RegulonDB RegulonDB 10.8: Gene Form
   

rnlA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rnlA yfjP rnlB yfjM IscR anti-terminator anti-anti-terminator terminator anti-anti-terminator anti-terminator yfjPp6 yfjPp6 yfjPp5 yfjPp5 yfjPp8 yfjPp8 TSS_2981 TSS_2981 rnlBp2 rnlBp2 TSS_2980 TSS_2980 rnlBp rnlBp yfjMp3 yfjMp3 rnlAp rnlAp TSS_2978 TSS_2978 TSS_2977 TSS_2977 rnlAp2 rnlAp2

Gene      
Name: rnlA    Texpresso search in the literature
Synonym(s): ECK2626, G7365, b2630, std, yfjN
Genome position(nucleotides): 2765918 --> 2766991 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
44.32
External database links:  
ASAP:
ABE-0008659
ECHOBASE:
EB2992
OU-MICROARRAY:
b2630
PortEco:
rnlA
STRING:
511145.b2630
COLOMBOS: rnlA


Product      
Name: CP4-57 prophage; RNase LS, toxin of the RnlAB toxin-antitoxin system
Synonym(s): RnlA, Std, YfjN
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 40.061
Isoelectric point: 6.854
Motif(s):
 
Type Positions Sequence
98 -> 325 EQVNMVLQGFVETSVLPVLELSADESHIEFREHSRNAHTVVWKIISTSYQDELTVSLHITTGKLQIQGRPLSCYRVFTFNLAALLDLQGLEKVLIRQEDGKANIVQQEVARTYLQTVMADAYPHLHVTAEKLLVSGLCVKLAAPDLPDYCMLLYPELRTIEGVLKSKMSGLGMPVQQPAGFGTYFDKPAAHYILKPQFAATLRPEQINIISTAYTFFNVERHSLFHME
188 -> 196 EKVLIRQED
327 -> 357 VVDASRMISDMARLMGKATRAWGIIKDLYIV

 

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
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0004521 - endoribonuclease activity
GO:0042803 - protein homodimerization activity
biological_process GO:0006402 - mRNA catabolic process
GO:0051607 - defense response to virus
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic
External database links:  
DIP:
DIP-12079N
ECOCYC:
G7365-MONOMER
ECOLIWIKI:
b2630
INTERPRO:
IPR031845
MINT:
MINT-1290895
PDB:
4I8O
PFAM:
PF15935
PRIDE:
P52129
REFSEQ:
NP_417119
SMR:
P52129
UNIPROT:
P52129


Operon      
Name: rnlAB         
Operon arrangement:
Transcription unit        Promoter
rnlAB
rnlA
rnlB
rnlB


Transcriptional Regulation      
Display Regulation             
Repressed by: IscR


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_2977 2765896 forward nd [RS-EPT-CBR] [1]
  promoter TSS_2978 2765900 forward nd [RS-EPT-CBR] [1]
  promoter yfjMp3 2765985 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_2980 2766837 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2981 2767514 reverse nd [RS-EPT-CBR] [1]
  promoter yfjPp8 2767540 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yfjPp5 2767642 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter yfjPp6 2767644 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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