Human Gene PDE4D (ENST00000340635.11_8) from GENCODE V47lift37
  Description: phosphodiesterase 4D, transcript variant 1 (from RefSeq NM_001104631.2)
Gencode Transcript: ENST00000340635.11_8
Gencode Gene: ENSG00000113448.21_18
Transcript (Including UTRs)
   Position: hg19 chr5:58,264,865-59,189,553 Size: 924,689 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr5:58,270,491-59,189,449 Size: 918,959 Coding Exon Count: 15 

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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 (chr5:58,264,865-59,189,553)mRNA (may differ from genome)Protein (809 aa)
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-  Comments and Description Text from UniProtKB
  ID: PDE4D_HUMAN
DESCRIPTION: RecName: Full=cAMP-specific 3',5'-cyclic phosphodiesterase 4D; EC=3.1.4.17; AltName: Full=DPDE3; AltName: Full=PDE43;
FUNCTION: Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes.
CATALYTIC ACTIVITY: Adenosine 3',5'-cyclic phosphate + H(2)O = adenosine 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 rolipram. Activated by phosphatidic acid.
PATHWAY: Purine metabolism; 3',5'-cyclic AMP degradation; AMP from 3',5'-cyclic AMP: step 1/1.
SUBUNIT: Homodimer for the long isoforms. Isoforms with truncated N-termini are monomeric. Isoform 3 is part of a ternary complex containing PRKAR2A, PRKAR2B and AKAP9. Interacts with PDE4DIP. Identified in a complex composed of RYR1, PDE4D, PKA, FKBP1A and protein phosphatase 1 (PP1) (By similarity). Isoform 5, isoform N3 and isoform 12 bind GNB2L1 via their unique N-terminus. Binds ARRB2.
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Membrane (By similarity). Cytoplasm, cytoskeleton (By similarity). Cytoplasm, cytoskeleton, centrosome (By similarity). Note=Found in the soluble fraction, associated with membranes, and associated with the cytoskeleton and the centrosome (By similarity).
TISSUE SPECIFICITY: Widespread; most abundant in skeletal muscle. Isoform 6 is detected in brain. Isoform 8 is detected in brain, placenta, lung and kidney. Isoform 7 is detected in heart and skeletal muscle.
PTM: Isoform 3 and isoform 7 are activated by phosphorylation (in vitro), but not isoform 6. Isoform N3 and isoform 12 are phosphorylated on Ser-49, Ser-51, Ser-55 and Ser-59.
PTM: Sumoylation of long isoforms by PIAS4 augments their activation by PKA phosphorylation and represses their inhibition by ERK phosphorylation.
DISEASE: Note=Genetic variations in PDE4D might be associated with susceptibility to stroke. PubMed:17006457 states that association with stroke has to be considered with caution.
DISEASE: Defects in PDE4D are the cause of acrodysostosis type 2, with or without hormone resistance (ACRDYS2) [MIM:614613]. ACRDYS2 is a pleiotropic disorder characterized by skeletal, endocrine, and neurological abnormalities. Skeletal features include brachycephaly, midface hypoplasia with a small upturned nose, brachydactyly, and lumbar spinal stenosis. Endocrine abnormalities include hypothyroidism and hypogonadism in males and irregular menses in females. Developmental disability is a common finding but is variable in severity and can be associated with significant behavioral problems.
SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase family. PDE4 subfamily.

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

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-  MalaCards Disease Associations
  MalaCards Gene Search: PDE4D
Diseases sorted by gene-association score: acrodysostosis 2, with or without hormone resistance* (1331), acrodysostosis* (281), chromosome 5q12 deletion syndrome* (247), acrodysostosis with multiple hormone resistance* (247), atrial fibrillation and stroke (18), ocular hypotension (8), stroke, ischemic (7), pseudopseudohypoparathyroidism (6), western equine encephalitis (6), cerebrovascular disease (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C433247 Cilomilast
  • D004958 Estradiol
  • C554440 1-((5-(1-aminoethyl)-2-(8-methoxy-2-(triflurormethyl)-5-quinolinyl)-4-oxazolyl) carbonyl)-4-((cyclopropylcarbonyl)amino)proline ethyl ester
  • C009505 4,4'-diaminodiphenylmethane
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D016604 Aflatoxin B1
  • D001280 Atrazine
  • D001554 Benzene
  • D001564 Benzo(a)pyrene
          more ... click here to view the complete list

+  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: 12.03 RPKM in Muscle - Skeletal
Total median expression: 113.02 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 -43.70104-0.420 Picture PostScript Text
3' UTR -1356.335626-0.241 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
IPR023088 - PDEase
IPR002073 - PDEase_catalytic_dom
IPR023174 - PDEase_CS

