PDE3B phosphodiesterase 3B [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDE3Bprovided by HGNC
Official Full Name: phosphodiesterase 3Bprovided by HGNC
Primary source: HGNC:HGNC:8779
See related: Ensembl:ENSG00000152270 MIM:602047; AllianceGenome:HGNC:8779
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HcGIP1; cGIPDE1
Summary: Enables 3',5'-cyclic-AMP phosphodiesterase activity. Involved in several processes, including negative regulation of angiogenesis; negative regulation of lipid catabolic process; and regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction. Located in membrane. Part of guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in fat (RPKM 53.0), lymph node (RPKM 8.6) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11p15.2

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (14643804..14899321)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (14739099..14995688)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (14665350..14920867)

Chromosome 11 - NC_000011.10 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PDE3B regulates KRT6B and increases the sensitivity of bladder cancer cells to copper ionophores.
Title: PDE3B regulates KRT6B and increases the sensitivity of bladder cancer cells to copper ionophores.
A novel link between circPDE3B and ferroptosis in esophageal squamous cell carcinoma progression.
Title: A novel link between circPDE3B and ferroptosis in esophageal squamous cell carcinoma progression.
Phosphodiesterase 2A and 3B variants are associated with primary aldosteronism.
Title: Phosphodiesterase 2A and 3B variants are associated with primary aldosteronism.
Impact of phosphodiesterases PDE3 and PDE4 on 5-hydroxytryptamine receptor4-mediated increase of cAMP in human atrial fibrillation.
Title: Impact of phosphodiesterases PDE3 and PDE4 on 5-hydroxytryptamine receptor4-mediated increase of cAMP in human atrial fibrillation.
In Vitro Inhibition of Phosphodiesterase 3B (PDE 3B) by Anthocyanin-Rich Fruit Juice Extracts and Selected Anthocyanins.
Title: In Vitro Inhibition of Phosphodiesterase 3B (PDE 3B) by Anthocyanin-Rich Fruit Juice Extracts and Selected Anthocyanins.
Phosphodiesterase 3B (PDE3B) antagonizes the anti-angiogenic actions of PKA in human and murine endothelial cells.
Title: Phosphodiesterase 3B (PDE3B) antagonizes the anti-angiogenic actions of PKA in human and murine endothelial cells.
ABHD15 associates with and stabilizes phosphodiesterase 3B (PDE3B).
Title: Loss of ABHD15 Impairs the Anti-lipolytic Action of Insulin by Altering PDE3B Stability and Contributes to Insulin Resistance.
Our results shed more light on phosphodiesterase 3A activation and could be relevant to the treatment of severe hypertension in the general population.
Title: Clinical effects of phosphodiesterase 3A mutations in inherited hypertension with brachydactyly.
Data indicate that genome-wide significant associations were found both at age 6 and 14 with single nucleotide polymorphisms (SNPs) on chromosome 11p15 in phosphodiesterase 3B, cGMP-inhibited protein PDE3B/cytochrome P-450 CYP2R1 genes.
Title: Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
PDE3B appears to be an important actor in regulation of energy metabolism and energy intake. Is inhibition of PDE3B a possible target for treatment of obesity or type 2 diabetes mellitus? [REVIEW]
Title: From PDE3B to the regulation of energy homeostasis.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat decreases the intracellular levels of cAMP and CREB ser-133 phosphorylation through a signal transduction pathway involving sequential activation of phosphatidylinositol 3-kinase, AKT, and cyclic nucleoside phosphodiesterases	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SGC34479 (e-PCR)
- UniSTS:39974

