RegulonDB

RegulonDB RegulonDB 10.9: Gene Form

ychJ gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	ychJ
Synonym(s):	ECK1228, EG12119, b1233
Genome position(nucleotides):	1288674 <-- 1289132 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	46.41
External database links:

ASAP:	ABE-0004140
ECHOBASE:	EB2040
ECOLIHUB:	ychJ
OU-MICROARRAY:	b1233
STRING:	511145.b1233
COLOMBOS:	ychJ

Product

Name:

NTF2-like domain-containing protein YchJ

Synonym(s):

YchJ

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

16.99

Isoelectric point:

7.293

Motif(s):

Type	Positions	Sequence
	34 -> 35	MR
	59 -> 61	AAA
	1 -> 19	MSQLCPCGSAVEYSLCCHP
	134 -> 151	RNDPCPCGSGKKFKKCCG
	29 -> 127	DPEHLMRSRYCAFVMQDADYLIKTWHPSCGAAALRAELMAGFAHTEWLGLTVFEHCWQDADNIGFVSFVARFTEGGKTGAIIERSRFLKENGQWYYIDG

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0005515 - protein binding

Note(s):

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

External database links:

DIP:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

INTERPRO:

PFAM:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

ychJ

Operon arrangement:

Transcription unit	Promoter
ychJ	ychJp

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	TSS_1556	1288063	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1557	1288077	reverse	nd	[RS-EPT-CBR]	[1]
promoter	purUp3	1288751	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.504. P-value: 8.632e-6 Read more >	[ICWHO], [RS-EPT-CBR]	[1], [2]
promoter	purUp5	1288753	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.928. P-value: 9.282e-7 Read more >	[ICWHO]	[2]
promoter	purUp4	1288756	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.29. P-value: 2.150e-6 Read more >	[ICWHO]	[2]
promoter	TSS_1560	1289150	reverse	nd	[RS-EPT-CBR]	[1]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] 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.
[2] 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

Reference(s)

[1] 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.

[2] 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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