Pfam Domains:
PF00233 - 3'5'-cyclic nucleotide phosphodiesterase
PF18100 - Phosphodiesterase 4 upstream conserved regions (UCR)

SCOP Domains:
101447 - Formin homology 2 domain (FH2 domain)
109604 - HD-domain/PDEase-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1E9K - NMR 1MKD - X-ray MuPIT 1OYN - X-ray MuPIT 1PTW - X-ray MuPIT 1Q9M - X-ray MuPIT 1TB7 - X-ray MuPIT 1TBB - X-ray MuPIT 1XOM - X-ray MuPIT 1XON - X-ray MuPIT 1XOQ - X-ray MuPIT 1XOR - X-ray MuPIT 1Y2B - X-ray MuPIT 1Y2C - X-ray MuPIT 1Y2D - X-ray MuPIT 1Y2E - X-ray MuPIT 1Y2K - X-ray MuPIT 1ZKN - X-ray MuPIT 2FM0 - X-ray MuPIT 2FM5 - X-ray MuPIT 2PW3 - X-ray MuPIT 2QYN - X-ray MuPIT 3G4G - X-ray MuPIT 3G4I - X-ray MuPIT 3G4K - X-ray MuPIT 3G4L - X-ray MuPIT 3G58 - X-ray MuPIT 3IAD - X-ray MuPIT 3IAK - X-ray MuPIT 3K4S - X-ray MuPIT 3SL3 - X-ray MuPIT 3SL4 - X-ray MuPIT 3SL5 - X-ray MuPIT 3SL6 - X-ray MuPIT 3SL8 - X-ray MuPIT 3V9B - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q08499
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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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
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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:0005515 protein binding
GO:0008081 phosphoric diester hydrolase activity
GO:0008144 drug binding
GO:0016787 hydrolase activity
GO:0019899 enzyme binding
GO:0030552 cAMP binding
GO:0031625 ubiquitin protein ligase binding
GO:0031698 beta-2 adrenergic receptor binding
GO:0044325 ion channel binding
GO:0046872 metal ion binding
GO:0051117 ATPase binding
GO:0097110 scaffold protein binding

Biological Process:
GO:0002027 regulation of heart rate
GO:0006198 cAMP catabolic process
GO:0006939 smooth muscle contraction
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007568 aging
GO:0010469 regulation of receptor activity
GO:0010880 regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
GO:0019933 cAMP-mediated signaling
GO:0030593 neutrophil chemotaxis
GO:0030814 regulation of cAMP metabolic process
GO:0032729 positive regulation of interferon-gamma production
GO:0032743 positive regulation of interleukin-2 production
GO:0032754 positive regulation of interleukin-5 production
GO:0033137 negative regulation of peptidyl-serine phosphorylation
GO:0035264 multicellular organism growth
GO:0045822 negative regulation of heart contraction
GO:0050852 T cell receptor signaling pathway
GO:0050900 leukocyte migration
GO:0060314 regulation of ryanodine-sensitive calcium-release channel activity
GO:0061028 establishment of endothelial barrier
GO:0071222 cellular response to lipopolysaccharide
GO:0071320 cellular response to cAMP
GO:0071872 cellular response to epinephrine stimulus
GO:0071875 adrenergic receptor signaling pathway
GO:0086004 regulation of cardiac muscle cell contraction
GO:0086024 adrenergic receptor signaling pathway involved in positive regulation of heart rate
GO:1901844 regulation of cell communication by electrical coupling involved in cardiac conduction
GO:1901898 negative regulation of relaxation of cardiac muscle

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005891 voltage-gated calcium channel complex
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0031965 nuclear membrane
GO:0034704 calcium channel complex


