RegulonDB RegulonDB 10.8: Gene Form
   

yniD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

thrS arpB ydiY yniD NsrR DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp DksA-ppGpp terminator yniDp6 yniDp6 thrSp thrSp TSS_2036 TSS_2036 TSS_2035 TSS_2035 TSS_2034 TSS_2034 TSS_2033 (cluster) TSS_2033 (cluster) TSS_2032 TSS_2032 TSS_2031 TSS_2031 TSS_2030 TSS_2030 TSS_2029 TSS_2029 infCp infCp TSS_2027 TSS_2027 TSS_2026 TSS_2026 TSS_2025 (cluster) TSS_2025 (cluster) TSS_2024 TSS_2024 infCp2 infCp2 TSS_2023 TSS_2023

Gene      
Name: yniD    Texpresso search in the literature
Synonym(s): ECK1719, G0-10453, b4535
Genome position(nucleotides): 1805165 --> 1805272 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.15
External database links:  
ASAP:
ABE-0285056
ECHOBASE:
EB4399
PortEco:
yniD
STRING:
511145.b4535
COLOMBOS: yniD


Product      
Name: uncharacterized protein YniD
Synonym(s): YniD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 4.115
Isoelectric point: 11.228
Motif(s):
 
Type Positions Sequence
9 -> 33 KHWKMVVVLLAICGAMLLLRWAAMI

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
MONOMER0-2675
ECOLIWIKI:
b4535
PRIDE:
Q2EES1
REFSEQ:
YP_588455
UNIPROT:
Q2EES1


Operon      
Name: yniD         
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_2023 1800817 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2024 1800819 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2025 (cluster) 1801170 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_2026 1801273 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2027 1801278 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2029 1801426 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2030 1801552 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2031 1801633 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2032 1802563 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2033 (cluster) 1802626 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_2034 1802634 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2035 1802637 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2036 1802699 reverse nd [RS-EPT-CBR] [1]
  promoter yniDp6 1805101 forward Similarity to the consensus
Read more >
[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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