RegulonDB

Gene
Name:	yciN
Synonym(s):	ECK1267, EG12868, b1273
Genome position(nucleotides):	1330417 <-- 1330668 Genome Browser
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	47.22
External database links:

ASAP:	ABE-0004269
ECHOBASE:	EB2709
OU-MICROARRAY:	b1273
PortEco:	yciN
STRING:	511145.b1273
COLOMBOS:	yciN

Product

Name:

protein YciN

Synonym(s):

YciN

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

9.386

Isoelectric point:

5.55

Motif(s):

Type	Positions	Sequence
	43 -> 83	LVFTGDYFLDEQGLPTAKSTAVFNMFKHLAHVLSEKYHLVD
	4 -> 81	ETQPIDRETLLKEANKIIREHEDTLAGIEATGVTQRNGVLVFTGDYFLDEQGLPTAKSTAVFNMFKHLAHVLSEKYHL

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:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

yciN

Operon arrangement:

Transcription unit	Promoter
yciN

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_1710	1330684	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1711 (cluster)	1330687	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1330686 to 1330687, where the highest frequency is at position 1328711. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	yciNp10	1330689	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.036. P-value: 6.841e-5 Read more >	[ICWHO]	[2]
promoter	yciNp8	1330702	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.125. P-value: 2.081e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1712	1330714	reverse	nd	[RS-EPT-CBR]	[1]
promoter	yciNp9	1330757	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.005. P-value: 2.300e-5 Read more >	[ICWHO]	[2]
promoter	yciNp11	1330790	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.213. P-value: 5.342e-6 Read more >	[ICWHO]	[2]
promoter	TSS_1713	1330791	forward	nd	[RS-EPT-CBR]	[1]
promoter	yciNp5	1330803	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.29. P-value: 8.356e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1715	1331232	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1716	1331471	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1717	1332403	forward	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