Pde4b phosphodiesterase 4B [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Pde4bprovided by RGD
Full Name: phosphodiesterase 4Bprovided by RGD
Primary source: RGD:3280
See related: EnsemblRapid:ENSRNOG00000005905 AllianceGenome:RGD:3280
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Pde4B1; Pde4B2; Pde4B3; Pde4B4; Pde4b5; PDE4/IVb; Pde4b_v1; Pde4b_v2; Pde4b_v3; Pde4b_v4
Summary: Enables 3',5'-cyclic-AMP phosphodiesterase activity. Predicted to be involved in T cell receptor signaling pathway; cAMP-mediated signaling; and positive regulation of cytokine production. Predicted to act upstream of or within several processes, including cellular response to lipopolysaccharide; neutrophil chemotaxis; and neutrophil homeostasis. Located in perinuclear region of cytoplasm. Human ortholog(s) of this gene implicated in alcohol dependence. Orthologous to human PDE4B (phosphodiesterase 4B). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Brain (RPKM 181.0), Heart (RPKM 165.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q33

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (122028956..122598267)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (116799819..117369155)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (121759236..122136814)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phosphodiesterase 4B activation exacerbates pulmonary hypertension induced by intermittent hypoxia by regulating mitochondrial injury and cAMP/PKA/p-CREB/PGC-1alpha signaling.
Title: Phosphodiesterase 4B activation exacerbates pulmonary hypertension induced by intermittent hypoxia by regulating mitochondrial injury and cAMP/PKA/p-CREB/PGC-1α signaling.
Fibroblast growth factor 23 decreases PDE4 expression in heart increasing the risk of cardiac arrhythmia; Klotho opposes these effects.
Title: Fibroblast growth factor 23 decreases PDE4 expression in heart increasing the risk of cardiac arrhythmia; Klotho opposes these effects.
Cold-Inducible RNA-Binding Protein Prevents an Excessive Heart Rate Response to Stress by Targeting Phosphodiesterase.
Title: Cold-Inducible RNA-Binding Protein Prevents an Excessive Heart Rate Response to Stress by Targeting Phosphodiesterase.
PDE4B is primarily responsible for muscle proteolysis in burn injury and it, thus, constitutes a unique target for selective manipulations with drugs to control muscle cachexia.
Title: Phosphodiesterase 4B knockout prevents skeletal muscle atrophy in rats with burn injury.
The mRNA expression of PDE4D was significantly increased in allergic rats, but PDE4B was not. PDE4B was mainly distributed in the cytoplasm, whereas PDE4D was mainly distributed in the cell membrane
Title: Anti‑inflammatory effect of ciclamilast in an allergic model involving the expression of PDE4B.
PDE4B mediates a crucial PKA-dependent feedback that controls beta1 adrenergic receptor-dependent cAMP signals in a restricted subsarcolemmal domain.
Title: PDE4B mediates local feedback regulation of β₁-adrenergic cAMP signaling in a sarcolemmal compartment of cardiac myocytes.
Upregulated PDE4 expression during cholestatic liver injury plays a potential pathogenic role in the development of inflammation and fibrosis.
Title: Rolipram attenuates bile duct ligation-induced liver injury in rats: a potential pathogenic role of PDE4.
Acutely after spinal cord injury, PDE4B is localized to activated microglia and is absent in uninjured spinal cord or inactive microglia.
Title: Proinflammatory cytokine regulation of cyclic AMP-phosphodiesterase 4 signaling in microglia in vitro and following CNS injury.
PDE3a, PDE4b and PDE4d isoforms mRNAs were highly expressed in the whole cervical ganglia with no modulation by hypoxia.
Title: Effect of oxygen on phosphodiesterases (PDE) 3 and 4 isoforms and PKA activity in the superior cervical ganglia.
ZNF804a regulates expression of the schizophrenia-associated genes PRSS16, COMT, PDE4B, and DRD2
Title: ZNF804a regulates expression of the schizophrenia-associated genes PRSS16, COMT, PDE4B, and DRD2.

Submit: New GeneRIF Correction See all GeneRIFs (22)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI535520 (e-PCR)
- UniSTS:248128

