RegulonDB RegulonDB 10.8: Gene Form
   

rne gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rne yceQ flgL3\' 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 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.65
External database links:  
ASAP:
ABE-0003668
CGSC:
269
ECHOBASE:
EB0852
OU-MICROARRAY:
b1084
PortEco:
rne
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
66 -> 66 G
407 -> 407 C
833 -> 850 ASPELASGKVWIRYPIVR
67 -> 67 F
169 -> 170 RT

 

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: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:  
DIP:
DIP-10727N
DISPROT:
DP00207
ECOCYC:
EG10859-MONOMER
ECOLIWIKI:
b1084
INTERPRO:
IPR004659
INTERPRO:
IPR003029
INTERPRO:
IPR019307
INTERPRO:
IPR028878
INTERPRO:
IPR012340
INTERPRO:
IPR021968
INTERPRO:
IPR022967
MINT:
P21513
MODBASE:
P21513
PDB:
6G63
PDB:
5F6C
PDB:
3H8A
PDB:
3H1C
PDB:
3GCM
PDB:
2VRT
PDB:
2VMK
PDB:
2FYM
PDB:
2C4R
PDB:
2C0B
PDB:
2BX2
PDB:
1SN8
PDB:
1SMX
PDB:
1SLJ
PDB:
3GME
PFAM:
PF12111
PFAM:
PF00575
PFAM:
PF10150
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 For this promoter, there
Read more >
[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 Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1364 (cluster) 1144680 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]


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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