuclease activity, producing 5'-phosphomonoesters
GO:0008270 - zinc ion binding
GO:0016891 - endoribonuclease activity, producing 5'-phosphomonoesters
GO:0042781 - 3'-tRNA processing endoribonuclease activity
GO:0042803 - protein homodimerization activity
biological_process GO:0008033 - tRNA processing
GO:0042779 - tRNA 3'-trailer cleavage
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic
GO:0034414 - tRNA 3'-trailer cleavage, endonucleolytic
External database links:  
DIP:
DIP-9498N
ECOCYC:
G7175-MONOMER
ECOLIWIKI:
b2268
INTERPRO:
IPR001279
INTERPRO:
IPR013471
INTERPRO:
IPR036866
INTERPRO:
IPR013469
MINT:
MINT-1275952
MODBASE:
P0A8V0
PDB:
2CBN
PFAM:
PF12706
PRIDE:
P0A8V0
PRODB:
PRO_000023801
REFSEQ:
NP_416771
SMART:
SM00849
SMR:
P0A8V0
SWISSMODEL:
P0A8V0
UNIPROT:
P0A8V0


Operon      
Name: rbn         
Operon arrangement:
Transcription unit        Promoter
 


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_2525 2381535 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2526 2381563 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2527 2381565 reverse nd [RS-EPT-CBR] [1]
  promoter rbnp4 2381581 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_2528 2381582 forward nd [RS-EPT-CBR] [1]
  promoter elaAp3 2381614 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter elaAp4 2381686 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter elaDp8 2382654 forward Similarity to the consensus
Read more >
[ICWHO] [2]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] 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.

 [2] 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


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