RegulonDB RegulonDB 10.8: Gene Form
   

ydcJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

opgD ydcJ ydcI unknown TSS_1808 TSS_1808 TSS_1807 TSS_1807 TSS_1806 TSS_1806 opgDp9 opgDp9 opgDp7 opgDp7 opgDp8 opgDp8 opgDp4 opgDp4 ydcJp11 ydcJp11 ydcIp ydcIp ydcJp10 ydcJp10 ydcIp4 ydcIp4

Gene      
Name: ydcJ    Texpresso search in the literature
Synonym(s): ECK1417, G6738, b1423
Genome position(nucleotides): 1495288 --> 1496631 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.68
External database links:  
ASAP:
ABE-0004750
ECHOBASE:
EB3516
ECOO157CYC:
Z2297
ECOO157CYC:
Z2298
ECOO157CYC:
Z2296
OU-MICROARRAY:
b1423
PortEco:
ydcJ
STRING:
511145.b1423
COLOMBOS: ydcJ


Product      
Name: DUF1338 domain-containing protein YdcJ
Synonym(s): YdcJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 51.043
Isoelectric point: 5.245
Motif(s):
 
Type Positions Sequence
9 -> 401 EIREQFSQAMSAMYQQEVPQYGTLLELVADVNLAVLENNPQLHEKMVNADELARLNVERHGAIRVGTAQELATLRRMFAIMGMYPVSYYDLSQAGVPVHSTAFRPIDDASLARNPFRVFTSLLRLELIENEILRQKAAEILRQRDIFTPRCRQLLEEYEQQGGFNETQAQEFVQEALETFRWHQSATVDEETYRALHNEHRLIADVVCFPGCHINHLTPRTLDIDRVQSMMPECGIEPKILIEGPPRREVPILLRQTSFKALEETVLFAGQKQGTHTARFGEIEQRGVALTPKGRQLYDDLLRNAGTGQDNLTHQMHLQETFRTFPDSEFLMRQQGLAWFRYRLTPSGEAHRQAIHPGDDPQPLIERGWVVAQPITYEDFLPVSAAGIFQSNL

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11646N
ECOCYC:
G6738-MONOMER
ECOLIWIKI:
b1423
ECOO157CYC:
Z2298-MONOMER
ECOO157CYC:
Z2297-MONOMER
ECOO157CYC:
Z2296-MONOMER
INTERPRO:
IPR009770
PFAM:
PF07063
PRIDE:
P76097
REFSEQ:
NP_415940
SMART:
SM01150
SMR:
P76097
UNIPROT:
P76097


Operon      
Name: ydcJ         
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 ydcIp4 1495117 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter ydcJp10 1495133 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter ydcJp11 1495154 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter opgDp4 1496645 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter opgDp8 1496655 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter opgDp7 1496682 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter opgDp9 1496776 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_1806 1497690 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1807 1497713 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1808 1497832 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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