RegulonDB RegulonDB 10.9: Gene Form
   

rpsF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rpsF priB yjfY CRP TSS_5060 TSS_5060 TSS_5059 TSS_5059 TSS_5058 TSS_5058 TSS_5057 TSS_5057 rpsFp rpsFp TSS_5055 TSS_5055 yjfYp2 yjfYp2

Gene      
Name: rpsF    Texpresso search in the literature
Synonym(s): ECK4196, EG10905, b4200, sdgH
Genome position(nucleotides): 4425118 --> 4425513 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.53
External database links:  
ASAP:
ABE-0013740
CGSC:
225
ECHOBASE:
EB0898
ECOLIHUB:
rpsF
OU-MICROARRAY:
b4200
STRING:
511145.b4200
COLOMBOS: rpsF


Product      
Name: 30S ribosomal subunit protein S6
Synonym(s): RpsF, SdgH
Sequence: Get amino acid sequence Fasta Format
Cellular location: ribosome,cytosol
Molecular weight: 15.187
Isoelectric point: 5.067
Motif(s):
 
Type Positions Sequence
14 -> 14 Q
20 -> 20 G
3 -> 91 HYEIVFMVHPDQSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFRFNDAVIRSMVMR

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  2 - information transfer --> 2.3 - protein related --> 2.3.8 - ribosomal proteins
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0005840 - ribosome
GO:0022627 - cytosolic small ribosomal subunit
molecular_function GO:0003735 - structural constituent of ribosome
GO:0005515 - protein binding
GO:0003723 - RNA binding
GO:0019843 - rRNA binding
GO:0048027 - mRNA 5'-UTR binding
GO:0070181 - small ribosomal subunit rRNA binding
biological_process GO:0006412 - translation
Note(s): Note(s): ...[more].
Reference(s): [1] Mulder AM., et al., 2010
[2] Svensson P., et al., 1988
[3] Tang X., et al., 2014
External database links:  
DIP:
DIP-10782N
ECOCYC:
EG10905-MONOMER
ECOLIWIKI:
b4200
INTERPRO:
IPR000529
INTERPRO:
IPR014717
INTERPRO:
IPR035980
INTERPRO:
IPR020814
INTERPRO:
IPR020815
MODBASE:
P02358
PANTHER:
PTHR21011
PDB:
1EG0
PDB:
1M5G
PDB:
2YKR
PDB:
3IY8
PDB:
3J9Y
PDB:
3J9Z
PDB:
3JA1
PDB:
3JBU
PDB:
3JBV
PDB:
3JCD
PDB:
3JCE
PDB:
3JCJ
PDB:
3JCN
PDB:
4A2I
PDB:
4ADV
PDB:
4U1U
PDB:
4U1V
PDB:
4U20
PDB:
4U24
PDB:
4U25
PDB:
4U26
PDB:
4U27
PDB:
4V47
PDB:
4V48
PDB:
4V4H
PDB:
4V4Q
PDB:
4V4V
PDB:
4V4W
PDB:
4V50
PDB:
4V52
PDB:
4V53
PDB:
4V54
PDB:
4V55
PDB:
4V56
PDB:
4V57
PDB:
4V5B
PDB:
4V5H
PDB:
4V5Y
PDB:
4V64
PDB:
4V65
PDB:
4V66
PDB:
4V69
PDB:
4V6C
PDB:
4V6D
PDB:
4V6E
PDB:
4V6K
PDB:
4V6L
PDB:
4V6M
PDB:
4V6N
PDB:
4V6O
PDB:
4V6P
PDB:
4V6Q
PDB:
4V6R
PDB:
4V6S
PDB:
4V6T
PDB:
4V6V
PDB:
4V6Y
PDB:
4V6Z
PDB:
4V70
PDB:
4V71
PDB:
4V72
PDB:
4V73
PDB:
4V74
PDB:
4V75
PDB:
4V76
PDB:
4V77
PDB:
4V78
PDB:
4V79
PDB:
4V7A
PDB:
4V7B
PDB:
4V7C
PDB:
4V7D
PDB:
4V7I
PDB:
4V7S
PDB:
4V7T
PDB:
4V7U
PDB:
4V7V
PDB:
4V85
PDB:
4V89
PDB:
4V9C
PDB:
4V9D
PDB:
4V9O
PDB:
4V9P
PDB:
4WF1
PDB:
4WOI
PDB:
4WWW
PDB:
4YBB
PDB:
5AFI
PDB:
5H5U
PDB:
5IQR
PDB:
5IT8
PDB:
5J5B
PDB:
5J7L
PDB:
5J88
PDB:
5J8A
PDB:
5J91
PDB:
5JC9
PDB:
5JTE
PDB:
5JU8
PDB:
5KCR
PDB:
5KCS
PDB:
5KPS
PDB:
5KPV
PDB:
5KPW
PDB:
5KPX
PDB:
5L3P
PDB:
5LZA
PDB:
5LZB
PDB:
5LZC
PDB:
5LZD
PDB:
5LZE
PDB:
5LZF
PDB:
5MDV
PDB:
5MDW
PDB:
5MDY
PDB:
5MDZ
PDB:
5ME0
PDB:
5ME1
PDB:
5MGP
PDB:
5MY1
PDB:
5NO2
PDB:
5NO3
PDB:
5NO4
PDB:
5NP6
PDB:
5NWY
PDB:
5O2R
PDB:
5U4I
PDB:
5U9F
PDB:
5U9G
PDB:
5UYK
PDB:
5UYL
PDB:
5UYM
PDB:
5UYN
PDB:
5UYP
PDB:
5UYQ
PDB:
5UZ4
PDB:
5WDT
PDB:
5WE4
PDB:
5WE6
PDB:
5WFK
PDB:
6BU8
PDB:
6BY1
PDB:
6C4I
PDB:
6DNC
PDB:
6ENF
PDB:
6ENJ
PDB:
6ENU
PDB:
6GWT
PDB:
6GXM
PDB:
6GXN
PDB:
6GXO
PDB:
6GXP
PDB:
6H4N
PDB:
6H58
PDB:
6HRM
PDB:
6I7V
PDB:
6NQB
PDB:
6O9J
PDB:
6O9K
PDB:
6OFX
PDB:
6OG7
PDB:
6ORE
PDB:
6ORL
PDB:
6OST
PDB:
6OT3
PDB:
6OUO
PDB:
6Q97
PDB:
6Q98
PDB:
6Q9A
PDB:
6SZS
PDB:
6TBV
PDB:
6TC3
PFAM:
PF01250
PRIDE:
P02358
PRODB:
PRO_000023859
PROSITE:
PS01048
REFSEQ:
NP_418621
SMR:
P02358
UNIPROT:
P02358


