RegulonDB RegulonDB 10.7: Gene Form
   

intF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

intF yagN nc1 ykgV yagNp4 yagNp4 yagNp5 yagNp5 yagNp3 yagNp3 yagNp8 yagNp8 TSS_474 (cluster) TSS_474 (cluster)

Gene      
Name: intF    Texpresso search in the literature
Synonym(s): ECK0280, G6152, b0281, yagO
Genome position(nucleotides): 295696 <-- 297096 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
44.33
External database links:  
ASAP:
ABE-0000979
ECHOBASE:
EB3324
ECOO157CYC:
Z1835
OU-MICROARRAY:
b0281
PORTECO:
intF
REGULONDB:
b0281
STRING:
511145.b0281
M3D: intF
COLOMBOS: intF
PortEco: b0281


Product      
Name: CP4-6 prophage; putative phage integrase
Synonym(s): IntF, YagO
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 53.074
Isoelectric point: 10.511
Motif(s):
 
Type Positions Sequence
268 -> 445 KADDCLQKEQLKSWFSAVRSLNNPIASAYLQVLLLTGARREEIASLRWSDVDFKWSSMRIKDKIEGERIIPLTPYVSELLNVLAQSPNSDVNKEGWVFRSNSKSGKIIEPRSAHNRALVLAELPHISLHGLRRSFGTLAEWVEVPTGIVAQIMGHKPSALAEKHYRRRPLDLLRKWHE
273 -> 433 LQKEQLKSWFSAVRSLNNPIASAYLQVLLLTGARREEIASLRWSDVDFKWSSMRIKDKIEGERIIPLTPYVSELLNVLAQSPNSDVNKEGWVFRSNSKSGKIIEPRSAHNRALVLAELPHISLHGLRRSFGTLAEWVEVPTGIVAQIMGHKPSALAEKHYR
54 -> 119 DADVTTLACRATSGAKAFVFQSVYAGKTLRMTIGNINDWKIDDARAEARRLQTLIDTGIDPRIAKA

 

Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
molecular_function GO:0003677 - DNA binding
biological_process GO:0010165 - response to X-ray
GO:0044826 - viral genome integration into host DNA
GO:0006310 - DNA recombination
GO:0015074 - DNA integration
GO:0046718 - viral entry into host cell
GO:0075713 - establishment of integrated proviral latency
Note(s): Note(s): ...[more].
Reference(s): [1] Sargentini NJ., et al., 2016
External database links:  
ECOCYC:
G6152-MONOMER
ECOLIWIKI:
b0281
ECOO157CYC:
Z1835-MONOMER
INTERPRO:
IPR025166
INTERPRO:
IPR038488
INTERPRO:
IPR011010
INTERPRO:
IPR010998
INTERPRO:
IPR002104
INTERPRO:
IPR013762
MODBASE:
P71298
PFAM:
PF13356
PFAM:
PF00589
PRIDE:
P71298
PROSITE:
PS51898
PROTEINMODELPORTAL:
P71298
REFSEQ:
NP_414815
SMR:
P71298
UNIPROT:
P71298


Operon      
Name: intF         
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_474 (cluster) 295620 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter yagNp8 295656 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yagNp3 295660 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yagNp5 295663 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter yagNp4 295671 reverse Similarity to the consensus
Read more >
[ICWHO] [3]


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] Sargentini NJ., Gularte NP., Hudman DA., 2016, Screen for genes involved in radiation survival of Escherichia coli and construction of a reference database., Mutat Res 793-794:1-14

 [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.

 [3] 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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