RegulonDB

Gene
Name:	ryfD
Synonym(s):	ECK4418, G0-10600, b4609
Genome position(nucleotides):	2734153 <-- 2734295 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	40.56
External database links:

PortEco:	ryfD
COLOMBOS:	ryfD

Product

Name:

RyfD

Synonym(s):

ig: 1603, small regulatory RNA RyfD

Type:

small RNA

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	biological_process	GO:1900191 - negative regulation of single-species biofilm formation GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility

Note(s):

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

Evidence:

[IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype

Reference(s):

[1] Bak G., et al., 2015
[2] Kawano M., et al., 2005

External database links:

ECOCYC:

ECOLIWIKI:

Operon

Name:

ryfD

Operon arrangement:

Transcription unit	Promoter
ryfD	ryfDp

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	TSS_2902	2731272	reverse	nd	[RS-EPT-CBR]	[3]
promoter	TSS_2903 (cluster)	2733127	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2733126 to 2733127, where the highest frequency is at position 2731149. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[3]
promoter	TSS_2904 (cluster)	2734197	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2734196 to 2734197, where the highest frequency is at position 2732219. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[3]
promoter	TSS_2905	2734202	reverse	nd	[RS-EPT-CBR]	[3]
promoter	TSS_2907	2734207	reverse	nd	[RS-EPT-CBR]	[3]
promoter	TSS_2908 (cluster)	2734293	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 2734292 to 2734293, where the highest frequency is at position 2732315. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[3]

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

Reference(s)
[1] Bak G., Lee J., Suk S., Kim D., Young Lee J., Kim KS., Choi BS., Lee Y., 2015, Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli., Sci Rep 5:15287
[2] 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
[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.