RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

yagN gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	yagN
Synonym(s):	ECK0279, G6151, b0280
Genome position(nucleotides):	295139 <-- 295579 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	43.54
External database links:

ASAP:	ABE-0000976
ECHOBASE:	EB3323
OU-MICROARRAY:	b0280
PortEco:	yagN
STRING:	511145.b0280
COLOMBOS:	yagN

Product

Name:

CP4-6 prophage; protein YagN

Synonym(s):

YagN

Sequence:

Get amino acid sequence Fasta Format

Molecular weight:

15.815

Isoelectric point:

9.663

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)

Note(s):

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

External database links:

ECOCYC:

ECOLIWIKI:

PRIDE:

REFSEQ:

UNIPROT:

Operon

Name:

yagN

Operon arrangement:

Transcription unit	Promoter

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	yagLp7	294031		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]	[1]
	promoter	TSS_474 (cluster)	295620		reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 295619 to 295620, where the highest frequency is at position 294844. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[2]
	promoter	yagNp8	295656		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.156. P-value: 5.222e-5 Read more >	[ICWHO]	[1]
	promoter	yagNp3	295660		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.583. P-value: 6.841e-5 Read more >	[ICWHO]	[1]
	promoter	yagNp5	295663		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.71. P-value: 5.601e-5 Read more >	[ICWHO]	[1]
	promoter	yagNp4	295671		reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 3.585. P-value: 4.362e-5 Read more >	[ICWHO]	[1]

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] 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

[2] 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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