RegulonDB RegulonDB 11.1: Gene Form
   

xseB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dxs thiI ispA xseB TSS_539 TSS_539 thiIp thiIp xseBp xseBp TSS_538 (cluster) TSS_538 (cluster)

Gene      
Name: xseB    Texpresso search in the literature
Synonym(s): ECK0416, EG11098, b0422, yajE
Genome position(nucleotides): 441101 <-- 441343
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.14
External database links:  
ASAP:
 ABE-0001466
CGSC:
 17557
ECHOBASE:
 EB1090
ECOLIHUB:
 xseB
OU-MICROARRAY:
 b0422
STRING:
 511145.b0422
COLOMBOS: xseB


Shine dalgarno      
Sequence: gaaaaatattGAGAGTcagacattcatTAT


Product      
Name: exodeoxyribonuclease VII subunit XseB
Synonym(s): XseB, YajE, exonuclease VII, small subunit
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 8.952
Isoelectric point: 4.075
Motif(s):
 
Type Positions Sequence Comment
2 -> 80 PKKNEAPASFEKALSELEQIVTRLESGDLPLEEALNEFERGVQLARQGQAKLQQAEQRVQILLSDNEDASLTPFTPDNE UniProt: Exodeoxyribonuclease 7 small subunit.
11 -> 62 FEKALSELEQIVTRLESGDLPLEEALNEFERGVQLARQGQAKLQQAEQRVQI

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.2 - DNA
  2 - information transfer --> 2.1 - DNA related --> 2.1.4 - DNA repair
  2 - information transfer --> 2.1 - DNA related --> 2.1.5 - DNA degradation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0009318 - exodeoxyribonuclease VII complex
molecular_function GO:0004518 - nuclease activity
GO:0004527 - exonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0008855 - exodeoxyribonuclease VII activity
biological_process GO:0006308 - DNA catabolic process
GO:0006298 - mismatch repair
GO:0000738 - DNA catabolic process, exonucleolytic
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P0A8G9
DIP:
 DIP-48031N
ECOCYC:
 EG11098-MONOMER
ECOLIWIKI:
 b0422
INTERPRO:
 IPR003761
INTERPRO:
 IPR037004
PANTHER:
 PTHR34137
PFAM:
 PF02609
PRIDE:
 P0A8G9
PRODB:
 PRO_000024238
REFSEQ:
 NP_414956
SMR:
 P0A8G9
SWISSMODEL:
 P0A8G9
UNIPROT:
 P0A8G9


Operon      
Name: xseB-ispA-dxs-yajO         
Operon arrangement:
Transcription unit        Promoter
xseB-ispA-dxs-yajO
yajO


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_538 (cluster) 439919 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_539 441469 forward nd [RS-EPT-CBR] [1]


Evidence    

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


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.

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