Human Gene PDE3B (ENST00000282096.9_6) from GENCODE V47lift37
  Description: phosphodiesterase 3B, transcript variant 1 (from RefSeq NM_001363570.2)
Gencode Transcript: ENST00000282096.9_6
Gencode Gene: ENSG00000152270.9_10
Transcript (Including UTRs)
   Position: hg19 chr11:14,665,350-14,893,590 Size: 228,241 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr11:14,665,622-14,891,206 Size: 225,585 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:14,665,350-14,893,590)mRNA (may differ from genome)Protein (1112 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDE3B_HUMAN
DESCRIPTION: RecName: Full=cGMP-inhibited 3',5'-cyclic phosphodiesterase B; EC=3.1.4.17; AltName: Full=CGIPDE1; Short=CGIP1; AltName: Full=Cyclic GMP-inhibited phosphodiesterase B; Short=CGI-PDE B;
FUNCTION: Cyclic nucleotide phosphodiesterase with a dual- specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes. May play a role in fat metabolism. Regulates cAMP binding of RAPGEF3. Through simultaneous binding to RAPGEF3 and PIK3R6 assembles a signaling complex in which the PI3K gamma complex is activated by RAPGEF3 and which is involved in angiogenesis.
CATALYTIC ACTIVITY: Nucleoside 3',5'-cyclic phosphate + H(2)O = nucleoside 5'-phosphate.
COFACTOR: Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions, while site 2 has a preference for magnesium and/or manganese ions.
ENZYME REGULATION: Inhibited by cGMP.
SUBUNIT: Interacts with PIK3CG (By similarity). Interacts with RAPGEF3 and PIK3R6.
INTERACTION: P48736:PIK3CG; NbExp=3; IntAct=EBI-6172856, EBI-1030384; Q5UE93:PIK3R6; NbExp=3; IntAct=EBI-6172856, EBI-6172907; O95398:RAPGEF3; NbExp=8; IntAct=EBI-6172856, EBI-6172806;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
TISSUE SPECIFICITY: Abundant in adipose tissues.
SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase family. PDE3 subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PDE3B
Diseases sorted by gene-association score: pseudohypoparathyroidism, type ii (18), pelizaeus-merzbacher disease (7), lipodystrophy, familial partial, type 2 (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.01 RPKM in Colon - Sigmoid
Total median expression: 81.08 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -138.00272-0.507 Picture PostScript Text
3' UTR -507.202384-0.213 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003607 - HD/PDEase_dom
IPR002073 - PDEase_catalytic_dom
IPR023174 - PDEase_CS

Pfam Domains:
PF00233 - 3'5'-cyclic nucleotide phosphodiesterase

SCOP Domains:
109604 - HD-domain/PDEase-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1SO2 - X-ray MuPIT 1SOJ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q13370
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0004115 3',5'-cyclic-AMP phosphodiesterase activity
GO:0004119 cGMP-inhibited cyclic-nucleotide phosphodiesterase activity
GO:0005515 protein binding
GO:0008081 phosphoric diester hydrolase activity
GO:0016787 hydrolase activity
GO:0043422 protein kinase B binding
GO:0046872 metal ion binding
GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity

Biological Process:
GO:0001525 angiogenesis
GO:0006198 cAMP catabolic process
GO:0007162 negative regulation of cell adhesion
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0016525 negative regulation of angiogenesis
GO:0032869 cellular response to insulin stimulus
GO:0033629 negative regulation of cell adhesion mediated by integrin
GO:0043951 negative regulation of cAMP-mediated signaling
GO:0050995 negative regulation of lipid catabolic process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0032045 guanyl-nucleotide exchange factor complex


-  Descriptions from all associated GenBank mRNAs
  BC150307 - Homo sapiens phosphodiesterase 3B, cGMP-inhibited, mRNA (cDNA clone MGC:167096 IMAGE:8860429), complete cds.
AY459346 - Homo sapiens cGMP-inhibited cAMP phophodiesterase (PDE3B) mRNA, complete cds.
BC136565 - Homo sapiens phosphodiesterase 3B, cGMP-inhibited, mRNA (cDNA clone MGC:168178 IMAGE:9020555), complete cds.
BC136566 - Homo sapiens phosphodiesterase 3B, cGMP-inhibited, mRNA (cDNA clone MGC:168179 IMAGE:9020556), complete cds.
BC144248 - Homo sapiens phosphodiesterase 3B, cGMP-inhibited, mRNA (cDNA clone MGC:177785 IMAGE:9052768), complete cds.
BC146828 - Synthetic construct Homo sapiens clone IMAGE:100000975, MGC:167370 phosphodiesterase 3B, cGMP-inhibited (PDE3B) mRNA, encodes complete protein.
BC150322 - Synthetic construct Homo sapiens clone IMAGE:100013672, MGC:167371 phosphodiesterase 3B, cGMP-inhibited (PDE3B) mRNA, encodes complete protein.
KJ897308 - Synthetic construct Homo sapiens clone ccsbBroadEn_06702 PDE3B gene, encodes complete protein.
X95520 - H.sapiens mRNA for cyclic nucleotide phosphodiesterase.
AB209326 - Homo sapiens mRNA for phosphodiesterase 3B, cGMP-inhibited variant protein.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_no1Pathway - Actions of Nitric Oxide in the Heart

Reactome (by CSHL, EBI, and GO)

Protein Q13370 (Reactome details) participates in the following event(s):

R-HSA-162363 p-T309,S474-AKT2:PIP3 phosphorylates PDE3B
R-HSA-162425 p-S295-PDE3B hydrolyses cAMP to AMP
R-HSA-418456 cGMP is degraded by PDEs
R-HSA-418553 cAMP degradation by Phosphodiesterases
R-HSA-165160 PDE3B signalling
R-HSA-109703 PKB-mediated events
R-HSA-109704 PI3K Cascade
R-HSA-418457 cGMP effects
R-HSA-418555 G alpha (s) signalling events
R-HSA-112399 IRS-mediated signalling
R-HSA-392154 Nitric oxide stimulates guanylate cyclase
R-HSA-388396 GPCR downstream signalling
R-HSA-74751 Insulin receptor signalling cascade
R-HSA-2428928 IRS-related events triggered by IGF1R
R-HSA-418346 Platelet homeostasis
R-HSA-372790 Signaling by GPCR
R-HSA-74752 Signaling by Insulin receptor
R-HSA-2428924 IGF1R signaling cascade
R-HSA-109582 Hemostasis
R-HSA-162582 Signal Transduction
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-2404192 Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)

-  Other Names for This Gene
  Alternate Gene Symbols: B7ZM37, ENST00000282096.1, ENST00000282096.2, ENST00000282096.3, ENST00000282096.4, ENST00000282096.5, ENST00000282096.6, ENST00000282096.7, ENST00000282096.8, NM_001363570, O00639, PDE3B , PDE3B_HUMAN, Q13370, Q14408, Q6SEI4, uc317jyj.1, uc317jyj.2
UCSC ID: ENST00000282096.9_6
RefSeq Accession: NM_000922.4
Protein: Q13370 (aka PDE3B_HUMAN or CN3B_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.