RegulonDB RegulonDB 11.1: Gene Form
   

ymdE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ycdU ymdE insEF4 insE4 serX insF4 Cis-reg Cis-reg TSS_1320 TSS_1320 ycdUp11 ycdUp11 ycdUp1 ycdUp1 ycdUp9 ycdUp9 insFp4 insFp4 insFp5 insFp5

Gene      
Name: ymdE    Texpresso search in the literature
Synonym(s): ECK1016, G6535, b1028
Type: Pseudo Gene
Genome position(nucleotides): 1095544 --> 1095846
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 41.25
External database links:  
ASAP:
 ABE-0003486
ECHOBASE:
 EB4103
ECOLIHUB:
 ymdE
OU-MICROARRAY:
 b1028
COLOMBOS: ymdE


Product      
Name: putative uncharacterized protein YmdE
Sequence: Get amino acid sequence Fasta Format
Isoelectric point: 6.956
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 Q7DFV4
ECOCYC:
 G6535-MONOMER
ECOLIWIKI:
 b1028
INTERPRO:
 IPR001227
INTERPRO:
 IPR016035
MODBASE:
 P75909
PRIDE:
 Q7DFV4
REFSEQ:
 NP_415547
UNIPROT:
 Q7DFV4


Operon      
Name: ymdE-ycdU         
Operon arrangement:
Transcription unit        Promoter
ymdE-ycdU


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 insFp5 1095155 reverse nd [COMP-AINF] [1]
  promoter insFp4 1095196 reverse nd [COMP-AINF] [1]
  promoter ycdUp9 1095633 forward nd [COMP-AINF] [1]
  promoter ycdUp1 1095693 forward nd [COMP-AINF] [1]
  promoter ycdUp11 1095759 forward nd [COMP-AINF] [1]
  promoter TSS_1320 1097652 reverse nd [RS-EPT-CBR] [2]


Evidence    

 [COMP-AINF] 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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