RegulonDB RegulonDB 11.1: Gene Form
   

ydiZ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pfkB yniA ydiZ yniAp5 yniAp5 TSS_2040 TSS_2040 yniAp1 yniAp1 yniAp7 yniAp7 TSS_2039 TSS_2039 TSS_2038 TSS_2038

Gene      
Name: ydiZ    Texpresso search in the literature
Synonym(s): ECK1722, G6929, b1724
Genome position(nucleotides): 1807400 --> 1807690
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 43.3
External database links:  
ASAP:
 ABE-0005751
ECHOBASE:
 EB3741
ECOLIHUB:
 ydiZ
OU-MICROARRAY:
 b1724
STRING:
 511145.b1724
COLOMBOS: ydiZ


Product      
Name: putative endoribonuclease YdiZ
Synonym(s): YdiZ
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 10.865
Isoelectric point: 3.961
Motif(s):
 
Type Positions Sequence Comment
3 -> 94 SGDLVRYVITVMLHEDTLTEINELNNYLTRDGFLLTMTDDEGNIHELGTNTFGLISTQSEEEIRELVSGLTQSATGKDPEITITTWEEWNSN

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
molecular_function GO:0004521 - endoribonuclease activity
biological_process GO:0006974 - cellular response to DNA damage stimulus
GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
ALPHAFOLD:
 P64479
DIP:
 DIP-48166N
ECOCYC:
 G6929-MONOMER
ECOLIWIKI:
 b1724
INTERPRO:
 IPR022597
INTERPRO:
 IPR038241
PFAM:
 PF11080
PRIDE:
 P64479
REFSEQ:
 NP_416238
UNIPROT:
 P64479


Operon      
Name: ydiZ         
Operon arrangement:
Transcription unit        Promoter
ydiZ


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_2038 1807375 forward nd [RS-EPT-CBR] [2]
  promoter TSS_2039 1807377 forward nd [RS-EPT-CBR] [2]
  promoter yniAp7 1807579 forward nd [COMP-AINF] [3]
  promoter yniAp1 1807719 forward nd [COMP-AINF] [3]
  promoter TSS_2040 1807770 forward nd [RS-EPT-CBR] [2]
  promoter yniAp5 1807775 forward nd [COMP-AINF] [3]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [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.

 [3] 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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