RegulonDB RegulonDB 10.8: Gene Form
   

yccF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yccS helD yccF sxy TSS_1287 TSS_1287 TSS_1286 TSS_1286 helDp helDp yccFp yccFp yccSp2 yccSp2 yccSp3 yccSp3

Gene      
Name: yccF    Texpresso search in the literature
Synonym(s): ECK0952, G6496, b0961
Genome position(nucleotides): 1023902 <-- 1024348 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.32
External database links:  
ASAP:
ABE-0003253
ECHOBASE:
EB2212
OU-MICROARRAY:
b0961
PortEco:
yccF
STRING:
511145.b0961
COLOMBOS: yccF


Product      
Name: PF03733 family inner membrane protein YccF
Synonym(s): YccF
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 16.275
Isoelectric point: 9.516
Motif(s):
 
Type Positions Sequence
77 -> 127 VLNIFWLIFFGWWLCLMHIATGIAQCISIIGIPVGIANFKIAAIALWPVGR
103 -> 125 ISIIGIPVGIANFKIAAIALWPV
4 -> 53 VLNILNFVLGGFATTLGWLLATLVSIVLIFTLPLTRSCWEITKLSLVPYG
15 -> 37 FATTLGWLLATLVSIVLIFTLPL

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0016021 - integral component of membrane
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
G6496-MONOMER
ECOLIWIKI:
b0961
INTERPRO:
IPR005185
INTERPRO:
IPR031308
PFAM:
PF03733
PRIDE:
P0AB12
REFSEQ:
NP_415481
UNIPROT:
P0AB12


Operon      
Name: yccFS         
Operon arrangement:
Transcription unit        Promoter
yccFS


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 yccSp3 1023976 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter yccSp2 1023994 reverse Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_1286 1024442 forward nd [RS-EPT-CBR] [2]
  promoter TSS_1287 1025511 forward nd [RS-EPT-CBR] [2]


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] 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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