D11S2560 (e-PCR)
- UniSTS:37928

D8S2279 (e-PCR)
- UniSTS:473907

RH16485 (e-PCR)
- UniSTS:8287

D11S4193 (e-PCR), detects polymorphism
- UniSTS:1640

D15S1477 (e-PCR)
- UniSTS:474482

SHGC-145708 (e-PCR)
- UniSTS:174739

RH80346 (e-PCR)
- UniSTS:88735

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3',5'-cGMP-inhibited cyclic-nucleotide phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
enables 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity	IEA Inferred from Electronic Annotation more info
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	TAS Traceable Author Statement 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	EXP Inferred from Experiment more info	PubMed
enables 3',5'-cyclic-nucleotide phosphodiesterase activity	IDA Inferred from Direct Assay more info	PubMed
enables 3',5'-cyclic-nucleotide phosphodiesterase activity	TAS Traceable Author Statement more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase B binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	TAS Traceable Author Statement more info
involved_in angiogenesis	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 insulin stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cell adhesion mediated by integrin	IC Inferred by Curator more info	PubMed
involved_in negative regulation of lipid catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	ISS Inferred from Sequence or Structural Similarity more info
part_of guanyl-nucleotide exchange factor complex	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B

Names: CGI-PDE B; CGIP1; cGMP-inhibited 3',5'-cyclic phosphodiesterase B; cyclic GMP-inhibited phosphodiesterase B; cyclic nucleotide phosphodiesterase; phosphodiesterase 3B, cGMP-inhibited

NP_000913.2

EC 3.1.4.17

NP_001350498.1

EC 3.1.4.17

NP_001350499.1

EC 3.1.4.17

NP_001416628.1

EC 3.1.4.17

NP_001416629.1

EC 3.1.4.17

XP_006718312.1

EC 3.1.4.17

XP_047283071.1

EC 3.1.4.17

XP_054225082.1

EC 3.1.4.17

XP_054225083.1

EC 3.1.4.17

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_000922.4 → NP_000913.2 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 2

See identical proteins and their annotated locations for NP_000913.2

Status: VALIDATED

Source sequence(s)

AC090835, BC136565, BC150307

Consensus CDS

CCDS7817.1

UniProtKB/Swiss-Prot

B7ZM37, O00639, Q13370, Q14408, Q6SEI4

UniProtKB/TrEMBL

A7E2E5

Related

ENSP00000282096.4, ENST00000282096.9

Conserved Domains (2) summary

pfam00233
Location:736 → 1010

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam06532
Location:136 → 282

DUF1109; Protein of unknown function (DUF1109)
NM_001363569.2 → NP_001350498.1 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 3

Status: VALIDATED

Source sequence(s)

AC018795, AC087207, AC090835

Consensus CDS

CCDS91445.1

UniProtKB/TrEMBL

A7E2E5

Related

ENSP00000388644.2, ENST00000455098.2

Conserved Domains (2) summary

pfam00233
Location:685 → 959

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam06532
Location:136 → 282

DUF1109; Protein of unknown function (DUF1109)
NM_001363570.2 → NP_001350499.1 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 1

Status: VALIDATED

Source sequence(s)

AC018795, AC087207, AC090835

UniProtKB/TrEMBL

A7E2E5

Conserved Domains (2) summary

pfam00233
Location:814 → 1088

PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

pfam06532
Location:136 → 282

DUF1109; Protein of unknown function (DUF1109)
NM_001429699.1 → NP_001416628.1 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 4

Status: VALIDATED

Source sequence(s)

AC018795, AC087207, AC090835

UniProtKB/TrEMBL

A7E2E5
NM_001429700.1 → NP_001416629.1 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 5

Status: VALIDATED

Source sequence(s)

AC018795, AC087207, AC090835

UniProtKB/TrEMBL

A7E2E5

RNA

NR_190763.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC018795, AC087207, AC090835
NR_190764.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC018795, AC087207, AC090835
NR_190765.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC018795, AC087207, AC090835
NR_190766.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC018795, AC087207, AC090835

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

14643804..14899321

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006718249.4 → XP_006718312.1 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X1

Conserved Domains (1) summary

pfam06532
Location:136 → 282

DUF1109; Protein of unknown function (DUF1109)
XM_047427115.1 → XP_047283071.1 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

14739099..14995688

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054369107.1 → XP_054225082.1 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X1
XM_054369108.1 → XP_054225083.1 cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X2