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PDE3B phosphodiesterase 3B [ Homo sapiens (human) ]

Gene ID: 5140, updated on 3-Nov-2024

Summary

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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, Nov 2024]
Expression
Biased expression in fat (RPKM 53.0), lymph node (RPKM 8.6) and 12 other tissues See more
Orthologs
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Genomic context

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See PDE3B in Genome Data Viewer
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_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4474 Neighboring gene RNA, U7 small nuclear 49 pseudogene Neighboring gene COPI coat complex subunit beta 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:14541725-14542339 Neighboring gene proteasome 20S subunit alpha 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14654809-14655398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3173 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:14683201-14683380 Neighboring gene mortality factor 4 like 1 pseudogene 3 Neighboring gene uncharacterized LOC107984315 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14737137-14737723 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14737724-14738309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:14748217-14748780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:14764591-14765090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14799188-14799688 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:14838787-14838962 Neighboring gene uncharacterized LOC124902639 Neighboring gene MPRA-validated peak1207 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14929307-14929806 Neighboring gene cytochrome P450 family 2 subfamily R member 1 Neighboring gene calcitonin pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14993078-14993724 Neighboring gene calcitonin related polypeptide alpha

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Benzyl vinylogous amide substituted aryldihydropyridazinones and aryldimethylpyrazolones as potent and selective PDE3B inhibitors. Edmondson SD, et al. Bioorg Med Chem Lett, 2003 Nov 17. PMID 14592490
  2. A selective phosphodiesterase 3 inhibitor rescues low PO2-induced ATP release from erythrocytes of humans with type 2 diabetes: implication for vascular control. Sprague RS, et al. Am J Physiol Heart Circ Physiol, 2011 Dec. PMID 21963837, Free PMC Article
  3. Systematic search for single nucleotide polymorphisms in the 5' flanking region of the human phosphodiesterase 3B gene: absence of evidence for major effects of identified polymorphisms on susceptibility to Japanese type 2 diabetes. Osawa H, et al. Mol Genet Metab, 2003 May. PMID 12765845
  4. A novel link between circPDE3B and ferroptosis in esophageal squamous cell carcinoma progression. Zhou P, et al. Genomics, 2024 Jan. PMID 38092323
  5. Crystal structure of human phosphodiesterase 3B: atomic basis for substrate and inhibitor specificity. Scapin G, et al. Biochemistry, 2004 May 25. PMID 15147193

See all (73) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. Phosphodiesterase 2A and 3B variants are associated with primary aldosteronism.
    Title: Phosphodiesterase 2A and 3B variants are associated with primary aldosteronism.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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
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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 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
NP_001350498.1
NP_001350499.1
NP_001416628.1
NP_001416629.1
XP_006718312.1
XP_047283071.1
XP_054225082.1
XP_054225083.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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)

  1. 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)

  2. 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)

  3. 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)

  4. NM_001429699.1 → NP_001416628.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC018795, AC087207, AC090835

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

    Status: VALIDATED

    Source sequence(s)
    AC018795, AC087207, AC090835

RNA

  1. NR_190763.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC018795, AC087207, AC090835

  2. NR_190764.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC018795, AC087207, AC090835

  3. NR_190765.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC018795, AC087207, AC090835

  4. 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

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    14643804..14899321
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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)

  2. XM_047427115.1 → XP_047283071.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    14739099..14995688
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13370.2 GenPept UniProtKB/Swiss-Prot:Q13370

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
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