RegulonDB

RegulonDB RegulonDB 10.8: Gene Form

yceD gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	yceD
Synonym(s):	ECK1074, EG11119, b1088
Genome position(nucleotides):	1146794 --> 1147315 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.62
External database links:

ASAP:	ABE-0003684
ECHOBASE:	EB1109
OU-MICROARRAY:	b1088
PortEco:	yceD
STRING:	511145.b1088
COLOMBOS:	yceD

Product

Name:

DUF177 domain-containing protein YceD

Synonym(s):

G30K, YceD

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

19.315

Isoelectric point:

4.177

Motif(s):

Type	Positions	Sequence
	61 -> 171	LNGDAKVTVTLECQRCGKPFTHQVYTTYCFSPVRSDEQAEALPEAYEPIEVNEFGEIDLLAMVEDEIILALPVVPVHDSEHCEVSEADMVFGELPEEAQKPNPFAVLASLK

Classification:

Multifun Terms (GenProtEC)
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	biological_process	GO:0042254 - ribosome biogenesis

Note(s):

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

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PANTHER:

PFAM:

PRIDE:

REFSEQ:

UNIPROT:

Operon

Name:

yceD-rpmF-plsX-fabHDG-acpP-fabF

Operon arrangement:

Transcription unit	Promoter
yceD-rpmF	yceDp1
yceD-rpmF	yceDp2
rpmF-plsX-fabHDG	rpmFp
plsX-fabHDG	plsXp
fabHDG	fabHp
acpP	acpPp
acpP-fabF	acpPp
fabDG-acpP
fabF
fabG-acpP

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_1365	1146590	forward	nd	[RS-EPT-CBR]	[1]
promoter	yceFp8	1146607	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.009. P-value: 2.145e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1366	1146625	reverse	nd	[RS-EPT-CBR]	[1]
promoter	yceFp7	1146628	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 4.073. P-value: 3.947e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1368 (cluster)	1146701	reverse	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1146700 to 1146701, where the highest frequency is at position 1145924. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	yceFp9	1146749	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 5.175. P-value: 3.997e-6 Read more >	[ICWHO]	[2]
promoter	yceFp6	1146761	reverse	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.953. P-value: 4.233e-5 Read more >	[ICWHO]	[2]
promoter	TSS_1370	1146794	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1371	1146809	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1372	1147056	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1373	1147094	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1374	1147132	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1375 (cluster)	1147141	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1147141 to 1147142, where the highest frequency is at position 1146365. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_1376 (cluster)	1147146	forward	For this promoter, there is a cluster of 4 transcription start sites,in the interval 1147146 to 1147149, where the highest frequency is at position 1146370. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_1377	1147188	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1378	1147194	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1379 (cluster)	1147206	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1147206 to 1147207, where the highest frequency is at position 1146429. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_1380	1147213	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1381	1147215	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1382 (cluster)	1147300	forward	For this promoter, there is a cluster of 3 transcription start sites,in the interval 1147300 to 1147302, where the highest frequency is at position 1146523. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_1383	1147307	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1384 (cluster)	1147313	forward	For this promoter, there is a cluster of 3 transcription start sites,in the interval 1147313 to 1147315, where the highest frequency is at position 1146538. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[RS-EPT-CBR]	[1]
promoter	TSS_1385	1147350	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_1386 (cluster)	1147395	forward	For this promoter, there is a cluster of 2 transcription start sites,in the interval 1147395 to 1147396, where the highest frequency is at position 1146619. The most upstream position of this cluster is assigned as TSS position in the promoter. Read more >	[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

RegulonDB