RegulonDB RegulonDB 10.9: Gene Form
   

rpoN gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rpoN lptB hpf TSS_3525 TSS_3525 TSS_3524 TSS_3524 TSS_3523 TSS_3523 TSS_3522 TSS_3522 TSS_3521 TSS_3521 TSS_3520 TSS_3520 TSS_3519 TSS_3519 TSS_3518 TSS_3518 TSS_3517 TSS_3517 TSS_3516 TSS_3516 TSS_3515 TSS_3515 TSS_3514 (cluster) TSS_3514 (cluster) rpoNp rpoNp

Gene      
Name: rpoN    Texpresso search in the literature
Synonym(s): ECK3191, EG10898, b3202, glnF, ntrA
Genome position(nucleotides): 3344717 --> 3346150 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.86
External database links:  
ASAP:
ABE-0010514
CGSC:
17926
ECHOBASE:
EB0891
ECOLIHUB:
rpoN
OU-MICROARRAY:
b3202
STRING:
511145.b3202
COLOMBOS: rpoN


Shine dalgarno      
Sequence: cgttttagcaGGAGAGtacgattctgaacATG


Product      
Name: RNA polymerase, sigma 54 (sigma N) factor
Synonym(s): sigma;54, GlnF, NtrA, RpoN, sigma 54 factor, sigma N, sigma N factor
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 53.99
Isoelectric point: 4.368
Motif(s):
 
Type Positions Sequence
317 -> 475 QFIRSNLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASSTAIRALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQ
99 -> 103 GTSGD
5 -> 48 LQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLE
115 -> 303 ETTQTLQDYLMWQVELTPFSDTDRAIATSIVDAVDETGYLTVPLEDILESIGDEEIDIDEVEAVLKRIQRFDPVGVAAKDLRDCLLIQLSQFDKTTPWLEEARLIISDHLDLLANHDFRTLMRVTRLKEDVLKEAVNLIQSLDPRPGQSIQTGEPEYVIPDVLVRKHNGHWTVELNSDSIPRLQINQHY
366 -> 385 VLADIAQAVEMHESTISRVT

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.8 - metabolism of other compounds --> 1.8.3 - nitrogen metabolism
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.1 - sigma factors, anti-sigmafactors
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.3 - stimulon
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0032993 - protein-DNA complex
molecular_function GO:0003677 - DNA binding
GO:0016779 - nucleotidyltransferase activity
GO:0016740 - transferase activity
GO:0016987 - sigma factor activity
GO:0003899 - DNA-directed 5'-3' RNA polymerase activity
GO:0000976 - transcription regulatory region sequence-specific DNA binding
GO:0001216 - DNA-binding transcription activator activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006525 - arginine metabolic process
GO:0006352 - DNA-templated transcription, initiation
GO:0045893 - positive regulation of transcription, DNA-templated
GO:2000142 - regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Reference(s): [1] Bonocora RP., et al., 2015
External database links:  
DIP:
DIP-10776N
DISPROT:
DP01169
ECOCYC:
RPON-MONOMER
ECOLIWIKI:
b3202
INTERPRO:
IPR007634
INTERPRO:
IPR038709
INTERPRO:
IPR007046
INTERPRO:
IPR000394
PANTHER:
PTHR32248
PDB:
2MT3
PFAM:
PF04963
PFAM:
PF00309
PFAM:
PF04552
PRIDE:
P24255
PRINTS:
PR00045
PRODB:
PRO_000023850
PROSITE:
PS50044
PROSITE:
PS00718
PROSITE:
PS00717
REFSEQ:
NP_417669
SMR:
P24255
UNIPROT:
P24255


Operon      
Name: yrbG-kdsDC-lptCAB-rpoN-hpf-ptsN-rapZ-npr         
Operon arrangement:
Transcription unit        Promoter
yrbG-kdsD
yrbG-kdsDC-lptCAB
kdsC-lptCAB
kdsC-lptCAB
kdsC-lptCAB
lptAB
lptAB
lptB-rpoN-hpf-ptsN-yhbJ
rpoN-hpf-ptsN-yhbJ-npr


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_3514 (cluster) 3345196 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_3515 3345209 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3516 3345220 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3517 3345418 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3518 3345499 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3519 3345526 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3520 3345533 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3521 3345596 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3522 3345796 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3523 3345915 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3524 3346078 forward nd [RS-EPT-CBR] [2]
  promoter TSS_3525 3346195 forward nd [RS-EPT-CBR] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates



Reference(s)    

 [1] Bonocora RP., Smith C., Lapierre P., Wade JT., 2015, Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding., PLoS Genet 11(10):e1005552

 [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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