RegulonDB RegulonDB 11.1: Gene Form
   

yceD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yceD rpmF sraB yceF TSS_1386 (cluster) TSS_1386 (cluster) TSS_1385 TSS_1385 rpmFp rpmFp TSS_1384 (cluster) TSS_1384 (cluster) TSS_1383 TSS_1383 TSS_1382 (cluster) TSS_1382 (cluster) TSS_1381 TSS_1381 TSS_1380 TSS_1380 TSS_1379 (cluster) TSS_1379 (cluster) TSS_1378 TSS_1378 TSS_1377 TSS_1377 TSS_1376 (cluster) TSS_1376 (cluster) TSS_1375 (cluster) TSS_1375 (cluster) TSS_1374 TSS_1374 TSS_1373 TSS_1373 TSS_1372 TSS_1372 TSS_1371 TSS_1371 TSS_1370 TSS_1370 yceDp2 yceDp2 yceFp6 yceFp6 yceFp9 yceFp9 TSS_1368 (cluster) TSS_1368 (cluster) yceDp1 yceDp1 yceFp7 yceFp7 TSS_1366 TSS_1366 yceFp8 yceFp8 TSS_1365 TSS_1365 psrDp psrDp

Gene      
Name: yceD    Texpresso search in the literature
Synonym(s): ECK1074, EG11119, b1088
Genome position(nucleotides): 1146794 --> 1147315
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.62
External database links:  
ASAP:
 ABE-0003684
ECHOBASE:
 EB1109
ECOLIHUB:
 yceD
OU-MICROARRAY:
 b1088
STRING:
 511145.b1088
COLOMBOS: yceD


Product      
Name: DUF177 domain-containing protein YceD
Synonym(s): G30K, YceD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 19.315
Isoelectric point: 4.177
Motif(s):
 
Type Positions Sequence Comment
61 -> 171 LNGDAKVTVTLECQRCGKPFTHQVYTTYCFSPVRSDEQAEALPEAYEPIEVNEFGEIDLLAMVEDEIILALPVVPVHDSEHCEVSEADMVFGELPEEAQKPNPFAVLASLK

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
biological_process GO:0042254 - ribosome biogenesis
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P0AB28
ECOCYC:
 EG11119-MONOMER
ECOLIWIKI:
 b1088
INTERPRO:
 IPR003772
INTERPRO:
 IPR039255
PANTHER:
 PTHR38099
PFAM:
 PF02620
PRIDE:
 P0AB28
REFSEQ:
 NP_415606
UNIPROT:
 P0AB28


Operon      
Name: yceD-rpmF-plsX-fabHDG-acpP-fabF         
Operon arrangement:
Transcription unit        Promoter
yceD-rpmF
yceD-rpmF
rpmF-plsX-fabHDG
plsX-fabHDG
fabHDG
acpP
acpP-fabF
fabDG-acpP
fabF
fabG-acpP


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_1365 1146590 forward nd [RS-EPT-CBR] [1]
  promoter yceFp8 1146607 reverse nd [COMP-AINF] [2]
  promoter TSS_1366 1146625 reverse nd [RS-EPT-CBR] [1]
  promoter yceFp7 1146628 reverse nd [COMP-AINF] [2]
  promoter TSS_1368 (cluster) 1146701 reverse nd [RS-EPT-CBR] [1]
  promoter yceFp9 1146749 reverse nd [COMP-AINF] [2]
  promoter yceFp6 1146761 reverse nd [COMP-AINF] [2]
  promoter TSS_1370 1146794 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1371 1146809 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1372 1147056 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1373 1147094 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1374 1147132 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1375 (cluster) 1147141 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1376 (cluster) 1147146 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1377 1147188 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1378 1147194 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1379 (cluster) 1147206 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1380 1147213 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1381 1147215 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1382 (cluster) 1147300 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1383 1147307 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1384 (cluster) 1147313 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1385 1147350 forward nd [RS-EPT-CBR] [1]
  promoter TSS_1386 (cluster) 1147395 forward nd [RS-EPT-CBR] [1]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


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.

 [2] 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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