RegulonDB

Gene
Name:	sokC
Synonym(s):	ECK0019, G0-9581, b4413, sof
Genome position(nucleotides):	16952 --> 17006 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	47.27
External database links:

ASAP:	ABE-0047238
ECHOBASE:	EB4290
PortEco:	sokC
COLOMBOS:	sokC

Product

Name:

SokC

Synonym(s):

SokC, sof

Type:

small RNA

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.6 - antisense RNA
Gene Ontology Terms (GO)

Note(s):

Note(s): ...[more].

Evidence:

[HIFS] Human inference of function from sequence
[IDA] Inferred from direct assay

Reference(s):

[1] Kawano M., et al., 2005
[2] Pedersen K., et al., 1999

External database links:

ECOCYC:

ECOLIWIKI:

Operon

Name:

sokC

Operon arrangement:

Transcription unit	Promoter

RNA cis-regulatory element

Attenuation:	Translational

Elements in the selected gene context region unrelated to any object in RegulonDB

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	hokCp4	16951	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.208. P-value: 8.961e-5 Read more >	[ICWHO]	[3]
promoter	TSS_41	16961	reverse	nd	[RS-EPT-CBR]	[4]
promoter	TSS_42	18023	forward	nd	[RS-EPT-CBR]	[4]
promoter	TSS_43	18025	forward	nd	[RS-EPT-CBR]	[4]

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] Kawano M., Reynolds AA., Miranda-Rios J., Storz G., 2005, Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli., Nucleic Acids Res 33(3):1040-50
[2] Pedersen K., Gerdes K., 1999, Multiple hok genes on the chromosome of Escherichia coli., Mol Microbiol 32(5):1090-102
[3] 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
[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.