RegulonDB

Gene
Name:	rpnC
Synonym(s):	ECK0131, EG11748, b0132, yadD
Genome position(nucleotides):	146968 --> 147870 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	48.84
External database links:

ASAP:	ABE-0000463
ECHOBASE:	EB1698
ECOLIHUB:	yadD
OU-MICROARRAY:	b0132
STRING:	511145.b0132
COLOMBOS:	rpnC

Product

Name:

recombination-promoting nuclease RpnC

Synonym(s):

RpnC, YadD

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol

Molecular weight:

34.607

Isoelectric point:

5.092

Motif(s):

Type	Positions	Sequence
	7 -> 207	TPHDAVFKQFLMHAETARDFLEIHLPVELRELCDLNTLHLESGSFIEESLKGHSTDVLYSVQMQGNPGYLHVVIEHQSKPDKKMAFRMMRYSIAAMHRHLEADHDKLPLVVPILFYQGEATPYPLSMCWFDMFYSPELARRVYNSPFPLVDITITPDDEIMQHRRIAILELLQKHIRQRDLMLLLEQLVTLIDEGYTSGSQ

Classification:

Multifun Terms (GenProtEC)
Multifun Terms (GenProtEC)		5 - cell processes --> 5.4 - genetic exchange, recombination (for future)
Gene Ontology Terms (GO)
	cellular_component	GO:0005829 - cytosol
	molecular_function	GO:0004518 - nuclease activity GO:0004519 - endonuclease activity GO:0016787 - hydrolase activity GO:1990238 - double-stranded DNA endodeoxyribonuclease activity
	biological_process	GO:0006310 - DNA recombination GO:0090305 - nucleic acid phosphodiester bond hydrolysis

Note(s):

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

Evidence:

[IMP] Inferred from mutant phenotype

Reference(s):

[1] Kingston AW., et al., 2017

External database links:

ECOCYC:

ECOLIWIKI:

INTERPRO:

INTERPRO:

PFAM:

PRIDE:

REFSEQ:

SMR:

UNIPROT:

Operon

Name:

rpnC

Operon arrangement:

Transcription unit	Promoter
yadD

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	yadDp3	146898	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.814. P-value: 3.013e-5 Read more >	[ICWHO]	[2]
promoter	yadDp5	146957	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.953. P-value: 4.233e-5 Read more >	[ICWHO]	[2]
promoter	yadDp4	146959	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 4.199. P-value: 4.678e-5 Read more >	[ICWHO]	[2]
promoter	TSS_271	147583	forward	nd	[RS-EPT-CBR]	[3]

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] Kingston AW., Ponkratz C., Raleigh EA., 2017, Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer., J Bacteriol 199(7)
[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
[3] 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.