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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
    mouse all
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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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    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.

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