RH138148 (e-PCR)
- UniSTS:220235

RH138697 (e-PCR)
- UniSTS:220784

BF390420 (e-PCR)
- UniSTS:249464

PMC25763P1 (e-PCR)
- UniSTS:272286

Pde4b (e-PCR), detects polymorphism
- UniSTS:518826

22.MMHAP70FRH7.seq (e-PCR)
- UniSTS:123573

RH138005 (e-PCR)
- UniSTS:220092

BE120216 (e-PCR)
- UniSTS:247269

AU028135 (e-PCR)
- UniSTS:112624

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 3',5'-cyclic-AMP phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 3',5'-cyclic-AMP phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed
enables 3',5'-cyclic-AMP phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables 3',5'-cyclic-AMP phosphodiesterase activity	ISO Inferred from Sequence Orthology more info
enables 3',5'-cyclic-GMP phosphodiesterase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 3',5'-cyclic-nucleotide phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables cAMP binding	IEA Inferred from Electronic Annotation more info
enables cAMP binding	ISO Inferred from Sequence Orthology more info
enables calcium channel regulator activity	IEA Inferred from Electronic Annotation more info
enables gamma-tubulin binding	IEA Inferred from Electronic Annotation more info
enables gamma-tubulin binding	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transmembrane transporter binding	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane transporter binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in T cell receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in T cell receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cAMP catabolic process	IEA Inferred from Electronic Annotation more info
involved_in cAMP-mediated signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular response to epinephrine stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in cellular response to xenobiotic stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to xenobiotic stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within leukocyte migration	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of adenylate cyclase-activating adrenergic receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of relaxation of cardiac muscle	IEA Inferred from Electronic Annotation more info
involved_in neutrophil chemotaxis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neutrophil chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in neutrophil homeostasis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neutrophil homeostasis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-2 production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of interleukin-2 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of type II interferon production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of type II interferon production	ISO Inferred from Sequence Orthology more info
involved_in regulation of calcium ion transmembrane transport via high voltage-gated calcium channel	IEA Inferred from Electronic Annotation more info
involved_in regulation of cardiac muscle cell contraction	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info
NOT acts_upstream_of_or_within smooth muscle contraction	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Z disc	IEA Inferred from Electronic Annotation more info
located_in cell periphery	ISO Inferred from Sequence Orthology more info
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in dendritic spine	IEA Inferred from Electronic Annotation more info
located_in dendritic spine	ISO Inferred from Sequence Orthology more info
located_in excitatory synapse	IEA Inferred from Electronic Annotation more info
located_in excitatory synapse	ISO Inferred from Sequence Orthology more info
part_of gamma-tubulin complex	IEA Inferred from Electronic Annotation more info
part_of gamma-tubulin complex	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	ISO Inferred from Sequence Orthology more info
located_in synaptic vesicle	IEA Inferred from Electronic Annotation more info
located_in synaptic vesicle	ISO Inferred from Sequence Orthology more info
part_of voltage-gated calcium channel complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: 3',5'-cyclic-AMP phosphodiesterase 4B

Names: 3',5'-cyclic AMP phosphodiesterase; DPDE4; Phosphodiesterase 4B, cAMP-specific (dunce; cAMP-specific 3',5'-cyclic phosphodiesterase 4B; cAMP-specific phosphodiesterase 4B; phosphodiesterase 4B, cAMP specific; phosphodiesterase type 4B5

NP_001385864.1

EC 3.1.4.53

NP_058727.3

EC 3.1.4.53

XP_038965200.1

EC 3.1.4.53

XP_038965202.1

EC 3.1.4.53

XP_038965203.1

EC 3.1.4.53

XP_063143230.1

EC 3.1.4.53

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001398935.2 → NP_001385864.1 3',5'-cyclic-AMP phosphodiesterase 4B isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

P14646, Q5RKL0, Q8VD81, Q8VD82

UniProtKB/TrEMBL

A0A8I5ZY41, A6JRQ8

Related

ENSRNOP00000084515.1, ENSRNOT00000099065.2

Conserved Domains (2) summary

pfam00233
Location:405 → 646

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam18100
Location:166 → 281

PDE4_UCR; Phosphodiesterase 4 upstream conserved regions (UCR)
NM_001429342.1 → NP_001416271.1 3',5'-cyclic-AMP phosphodiesterase 4B isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A6JRR1, D3ZLB2, F1M1T9
NM_017031.4 → NP_058727.3 3',5'-cyclic-AMP phosphodiesterase 4B isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8I6AT13, A6JRQ9, F1M1T9

Related

ENSRNOP00000008278.6, ENSRNOT00000008278.8

Conserved Domains (2) summary

pfam00233
Location:390 → 631

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam18100
Location:151 → 266

PDE4_UCR; Phosphodiesterase 4 upstream conserved regions (UCR)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

122028956..122598267

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109275.2 → XP_038965203.1 3',5'-cyclic-AMP phosphodiesterase 4B isoform X3

Conserved Domains (2) summary

pfam18100
Location:166 → 281

PDE4_UCR; Phosphodiesterase 4 upstream conserved regions (UCR)

cl21469
Location:405 → 428

HDc; Metal dependent phosphohydrolases with conserved 'HD' motif
XM_039109272.2 → XP_038965200.1 3',5'-cyclic-AMP phosphodiesterase 4B isoform X1

Related

ENSRNOP00000096704.2, ENSRNOT00000098470.2

Conserved Domains (2) summary

pfam00233
Location:328 → 569

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam18100
Location:89 → 204

PDE4_UCR; Phosphodiesterase 4 upstream conserved regions (UCR)
XM_039109274.2 → XP_038965202.1 3',5'-cyclic-AMP phosphodiesterase 4B isoform X2

UniProtKB/TrEMBL

A0A8L2Q3F0, A6JRR2

Related

ENSRNOP00000007738.5, ENSRNOT00000007738.8

Conserved Domains (2) summary

pfam00233
Location:172 → 413

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam18100
Location:16 → 48

PDE4_UCR; Phosphodiesterase 4 upstream conserved regions (UCR)
XM_063287160.1 → XP_063143230.1 3',5'-cyclic-AMP phosphodiesterase 4B isoform X4