RegulonDB RegulonDB 11.1: Gene Form
   

csrA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

alaS csrA serV terminator TSS_3008 TSS_3008 TSS_3007 (cluster) TSS_3007 (cluster) TSS_3006 TSS_3006 csrAp1 csrAp1 csrAp csrAp csrAp2 csrAp2 csrAp3 csrAp3 csrAp4 csrAp4 csrAp5 csrAp5 serVp serVp TSS_3002 TSS_3002

Gene      
Name: csrA    Texpresso search in the literature
Synonym(s): ECK2691, EG11447, b2696, zfiA
Genome position(nucleotides): 2818961 <-- 2819146
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.46
Reference(s): [1] Romeo T., et al., 1993
[2] Romeo T., et al., 1993
External database links:  
ASAP:
 ABE-0008866
CGSC:
 34504
ECHOBASE:
 EB1416
ECOLIHUB:
 csrA
OU-MICROARRAY:
 b2696
STRING:
 511145.b2696
COLOMBOS: csrA


Product      
Name: carbon storage regulator
Synonym(s): CsrA, ZfiA, pleiotropic regulatory protein for carbon source metabolism, translational dual regulator CsrA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 6.856
Isoelectric point: 9.107
Motif(s):
 
Type Positions Sequence Comment
1 -> 52 MLILTRRVGETLMIGDEVTVTVLGVKGNQVRIGVNAPKEVSVHREEIYQRIQ
2 -> 7 LILTRR UniProt: Region 1, important for regulation and mRNA-binding; Sequence Annotation Type: region of interest.
3 -> 3 I UniProt: 80% loss of in vivo repression and activation, about 20% wild-type protein levels..
4 -> 4 L UniProt: 90% loss of in vivo repression and activation, 60-fold decreased affinity for RNA, about 60% wild-type protein levels..
6 -> 6 R UniProt: Nearly complete loss of in vivo repression and activation, 30-fold decreased affinity for RNA, about 175% wild-type protein levels..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.1 - carbon utilization --> 1.1.1 - carbon compounds
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.1 - glycolysis
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.9 - cytoplasmic polysaccharides
  1 - metabolism --> 1.7 - central intermediary metabolism
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.4 - global
  5 - cell processes --> 5.3 - motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003723 - RNA binding
GO:0048027 - mRNA 5'-UTR binding
biological_process GO:0031438 - negative regulation of mRNA cleavage
GO:0006417 - regulation of translation
GO:0045947 - negative regulation of translational initiation
GO:0006109 - regulation of carbohydrate metabolic process
GO:0006402 - mRNA catabolic process
GO:0017148 - negative regulation of translation
GO:0045948 - positive regulation of translational initiation
GO:0048255 - mRNA stabilization
GO:0045719 - negative regulation of glycogen biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [3] Sharan M., et al., 2017
External database links:  
ALPHAFOLD:
 P69913
DIP:
 DIP-47836N
ECOCYC:
 EG11447-MONOMER
ECOLIWIKI:
 b2696
INTERPRO:
 IPR003751
INTERPRO:
 IPR036107
PANTHER:
 PTHR34984
PDB:
 5Z38
PDB:
 1Y00
PFAM:
 PF02599
PRIDE:
 P69913
PRODB:
 PRO_000022345
REFSEQ:
 NP_417176
SMR:
 P69913
UNIPROT:
 P69913


Operon      
Name: csrA         
Operon arrangement:
Transcription unit        Promoter
csrA
csrA
 
csrA
csrA
csrA


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_3002 2818645 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_3006 2819585 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_3007 (cluster) 2819687 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_3008 2821435 reverse nd [RS-EPT-CBR] [4]


Evidence    

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


Reference(s)    

 [1] Romeo T., Gong M., 1993, Genetic and physical mapping of the regulatory gene csrA on the Escherichia coli K-12 chromosome., J Bacteriol 175(17):5740-1

 [2] Romeo T., Gong M., Liu MY., Brun-Zinkernagel AM., 1993, Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties., J Bacteriol 175(15):4744-55

 [3] Sharan M., Forstner KU., Eulalio A., Vogel J., 2017, APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins., Nucleic Acids Res 45(11):e96

 [4] 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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