RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

ryfA gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	ryfA
Synonym(s):	ECK2518, G0-8879, PAIR3b, b4440, tp1
Genome position(nucleotides):	2653855 --> 2654158 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.63
External database links:

ASAP:	ABE-0047260
ECHOBASE:	EB4526
PortEco:	ryfA
COLOMBOS:	ryfA

Product

Name:

RyfA

Synonym(s):

PAIR3, PAIR3b, Tp1, small regulatory RNA RyfA, tp1

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] Rivas E., et al., 2001
[3] Rudd KE. 1999

External database links:

ECOCYC:

ECOLIWIKI:

Operon

Name:

ryfA

Operon arrangement:

Transcription unit	Promoter

Regulation by small RNA
	Display Regulation
small RNA	IS129

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	ryfAp11	2653699		forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.705. P-value: 1.108e-5 Read more >	[ICWHO]	[4]

Evidence
[ICWHO] Inferred computationally without human oversight

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] Rivas E., Klein RJ., Jones TA., Eddy SR., 2001, Computational identification of noncoding RNAs in E. coli by comparative genomics., Curr Biol 11(17):1369-73
[3] Rudd KE., 1999, Novel intergenic repeats of Escherichia coli K-12., Res Microbiol 150(9-10):653-64
[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

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