Human Gene PDE3B (ENST00000282096.9) from GENCODE V44
  Description: Homo sapiens phosphodiesterase 3B (PDE3B), transcript variant 1, mRNA. (from RefSeq NM_001363570)
Gencode Transcript: ENST00000282096.9
Gencode Gene: ENSG00000152270.9
Transcript (Including UTRs)
   Position: hg38 chr11:14,643,804-14,872,044 Size: 228,241 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg38 chr11:14,644,076-14,869,660 Size: 225,585 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:14,643,804-14,872,044)mRNA (may differ from genome)Protein (1112 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBBioGrid 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
 

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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           more ... click here to view the complete list

-  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

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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-  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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  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
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00230 - Purine metabolism
hsa04910 - Insulin signaling pathway
hsa04914 - Progesterone-mediated oocyte maturation

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: ENST00000282096.1, ENST00000282096.2, ENST00000282096.3, ENST00000282096.4, ENST00000282096.5, ENST00000282096.6, ENST00000282096.7, ENST00000282096.8, NM_001363570, O00639, PDE3B_HUMAN, Q13370, Q14408, Q6SEI4, uc001mln.1, uc001mln.2, uc001mln.3, uc001mln.4, uc001mln.5
UCSC ID: ENST00000282096.9
RefSeq Accession: NM_000922
Protein: Q13370 (aka PDE3B_HUMAN or CN3B_HUMAN)
CCDS: CCDS7817.1

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