RegulonDB

Gene
Name:	pdeN
Synonym(s):	ECK2170, G7148, b2176, rtn
Genome position(nucleotides):	2270726 --> 2272282 Genome Browser
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	50.55
External database links:

ASAP:	ABE-0007203
ECHOBASE:	EB3830
OU-MICROARRAY:	b2176
PortEco:	rtn
STRING:	511145.b2176
COLOMBOS:	pdeN

Gene

Name:

pdeN

Synonym(s):

ECK2170, G7148, b2176, rtn

Genome position(nucleotides):

2270726 --> 2272282 Genome Browser

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

50.55

External database links:

ASAP:

ECHOBASE:

OU-MICROARRAY:

PortEco:

STRING:

COLOMBOS:

Type

Positions

Sequence

261 -> 514

RMRPGREIMTAIKREQFYVAYQPVVDTQALRVTGLEVLLRWRHPVAGEIPPDAFINFAESQKMIVPLTQHLFELIARDAAELEKVLPVGVKFGINIAPDHLHSESFKADIQKLLTSLPAHHFQIVLEITERDMLKEQEATQLFAWLHSVGVEIAIDDFGTGHSALIYLERFTLDYLKIDRGFINAIGTETITSPVLDAVLTLAKRLNMLTVAEGVETPEQARWLSERGVNFMQGYWISRPLPLDDFVRWLKKPY

42 -> 239

KYDTLITDVQKYLDTYFADLKSTTDRLQPLTLDTCQQANPELTARAAFSMNVRTFVLVKDKKTFCSSATGEMDIPLNELIPALDINKNVDMAILPGTPMVPNKPAIVIWYRNPLLKNSGVFAALNLNLTPSLFYSSRQEDYDGVALIIGNTALSTFSSRLMNVNELTDMPVRETKIAGIPLTVRLYADDWTWNDVWYA

236 -> 256

VWYAFLLGGMSGTVVGLLCYY

267 -> 500

EIMTAIKREQFYVAYQPVVDTQALRVTGLEVLLRWRHPVAGEIPPDAFINFAESQKMIVPLTQHLFELIARDAAELEKVLPVGVKFGINIAPDHLHSESFKADIQKLLTSLPAHHFQIVLEITERDMLKEQEATQLFAWLHSVGVEIAIDDFGTGHSALIYLERFTLDYLKIDRGFINAIGTETITSPVLDAVLTLAKRLNMLTVAEGVETPEQARWLSERGVNFMQGYWISRP

16 -> 36

CIVAGVMIAILVSCLQFLVAW

Type

Positions

Sequence

261 -> 514

42 -> 239

KYDTLITDVQKYLDTYFADLKSTTDRLQPLTLDTCQQANPELTARAAFSMNVRTFVLVKDKKTFCSSATGEMDIPLNELIPALDINKNVDMAILPGTPMVPNKPAIVIWYRNPLLKNSGVFAALNLNLTPSLFYSSRQEDYDGVALIIGNTALSTFSSRLMNVNELTDMPVRETKIAGIPLTVRLYADDWTWNDVWYA

236 -> 256

VWYAFLLGGMSGTVVGLLCYY

267 -> 500

16 -> 36

CIVAGVMIAILVSCLQFLVAW

482 -> 518

RWLSERGVNFMQGYWISRPLPLDDFVRWLKKPYTPQW

Multifun Terms (GenProtEC)

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol
GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane

molecular_function

GO:0016787 - hydrolase activity
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity

RNA cis-regulatory element

Attenuation:	Transcriptional

RNA cis-regulatory element

Attenuation:

Transcriptional

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	rtnp1	2270678	forward	Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: good homology. Score: 3.78. P-value: 7.869e-5 Read more >	[ICWHO]	[2]
promoter	yejAp	2272312	forward	nd	[AIPP]	[2]
promoter	TSS_2475	2272388	forward	nd	[RS-EPT-CBR]	[3]
promoter	TSS_2476	2273514	reverse	nd	[RS-EPT-CBR]	[3]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

rtnp1

2270678

forward

Similarity to the consensus
Read more >

[ICWHO]

[2]

promoter

yejAp

2272312

forward

[AIPP]

[2]

promoter

TSS_2475

2272388

forward

[RS-EPT-CBR]

[3]

promoter

TSS_2476

2273514

reverse

[RS-EPT-CBR]

[3]

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

Evidence

[ICWHO] Inferred computationally without human oversight

[AIPP] Automated inference of promoter position

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Sarenko O., Klauck G., Wilke FM., Pfiffer V., Richter AM., Herbst S., Kaever V., Hengge R., 2017, More than Enzymes That Make or Break Cyclic Di-GMP-Local Signaling in the Interactome of GGDEF/EAL Domain Proteins of Escherichia coli., MBio 8(5)
[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.

Reference(s)

[1] Sarenko O., Klauck G., Wilke FM., Pfiffer V., Richter AM., Herbst S., Kaever V., Hengge R., 2017, More than Enzymes That Make or Break Cyclic Di-GMP-Local Signaling in the Interactome of GGDEF/EAL Domain Proteins of Escherichia coli., MBio 8(5)

[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.