RegulonDB RegulonDB 11.1: Gene Form
   

rne gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rne yceQ flgO Cis-reg rnep2 rnep2 rnep1 rnep1 TSS_1364 (cluster) TSS_1364 (cluster) rnep4 rnep4 yceQp6 yceQp6 TSS_1363 TSS_1363 TSS_1362 TSS_1362 TSS_1361 TSS_1361 TSS_1360 TSS_1360 TSS_1359 TSS_1359 TSS_1358 TSS_1358 TSS_1357 TSS_1357 TSS_1356 TSS_1356 TSS_1355 TSS_1355 TSS_1354 TSS_1354 TSS_1353 TSS_1353 TSS_1352 (cluster) TSS_1352 (cluster)

Gene      
Name: rne    Texpresso search in the literature
Synonym(s): ECK1069, EG10859, ams, b1084, hmp1, smbB
Genome position(nucleotides): 1141182 <-- 1144367
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.65
External database links:  
ASAP:
 ABE-0003668
CGSC:
 269
ECHOBASE:
 EB0852
ECOLIHUB:
 rne
OU-MICROARRAY:
 b1084
STRING:
 511145.b1084
COLOMBOS: rne


Product      
Name: ribonuclease E
Synonym(s): Ams, Rne, SmbB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,inner membrane
Molecular weight: 118.197
Isoelectric point: 5.334
Motif(s):
 
Type Positions Sequence Comment
36 -> 118 QKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTT
39 -> 119 ANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTF UniProt: S1 motif.
57 -> 57 F UniProt: Reduces RNA cleavage by over 98%..
66 -> 66 G UniProt: Disrupts folding of the S1 motif..
67 -> 67 F UniProt: Reduces RNA cleavage by over 98%..

 
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:1902555 - endoribonuclease complex
GO:1990061 - bacterial degradosome
GO:0005737 - cytoplasm
GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0009898 - cytoplasmic side of plasma membrane
molecular_function GO:0017151 - DEAD/H-box RNA helicase binding
GO:0003676 - nucleic acid binding
GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0003723 - RNA binding
GO:0004540 - ribonuclease activity
GO:0000049 - tRNA binding
GO:0019843 - rRNA binding
GO:0008270 - zinc ion binding
GO:0004521 - endoribonuclease activity
GO:0000287 - magnesium ion binding
GO:0008312 - 7S RNA binding
GO:0042802 - identical protein binding
GO:0008995 - ribonuclease E activity
biological_process GO:1902280 - regulation of RNA helicase activity
GO:0006401 - RNA catabolic process
GO:0006402 - mRNA catabolic process
GO:0006396 - RNA processing
GO:0008033 - tRNA processing
GO:0006364 - rRNA processing
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0051289 - protein homotetramerization
GO:0000967 - rRNA 5'-end processing
GO:0090501 - RNA phosphodiester bond hydrolysis
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic
External database links:  
ALPHAFOLD:
 P21513
DIP:
 DIP-10727N
DISPROT:
 DP00207
ECOCYC:
 EG10859-MONOMER
ECOLIWIKI:
 b1084
INTERPRO:
 IPR028878
INTERPRO:
 IPR003029
INTERPRO:
 IPR004659
INTERPRO:
 IPR022967
INTERPRO:
 IPR012340
INTERPRO:
 IPR019307
INTERPRO:
 IPR021968
MINT:
 P21513
MODBASE:
 P21513
PDB:
 6G63
PDB:
 5F6C
PDB:
 3H8A
PDB:
 3H1C
PDB:
 3GME
PDB:
 3GCM
PDB:
 2VRT
PDB:
 2VMK
PDB:
 2FYM
PDB:
 2C4R
PDB:
 2C0B
PDB:
 2BX2
PDB:
 1SN8
PDB:
 1SLJ
PDB:
 1SMX
PFAM:
 PF00575
PFAM:
 PF10150
PFAM:
 PF12111
PRIDE:
 P21513
PRODB:
 PRO_000023789
PROSITE:
 PS50126
REFSEQ:
 NP_415602
SMART:
 SM00316
SMR:
 P21513
UNIPROT:
 P21513


Operon      
Name: rne         
Operon arrangement:
Transcription unit        Promoter
rne
rne
rne
rne


RNA cis-regulatory element    
   
Cis-reg RNase E 5' UTR element
   
   


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_1352 (cluster) 1141491 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1353 1141695 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1354 1141698 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1355 1141705 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1356 1141797 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1357 1142026 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1358 1142028 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1359 1142031 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1360 1142313 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1361 1143233 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1362 1144355 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1363 1144358 reverse nd [RS-EPT-CBR] [1]
  promoter yceQp6 1144380 forward nd [COMP-AINF] [2]
  promoter TSS_1364 (cluster) 1144680 reverse nd [RS-EPT-CBR] [1]


Evidence    

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

 [COMP-AINF] 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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