RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

yohJ gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	yohJ
Synonym(s):	ECK2134, EG12023, b2141
Genome position(nucleotides):	2230624 --> 2231022 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.37
External database links:

ASAP:	ABE-0007078
ECHOBASE:	EB1958
OU-MICROARRAY:	b2141
PortEco:	yohJ
STRING:	511145.b2141
COLOMBOS:	yohJ

Product

Name:

PF03788 family membrane protein YohJ

Synonym(s):

YohJ

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

inner membrane

Molecular weight:

14.579

Isoelectric point:

9.18

Motif(s):

Type	Positions	Sequence
	23 -> 113	YAGIFIASLLPVTIPGSIIGMLILFVLLALQILPAKWVNPGCYVLIRYMALLFVPIGVGVMQYFDLLRAQFGPVVVSCAVSTLVVFLVVSW
	63 -> 83	GCYVLIRYMALLFVPIGVGVM
	7 -> 27	IIWQYLRAFVLIYACLYAGIF
	31 -> 51	LLPVTIPGSIIGMLILFVLLA
	93 -> 113	FGPVVVSCAVSTLVVFLVVSW

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0016020 - membrane GO:0005886 - plasma membrane GO:0016021 - integral component of membrane

Note(s):

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

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PANTHER:

PFAM:

PRIDE:

REFSEQ:

UNIPROT:

Operon

Name:

yohJK

Operon arrangement:

Transcription unit	Promoter
yohJK	yohJp

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	yohJp4	2230493	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.338. P-value: 7.485e-5 Read more >	[ICWHO]	[1]
promoter	TSS_2454	2230603	forward	nd	[RS-EPT-CBR]	[2]
promoter	sanAp3	2232684	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: poor homology. Score: 4.029. P-value: 5.068e-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.

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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