-  Descriptions from all associated GenBank mRNAs
  JA482076 - Sequence 59 from Patent WO2011072091.
JE980368 - Sequence 59 from Patent EP2862929.
JA482075 - Sequence 58 from Patent WO2011072091.
JE980367 - Sequence 58 from Patent EP2862929.
JA482077 - Sequence 60 from Patent WO2011072091.
JE980369 - Sequence 60 from Patent EP2862929.
U02882 - Human rolipram-sensitive 3',5'-cyclic AMP phosphodiesterase mRNA, complete cds.
L20970 - Human phosphodiesterase mRNA, complete cds.
AF012073 - Homo sapiens cAMP-specific phosphodiesterase PDE4D5 (PDE4D) mRNA, complete cds.
L20969 - Homo sapiens cyclic AMP phosphodiesterase mRNA, complete cds.
HM005449 - Homo sapiens clone HTL-T-136 testicular tissue protein Li 136 mRNA, complete cds.
AF536976 - Homo sapiens cAMP-specific phosphodiesterase PDE4D7 (PDE4D) mRNA, complete cds; alternatively spliced.
U50159 - Human cAMP-specific phosphodiesterase HPDE4D3 variant (PDE4D) mRNA, complete cds.
AY245866 - Homo sapiens cAMP-specific phosphodiesterase variant PDE4D7 (PDE4D) mRNA, complete cds; alternatively spliced.
AJ250854 - Homo sapiens partial mRNA for cAMP-specific phosphodiesterase 4D (PDE4DN3 gene).
BC008390 - Homo sapiens phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila), mRNA (cDNA clone IMAGE:4280941), complete cds.
KJ901629 - Synthetic construct Homo sapiens clone ccsbBroadEn_11023 PDE4D gene, encodes complete protein.
BT007398 - Homo sapiens phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila) mRNA, complete cds.
AF012074 - Homo sapiens cAMP-specific phosphodiesterase PDE4D2 (PDE4D) mRNA, complete cds.
AY388960 - Homo sapiens cAMP-specific phosphodiesterase PDE4D9 (PDE4D) mRNA, complete cds.
AF536977 - Homo sapiens cAMP-specific phosphodiesterase PDE4D8 (PDE4D) mRNA, complete cds; alternatively spliced.
U50157 - Human cAMP-specific phosphodiesterase HPDE4D1 variant (PDE4D) mRNA, complete cds.
U50158 - Human cAMP-specific phosphodiesterase HPDE4D2 variant (PDE4D) mRNA, complete cds.
AY245867 - Homo sapiens cAMP-specific phosphodiesterase variant PDE4D9 (PDE4D) mRNA, complete cds; alternatively spliced.
AB528028 - Synthetic construct DNA, clone: pF1KB6242, Homo sapiens PDE4D gene for cAMP-specific 3',5'-cyclic phosphodiesterase 4D, without stop codon, in Flexi system.
AJ250852 - Homo sapiens partial mRNA for cAMP-specific phosphodiesterase 4D, (PDE4DN1 gene).
U79571 - Homo sapiens 3',5'-cyclic nucleotide phosphodiesterase 4D splice variant 1 (HSPDE4D) mRNA, partial cds.
AJ250855 - Homo sapiens partial mRNA for cAMP-specific phosphodiesterase 4D, (PDE4DN2 gene).
AF536980 - Homo sapiens cAMP-specific phosphodiesterase (PDE4D) mRNA, 3' untranslated region, partial sequence.
JD127400 - Sequence 108424 from Patent EP1572962.
JD198938 - Sequence 179962 from Patent EP1572962.
JD247501 - Sequence 228525 from Patent EP1572962.
JD504116 - Sequence 485140 from Patent EP1572962.
JD504296 - Sequence 485320 from Patent EP1572962.
JD534060 - Sequence 515084 from Patent EP1572962.
BC036319 - Homo sapiens phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila), mRNA (cDNA clone MGC:42769 IMAGE:4828512), complete cds.
JD549434 - Sequence 530458 from Patent EP1572962.
AF536975 - Homo sapiens cAMP-specific phosphodiesterase PDE4D6 (PDE4D) mRNA, complete cds; alternatively spliced.
JF432192 - Synthetic construct Homo sapiens clone IMAGE:100073352 phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila) (PDE4D) gene, encodes complete protein.
KJ897310 - Synthetic construct Homo sapiens clone ccsbBroadEn_06704 PDE4D gene, encodes complete protein.
CU690324 - Synthetic construct Homo sapiens gateway clone IMAGE:100019754 5' read PDE4D mRNA.
JD538589 - Sequence 519613 from Patent EP1572962.
JD341309 - Sequence 322333 from Patent EP1572962.
JD205830 - Sequence 186854 from Patent EP1572962.
JD526360 - Sequence 507384 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q08499 (Reactome details) participates in the following event(s):

R-HSA-111962 cAMP hydrolysis by PDE 4
R-HSA-418553 cAMP degradation by Phosphodiesterases
R-HSA-180024 DARPP-32 events
R-HSA-111885 Opioid Signalling
R-HSA-418555 G alpha (s) signalling events
R-HSA-418594 G alpha (i) signalling events
R-HSA-388396 GPCR downstream signalling
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: DPDE3, ENST00000340635.1, ENST00000340635.10, ENST00000340635.2, ENST00000340635.3, ENST00000340635.4, ENST00000340635.5, ENST00000340635.6, ENST00000340635.7, ENST00000340635.8, ENST00000340635.9, NM_001104631, O43433, PDE4D , PDE4D_HUMAN, Q08499, Q13549, Q13550, Q13551, Q7Z2L8, Q8IV84, Q8IVA9, Q8IVD2, Q8IVD3, Q96HL4, Q9HCX7, uc317vsx.1, uc317vsx.2
UCSC ID: ENST00000340635.11_8
RefSeq Accession: NM_001104631.2
Protein: Q08499 (aka PDE4D_HUMAN or CN4D_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.