RegulonDB RegulonDB 10.8: Gene Form
   

racR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

racR ydaS ydaG unknown racRp4 racRp4 ydaSp6 ydaSp6 ydaSp2 ydaSp2 ydaSp4 ydaSp4 racRp3 racRp3 racRp5 racRp5 ydaSp3 ydaSp3 TSS_1775 TSS_1775

Gene      
Name: racR    Texpresso search in the literature
Synonym(s): ECK1354, G6680, b1356, rarC, ydaR
Genome position(nucleotides): 1419765 <-- 1420241 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
41.93
External database links:  
ASAP:
ABE-0004548
ECHOBASE:
EB3143
OU-MICROARRAY:
b1356
PortEco:
racR
STRING:
511145.b1356
COLOMBOS: racR


Product      
Name: Rac prophage; DNA-binding transcriptional repressor RacR
Synonym(s): RacR, RarC, YdaR
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 17.663
Isoelectric point: 8.799
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0001217 - DNA-binding transcription repressor activity
biological_process GO:0006351 - transcription, DNA-templated
GO:2000143 - negative regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Evidence: [AIFS] Automated inference of function from sequence
[APPHINH] Assay of protein purified to homogeneity from its native host
[IEP] Inferred from expression pattern
[IHBCE] Inferred by a human based on computational evidence
Reference(s): [1] Bindal G., et al., 2017
[2] Krishnamurthi R., et al., 2017
[3] Perez-Rueda E., et al., 2000
[4] Perez-Rueda E., et al., 2004
External database links:  
ECOCYC:
G6680-MONOMER
ECOLIWIKI:
b1356
INTERPRO:
IPR010982
PRIDE:
P76062
PRODB:
PRO_000023674
REFSEQ:
NP_415874
SMR:
P76062
UNIPROT:
P76062


Operon      
Name: racR         
Operon arrangement:
Transcription unit        Promoter
 


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_1775 1419829 reverse nd [RS-EPT-CBR] [5]
  promoter ydaSp3 1420170 forward Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter racRp5 1420242 reverse Similarity to the consensus
Read more >
[ICWHO], [RS-EPT-CBR] [5], [6]
  promoter racRp3 1420244 reverse Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter ydaSp4 1420260 forward Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter ydaSp2 1420277 forward Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter ydaSp6 1420343 forward Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter racRp4 1420449 reverse Similarity to the consensus
Read more >
[ICWHO] [6]


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] Bindal G., Krishnamurthi R., Seshasayee ASN., Rath D., 2017, CRISPR-Cas-Mediated Gene Silencing Reveals RacR To Be a Negative Regulator of YdaS and YdaT Toxins in Escherichia coli K-12., mSphere 2(6)

 [2] Krishnamurthi R., Ghosh S., Khedkar S., Seshasayee ASN., 2017, Repression of YdaS Toxin Is Mediated by Transcriptional Repressor RacR in the Cryptic rac Prophage of Escherichia coli K-12., mSphere 2(6)

 [3] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [4] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [5] 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.

 [6] 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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