RegulonDB RegulonDB 10.8: Gene Form
   

ybcJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

folD ybcI ybcJ anti-terminator terminator TSS_679 TSS_679 ybcJp7 ybcJp7 ybcJp5 ybcJp5 ybcJp3 ybcJp3 ybcJp4 ybcJp4 ybcIp5 ybcIp5

Gene      
Name: ybcJ    Texpresso search in the literature
Synonym(s): ECK0521, EG12879, b0528
Genome position(nucleotides): 556661 <-- 556873 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
54.93
External database links:  
ASAP:
ABE-0001816
ECHOBASE:
EB2717
OU-MICROARRAY:
b0528
PortEco:
ybcJ
STRING:
511145.b0528
COLOMBOS: ybcJ


Product      
Name: putative RNA-binding protein YbcJ
Synonym(s): YbcJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 7.39
Isoelectric point: 8.258
Motif(s):
 
Type Positions Sequence
12 -> 68 VELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV
9 -> 69 HPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVV

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003723 - RNA binding
biological_process GO:0006412 - translation
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
[IGI] Inferred from genetic interaction
[IMP] Inferred from mutant phenotype
Reference(s): [1] Gagarinova A., et al., 2016
[2] Hu P., et al., 2009
[3] Volpon L., et al., 2003
External database links:  
DIP:
DIP-47878N
ECOCYC:
EG12879-MONOMER
ECOLIWIKI:
b0528
INTERPRO:
IPR002942
INTERPRO:
IPR036986
MINT:
MINT-1218447
MODBASE:
P0AAS7
PDB:
1P9K
PFAM:
PF13275
PRIDE:
P0AAS7
PROSITE:
PS50889
REFSEQ:
NP_415061
SMR:
P0AAS7
UNIPROT:
P0AAS7


Operon      
Name: folD-ybcJ         
Operon arrangement:
Transcription unit        Promoter
folD-ybcJ


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 ybcIp5 556632 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ybcJp4 556891 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ybcJp3 556967 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ybcJp5 557006 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter ybcJp7 557025 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_679 557596 reverse nd [RS-EPT-CBR] [5]


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] Gagarinova A., Stewart G., Samanfar B., Phanse S., White CA., Aoki H., Deineko V., Beloglazova N., Yakunin AF., Golshani A., Brown ED., Babu M., Emili A., 2016, Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery., Cell Rep 17(3):904-916

 [2] Hu P., Janga SC., Babu M., Diaz-Mejia JJ., Butland G., Yang W., Pogoutse O., Guo X., Phanse S., Wong P., Chandran S., Christopoulos C., Nazarians-Armavil A., Nasseri NK., Musso G., Ali M., Nazemof N., Eroukova V., Golshani A., Paccanaro A., Greenblatt JF., Moreno-Hagelsieb G., Emili A., 2009, Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins., PLoS Biol 7(4):e96

 [3] Volpon L., Lievre C., Osborne MJ., Gandhi S., Iannuzzi P., Larocque R., Cygler M., Gehring K., Ekiel I., 2003, The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding., J Bacteriol 185(14):4204-10

 [4] 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

 [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.


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