RegulonDB

Gene
Name:	ydcJ
Synonym(s):	ECK1417, G6738, b1423
Genome position(nucleotides):	1495288 --> 1496631 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.68
External database links:

ASAP:	ABE-0004750
ECHOBASE:	EB3516
ECOO157CYC:	Z2297
ECOO157CYC:	Z2298
ECOO157CYC:	Z2296
OU-MICROARRAY:	b1423
PortEco:	ydcJ
STRING:	511145.b1423
COLOMBOS:	ydcJ

Product

Name:

DUF1338 domain-containing protein YdcJ

Synonym(s):

YdcJ

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

51.043

Isoelectric point:

5.245

Motif(s):

Type	Positions	Sequence
	9 -> 401	EIREQFSQAMSAMYQQEVPQYGTLLELVADVNLAVLENNPQLHEKMVNADELARLNVERHGAIRVGTAQELATLRRMFAIMGMYPVSYYDLSQAGVPVHSTAFRPIDDASLARNPFRVFTSLLRLELIENEILRQKAAEILRQRDIFTPRCRQLLEEYEQQGGFNETQAQEFVQEALETFRWHQSATVDEETYRALHNEHRLIADVVCFPGCHINHLTPRTLDIDRVQSMMPECGIEPKILIEGPPRREVPILLRQTSFKALEETVLFAGQKQGTHTARFGEIEQRGVALTPKGRQLYDDLLRNAGTGQDNLTHQMHLQETFRTFPDSEFLMRQQGLAWFRYRLTPSGEAHRQAIHPGDDPQPLIERGWVVAQPITYEDFLPVSAAGIFQSNL

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
Gene Ontology Terms (GO)	cellular_component	GO:0005829 - cytosol

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

ECOO157CYC:

ECOO157CYC:

ECOO157CYC:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMART:

SMR:

UNIPROT:

Operon

Name:

ydcJ

Operon arrangement:

Transcription unit	Promoter

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	ydcIp4	1495117	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.764. P-value: 5.771e-5 Read more >	[ICWHO]	[1]
promoter	ydcJp10	1495133	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.743. P-value: 9.051e-5 Read more >	[ICWHO]	[1]
promoter	ydcJp11	1495154	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.934. P-value: 6.023e-6 Read more >	[ICWHO]	[1]
promoter	opgDp4	1496645	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.106. P-value: 4.586e-5 Read more >	[ICWHO]	[1]
promoter	opgDp8	1496655	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.195. P-value: 2.166e-5 Read more >	[ICWHO]	[1]
promoter	opgDp7	1496682	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.16. P-value: 2.467e-5 Read more >	[ICWHO]	[1]
promoter	opgDp9	1496776	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.876. P-value: 6.910e-5 Read more >	[ICWHO]	[1]
promoter	TSS_1806	1497690	forward	nd	[RS-EPT-CBR]	[2]
promoter	TSS_1807	1497713	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_1808	1497832	forward	nd	[RS-EPT-CBR]	[2]

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.