RegulonDB RegulonDB 10.10: Gene Form
   

yjdM gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rdcA yjdM naRNA1 rdcB rdcAp1 rdcAp1 rdcAp2 rdcAp2 yjdMp5 yjdMp5 TSS_4909 (cluster) TSS_4909 (cluster)

Gene      
Name: yjdM    Texpresso search in the literature
Synonym(s): ECK4101, EG10711, b4108, phnA
Genome position(nucleotides): 4326399 <-- 4326734 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 46.43
External database links:  
ASAP:
 ABE-0013451
ECHOBASE:
 EB0705
ECOLIHUB:
 yjdM
OU-MICROARRAY:
 b4108
STRING:
 511145.b4108
COLOMBOS: yjdM


Product      
Name: zinc ribbon domain-containing protein YjdM
Synonym(s): PhnA, YjdM
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 12.345
Isoelectric point: 4.736
Motif(s):
 
Type Positions Sequence
44 -> 111 VKDANGNLLADGDSVTIIKDLKVKGSSSMLKIGTKVKNIRLVEGDHNIDCKIDGFGPMKLKSEFVKKN
2 -> 30 SLPHCPKCNSEYTYEDNGMYICPECAYEW

 
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-48079N
ECOCYC:
 EG10711-MONOMER
ECOLIWIKI:
 b4108
INTERPRO:
 IPR013987
INTERPRO:
 IPR004624
INTERPRO:
 IPR013988
PANTHER:
 PTHR30305:SF3
PFAM:
 PF03831
PFAM:
 PF08274
PRIDE:
 P0AFJ1
PRODB:
 PRO_000023530
REFSEQ:
 NP_418532
SMR:
 P0AFJ1
UNIPROT:
 P0AFJ1


Operon      
Name: yjdM         
Operon arrangement:
Transcription unit        Promoter
yjdM


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_4909 (cluster) 4326796 reverse nd [RS-EPT-CBR] [1]
  promoter yjdMp5 4326836 reverse nd [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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