Operon      
Name: rpsF-priB-rpsR-rplI         
Operon arrangement:
Transcription unit        Promoter
rpsF-priB-rpsR-rplI


Transcriptional Regulation      
Display Regulation             
Activated by: CRP


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 yjfYp2 4424828 reverse Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_5055 4424843 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_5057 4425027 forward nd [RS-EPT-CBR] [5]
  promoter TSS_5058 4425138 forward nd [RS-EPT-CBR] [5]
  promoter TSS_5059 4425715 forward nd [RS-EPT-CBR] [5]
  promoter TSS_5060 4425821 forward nd [RS-EPT-CBR] [5]


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] Mulder AM., Yoshioka C., Beck AH., Bunner AE., Milligan RA., Potter CS., Carragher B., Williamson JR., 2010, Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit., Science 330(6004):673-7

 [2] Svensson P., Changchien LM., Craven GR., Noller HF., 1988, Interaction of ribosomal proteins, S6, S8, S15 and S18 with the central domain of 16 S ribosomal RNA., J Mol Biol 200(2):301-8

 [3] Tang X., Yin Y., Ge M., Chen D., 2014, [Antisense RNA mediated gene silencing of nonessential gene rpsF in Escherichia coli]., Wei Sheng Wu Xue Bao 54(4):449-54

 [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

 [5] 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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