RegulonDB

Gene
Name:	ybcJ
Synonym(s):	ECK0521, EG12879, b0528
Genome position(nucleotides):	556661 <-- 556873 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.93
External database links:

ASAP:	ABE-0001816
ECHOBASE:	EB2717
OU-MICROARRAY:	b0528
PortEco:	ybcJ
STRING:	511145.b0528
COLOMBOS:	ybcJ

Product

Name:

putative RNA-binding protein YbcJ

Synonym(s):

YbcJ

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

7.39

Isoelectric point:

8.258

Motif(s):

Type	Positions	Sequence
	12 -> 68	VELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQV
	9 -> 69	HPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVV

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0003723 - RNA binding
	biological_process	GO:0006412 - translation

Note(s):

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

Evidence:

[HIFS] Human inference of function from sequence
[IGI] Inferred from genetic interaction
[IMP] Inferred from mutant phenotype

Reference(s):

[1] Gagarinova A., et al., 2016
[2] Hu P., et al., 2009
[3] Volpon L., et al., 2003

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

MINT:

MODBASE:

PDB:

PFAM:

PRIDE:

PROSITE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

folD-ybcJ

Operon arrangement:

Transcription unit	Promoter
folD-ybcJ	folDp

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	ybcIp5	556632	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.688. P-value: 8.784e-5 Read more >	[ICWHO]	[4]
promoter	ybcJp4	556891	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.934. P-value: 6.144e-6 Read more >	[ICWHO]	[4]
promoter	ybcJp3	556967	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.804. P-value: 3.908e-5 Read more >	[ICWHO]	[4]
promoter	ybcJp5	557006	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.329. P-value: 2.699e-5 Read more >	[ICWHO]	[4]
promoter	ybcJp7	557025	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.746. P-value: 9.516e-5 Read more >	[ICWHO]	[4]
promoter	TSS_679	557596	reverse	nd	[RS-EPT-CBR]	[5]

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] Gagarinova A., Stewart G., Samanfar B., Phanse S., White CA., Aoki H., Deineko V., Beloglazova N., Yakunin AF., Golshani A., Brown ED., Babu M., Emili A., 2016, Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery., Cell Rep 17(3):904-916
[2] Hu P., Janga SC., Babu M., Diaz-Mejia JJ., Butland G., Yang W., Pogoutse O., Guo X., Phanse S., Wong P., Chandran S., Christopoulos C., Nazarians-Armavil A., Nasseri NK., Musso G., Ali M., Nazemof N., Eroukova V., Golshani A., Paccanaro A., Greenblatt JF., Moreno-Hagelsieb G., Emili A., 2009, Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins., PLoS Biol 7(4):e96
[3] Volpon L., Lievre C., Osborne MJ., Gandhi S., Iannuzzi P., Larocque R., Cygler M., Gehring K., Ekiel I., 2003, The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding., J Bacteriol 185(14):4204-10
[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
[5] 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.