RegulonDB RegulonDB 11.1: Gene Form
   

rnb gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rnb yciW ymiB FliZ anti-anti-terminator anti-terminator terminator rnbp1 rnbp1 rnbp2 rnbp2 TSS_1732 TSS_1732 pdeRp pdeRp TSS_1731 TSS_1731

Gene      
Name: rnb    Texpresso search in the literature
Synonym(s): ECK1281, EG11620, b1286
Genome position(nucleotides): 1346978 <-- 1348912
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.23
External database links:  
ASAP:
 ABE-0004320
CGSC:
 272
ECHOBASE:
 EB1577
ECOLIHUB:
 rnb
OU-MICROARRAY:
 b1286
STRING:
 511145.b1286
COLOMBOS: rnb


Shine dalgarno      
Sequence: gccaccaaaaTAGACAatTAT


Product      
Name: RNase II
Synonym(s): Rnb, exoribonuclease 2, exoribonuclease II, ribonuclease II
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 72.491
Isoelectric point: 5.308
Motif(s):
 
Type Positions Sequence Comment
24 -> 80 GVVKATEKGFGFLEVDAQKSYFIPPPQMKKVMHGDRIIAVIHSEKERESAEPEELVE
99 -> 175 IVPDHPLLKDAIPCRAARGLNHEFKEGDWAVAEMRRHPLKGDRSFYAELTQYITFGDDHFVPWWVTLARHNLEKEAP
189 -> 516 REDLTALDFVTIDSASTEDMDDALFAKALPDDKLQLIVAIADPTAWIAEGSKLDKAAKIRAFTNYLPGFNIPMLPRELSDDLCSLRANEVRPVLACRMTLSADGTIEDNIEFFAATIESKAKLVYDQVSDWLENTGDWQPESEAIAEQVRLLAQICQRRGEWRHNHALVFKDRPDYRFILGEKGEVLDIVAEPRRIANRIVEEAMIAANICAARVLRDKLGFGIYNVHMGFDPANADALAALLKTHGLHVDAEEVLTLDGFCKLRRELDAQPTGFLDSRIRRFQSFAEISTEPGPHFGLGLEAYATWTSPIRKYGDMINHRLLKAVIK
384 -> 384 I UniProt: In Ref. 1; CAA48112..
399 -> 399 C UniProt: In Ref. 1; CAA48112..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.1 - RNA
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003676 - nucleic acid binding
GO:0004518 - nuclease activity
GO:0004527 - exonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0008408 - 3'-5' exonuclease activity
GO:0003723 - RNA binding
GO:0004540 - ribonuclease activity
GO:0008859 - exoribonuclease II activity
biological_process GO:0016070 - RNA metabolic process
GO:0006401 - RNA catabolic process
GO:0006402 - mRNA catabolic process
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0016078 - tRNA catabolic process
GO:0090501 - RNA phosphodiester bond hydrolysis
GO:0090503 - RNA phosphodiester bond hydrolysis, exonucleolytic
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P30850
DIP:
 DIP-10724N
ECOCYC:
 EG11620-MONOMER
ECOLIWIKI:
 b1286
INTERPRO:
 IPR012340
INTERPRO:
 IPR011129
INTERPRO:
 IPR004476
INTERPRO:
 IPR003029
INTERPRO:
 IPR013223
INTERPRO:
 IPR022966
INTERPRO:
 IPR040476
INTERPRO:
 IPR001900
INTERPRO:
 IPR011804
MODBASE:
 P30850
PDB:
 2IX1
PDB:
 2ID0
PDB:
 2IX0
PFAM:
 PF00575
PFAM:
 PF00773
PFAM:
 PF08206
PFAM:
 PF17876
PRIDE:
 P30850
PRODB:
 PRO_000023787
PROSITE:
 PS01175
REFSEQ:
 NP_415802
SMART:
 SM00357
SMART:
 SM00955
SMR:
 P30850
UNIPROT:
 P30850


Operon      
Name: rnb         
Operon arrangement:
Transcription unit        Promoter
rnb
rnb


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_1731 1346842 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1732 1348735 reverse nd [RS-EPT-CBR] [1]


Evidence    

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


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.

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