RegulonDB RegulonDB 10.10: Gene Form
   

yggL gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mutY trmB yggN yggL anti-anti-terminator anti-terminator terminator TSS_3294 TSS_3294 yggXp yggXp mutYp1 mutYp1 mutYp2 mutYp2 TSS_3292 TSS_3292 TSS_3291 TSS_3291 TSS_3290 TSS_3290 yggLp3 yggLp3 yggLp2 yggLp2 TSS_3288 TSS_3288 TSS_3287 (cluster) TSS_3287 (cluster) TSS_3286 (cluster) TSS_3286 (cluster) TSS_3285 (cluster) TSS_3285 (cluster) TSS_3284 TSS_3284 yggNp1 yggNp1 yggNp2 yggNp2 yggNp2b yggNp2b TSS_3283 TSS_3283

Gene      
Name: yggL    Texpresso search in the literature
Synonym(s): ECK2954, EG12443, b2959
Genome position(nucleotides): 3101807 <-- 3102133 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.62
External database links:  
ASAP:
ABE-0009712
ECHOBASE:
EB2337
ECOLIHUB:
yggL
OU-MICROARRAY:
b2959
STRING:
511145.b2959
COLOMBOS: yggL


Product      
Name: putative ribosome assembly factor YggL
Synonym(s): DUF469 domain-containing protein YggL, YggL
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 12.881
Isoelectric point: 4.596
Motif(s):
 
Type Positions Sequence
73 -> 73 E
7 -> 107 RRLRKKMHIDEFQELGFSVAWRFPEGTSEEQIDKTVDDFINEVIEPNKLAFDGSGYLAWEGLICMQEIGKCTEEHQAIVRKWLEERKLDEVRTSELFDVWW

 

Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0043022 - ribosome binding
GO:0043023 - ribosomal large subunit binding
biological_process GO:0042255 - ribosome assembly
Note(s): Note(s): ...[more].
Reference(s): [1] Chen SS., et al., 2013
[2] Hor J., et al., 2020
External database links:  
DIP:
DIP-12189N
ECOCYC:
EG12443-MONOMER
ECOLIWIKI:
b2959
INTERPRO:
IPR007416
PANTHER:
PTHR38778
PFAM:
PF04320
PRIDE:
P38521
REFSEQ:
NP_417434
UNIPROT:
P38521


Operon      
Name: trmB-yggL         
Operon arrangement:
Transcription unit        Promoter
trmB-yggL


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_3283 3101055 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3284 3102157 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3285 (cluster) 3102193 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3286 (cluster) 3102200 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3287 (cluster) 3102236 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3288 3102247 reverse nd [RS-EPT-CBR] [3]
  promoter yggLp2 3102250 reverse nd [ICWHO], [RS-EPT-CBR] [3], [4]
  promoter yggLp3 3102254 reverse nd [ICWHO] [4]
  promoter TSS_3290 3102279 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3291 3102291 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3292 3102390 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_3294 3104042 forward nd [RS-EPT-CBR] [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] Chen SS., Williamson JR., 2013, Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry., J Mol Biol 425(4):767-79

 [2] Hor J., Di Giorgio S., Gerovac M., Venturini E., Forstner KU., Vogel J., 2020, Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli., Nucleic Acids Res 48(16):9301-9319

 [3] 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.

 [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


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