RegulonDB RegulonDB 10.7: Gene Form
   

yneJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

sad yneK yneJ yneKp5 yneKp5 yneKp6 yneKp6 TSS_1840 TSS_1840 sadp5 sadp5 yneJp6 yneJp6 yneJp5 yneJp5

Gene      
Name: yneJ    Texpresso search in the literature
Synonym(s): ECK1519, G6812, b1526
Genome position(nucleotides): 1614804 --> 1615685 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.51
External database links:  
ASAP:
ABE-0005096
ECHOBASE:
EB3579
OU-MICROARRAY:
b1526
PORTECO:
yneJ
REGULONDB:
b1526
STRING:
511145.b1526
M3D: yneJ
COLOMBOS: yneJ
PortEco: b1526


Product      
Name: putative LysR-type DNA-binding transcriptional regulator YneJ
Synonym(s): YneJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 32.483
Isoelectric point: 6.795
Motif(s):
 
Type Positions Sequence
3 -> 61 LTQLEMFNAVAEAGSITQAAAKVHRVPSNLTTRLRQLETELGVDLFIRENQRLRLSPAG
18 -> 38 ITQAAAKVHRVPSNLTTRLRQ
85 -> 282 DEPQGLFSLGSLESTAAVRIPATLAEFNRRYPKIQFSLSTGPSGTMLDGVLEGKLNAAFIDGPINHTAIDGIPVYREELMIVTPQGYAPVTRASQVNGSNIYAFRANCSYRRHFESWFHADGAAPGTIHEMESYHGMLACVIAGAGIALIPRSMLESMPGHHQVEAWPLAEQWRWLTTWLVWRRGAKTRPLEAFIQLL
1 -> 58 MDLTQLEMFNAVAEAGSITQAAAKVHRVPSNLTTRLRQLETELGVDLFIRENQRLRLS

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
Reference(s): [1] Paradis-Bleau C., et al., 2014
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
External database links:  
ECOCYC:
G6812-MONOMER
ECOLIWIKI:
b1526
INTERPRO:
IPR005119
INTERPRO:
IPR000847
INTERPRO:
IPR036388
INTERPRO:
IPR036390
MODBASE:
P77309
PFAM:
PF03466
PFAM:
PF00126
PRIDE:
P77309
PROSITE:
PS50931
PROTEINMODELPORTAL:
P77309
REFSEQ:
NP_416043
SMR:
P77309
UNIPROT:
P77309


Operon      
Name: yneJ         
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 yneJp5 1614780 forward Similarity to the consensus
Read more >
[ICWHO], [RS-EPT-CBR] [4], [5]
  promoter yneJp6 1614788 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter sadp5 1614799 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1840 1614845 reverse nd [RS-EPT-CBR] [5]
  promoter yneKp6 1615550 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter yneKp5 1615731 forward Similarity to the consensus
Read more >
[ICWHO] [4]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [2] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [3] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [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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