RegulonDB RegulonDB 10.10: Gene Form
   

rnhA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

gloB dnaQ yafS rnhA rnhAp rnhAp TSS_433 TSS_433 TSS_432 (cluster) TSS_432 (cluster) dnaQp2 dnaQp2 TSS_431 TSS_431 dnaQp1 dnaQp1 gloBp5 gloBp5 TSS_430 TSS_430 yafSp2 yafSp2

Gene      
Name: rnhA    Texpresso search in the literature
Synonym(s): ECK0214, EG10860, b0214, cer, dasF, herA, rnh, sdrA, sin
Genome position(nucleotides): 235535 <-- 236002 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.43
External database links:  
ASAP:
 ABE-0000717
CGSC:
 268
ECHOBASE:
 EB0853
ECOLIHUB:
 rnhA
MIM:
 616479
OU-MICROARRAY:
 b0214
STRING:
 511145.b0214
COLOMBOS: rnhA


Product      
Name: ribonuclease HI
Synonym(s): Cer, DasF, HerA, RNase H, RNase HI, RNase HI, degrades RNA of DNA-RNA hybrids, participates in DNA replication, Rnh, RnhA, SdrA, Sin, type I RNase H
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 17.597
Isoelectric point: 8.478
Motif(s):
 
Type Positions Sequence
70 -> 70 D
3 -> 141 KQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAA
10 -> 10 D
130 -> 130 N
1 -> 142 MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHCEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERCDELARAAAM

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.1 - RNA
  2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication
  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:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0004523 - RNA-DNA hybrid ribonuclease activity
GO:0000287 - magnesium ion binding
biological_process GO:0006401 - RNA catabolic process
GO:0043137 - DNA replication, removal of RNA primer
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-47864N
ECOCYC:
 EG10860-MONOMER
ECOLIWIKI:
 b0214
INTERPRO:
 IPR002156
INTERPRO:
 IPR012337
INTERPRO:
 IPR022892
INTERPRO:
 IPR036397
MODBASE:
 P0A7Y4
PDB:
 1RBT
PDB:
 4Z0U
PDB:
 3QIO
PDB:
 3QIN
PDB:
 3HYF
PDB:
 3AA5
PDB:
 3AA4
PDB:
 1F21
PDB:
 1G15
PDB:
 1GOA
PDB:
 1GOB
PDB:
 1GOC
PDB:
 1JL1
PDB:
 1JL2
PDB:
 1JXB
PDB:
 1KVA
PDB:
 1KVB
PDB:
 1KVC
PDB:
 1LAV
PDB:
 1LAW
PDB:
 1RBR
PDB:
 1RBS
PDB:
 1RBU
PDB:
 1RBV
PDB:
 1RCH
PDB:
 1RDA
PDB:
 1RDB
PDB:
 1RDC
PDB:
 1RDD
PDB:
 1RNH
PDB:
 1WSE
PDB:
 1WSF
PDB:
 1WSG
PDB:
 1WSH
PDB:
 1WSI
PDB:
 1WSJ
PDB:
 2RN2
PDB:
 2YV0
PDB:
 2Z1G
PDB:
 2Z1H
PDB:
 2Z1I
PDB:
 2Z1J
PDB:
 3AA2
PDB:
 3AA3
PFAM:
 PF00075
PRIDE:
 P0A7Y4
PRODB:
 PRO_000023795
PROSITE:
 PS50879
REFSEQ:
 NP_414750
SMR:
 P0A7Y4
UNIPROT:
 P0A7Y4


Operon      
Name: rnhA         
Operon arrangement:
Transcription unit        Promoter
rnhA


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 yafSp2 234784 forward nd [ICWHO] [1]
  promoter TSS_430 234785 forward nd [RS-EPT-CBR] [2]
  promoter gloBp5 234926 reverse nd [ICWHO] [1]
  promoter TSS_431 235937 forward nd [RS-EPT-CBR] [2]
  promoter TSS_432 (cluster) 236020 forward nd [RS-EPT-CBR] [2]
  promoter TSS_433 236027 forward nd [RS-EPT-CBR] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] 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

 [2] 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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