Human Gene PDE1A (ENST00000409365.6_11) from GENCODE V47lift37
  Description: phosphodiesterase 1A, transcript variant 6 (from RefSeq NM_001363871.4)
Gencode Transcript: ENST00000409365.6_11
Gencode Gene: ENSG00000115252.19_14
Transcript (Including UTRs)
   Position: hg19 chr2:183,004,768-183,291,763 Size: 286,996 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr2:183,011,806-183,291,357 Size: 279,552 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:183,004,768-183,291,763)mRNA (may differ from genome)Protein (529 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCHuman Cortex Gene ExpressionMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDE1A_HUMAN
DESCRIPTION: RecName: Full=Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A; Short=Cam-PDE 1A; EC=3.1.4.17; AltName: Full=61 kDa Cam-PDE; AltName: Full=hCam-1;
FUNCTION: Cyclic nucleotide phosphodiesterase with a dual- specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes. Has a higher affinity for cGMP than for cAMP.
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 (By similarity).
ENZYME REGULATION: Type I PDE are activated by the binding of calmodulin in the presence of Ca(2+).
SUBUNIT: Homodimer (By similarity).
TISSUE SPECIFICITY: Several tissues, including brain, kidney, testes and heart.
SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase family. PDE1 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           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: 21.67 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 181.82 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 -135.80406-0.334 Picture PostScript Text
3' UTR -699.203041-0.230 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
IPR013706 - PDEase_N

Pfam Domains:
PF00233 - 3'5'-cyclic nucleotide phosphodiesterase
PF08499 - 3'5'-cyclic nucleotide phosphodiesterase N-terminal

SCOP Domains:
48264 - Cytochrome P450
109604 - HD-domain/PDEase-like
52499 - Isochorismatase-like hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1LXQ - Model


ModBase Predicted Comparative 3D Structure on P54750
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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:0004117 calmodulin-dependent cyclic-nucleotide phosphodiesterase activity
GO:0005516 calmodulin binding
GO:0008081 phosphoric diester hydrolase activity
GO:0016787 hydrolase activity
GO:0030553 cGMP binding
GO:0046872 metal ion binding
GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity
GO:0048101 calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity

Biological Process:
GO:0006198 cAMP catabolic process
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0034391 regulation of smooth muscle cell apoptotic process
GO:0046069 cGMP catabolic process
GO:0048660 regulation of smooth muscle cell proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043025 neuronal cell body


-  Descriptions from all associated GenBank mRNAs
  BC022480 - Homo sapiens phosphodiesterase 1A, calmodulin-dependent, mRNA (cDNA clone MGC:26303 IMAGE:4814064), complete cds.
AK295657 - Homo sapiens cDNA FLJ59536 complete cds, highly similar to Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A (EC 3.1.4.17).
AK294239 - Homo sapiens cDNA FLJ56062 complete cds, highly similar to Calcium/calmodulin-dependent 3',5'-cyclicnucleotide phosphodiesterase 1A (EC 3.1.4.17).
DQ892369 - Synthetic construct clone IMAGE:100004999; FLH185644.01X; RZPDo839D05148D phosphodiesterase 1A, calmodulin-dependent (PDE1A) gene, encodes complete protein.
DQ893372 - Synthetic construct clone IMAGE:100006002; FLH196730.01X; RZPDo839H06156D phosphodiesterase 1A, calmodulin-dependent (PDE1A) gene, encodes complete protein.
DQ895578 - Synthetic construct Homo sapiens clone IMAGE:100010038; FLH185640.01L; RZPDo839D05147D phosphodiesterase 1A, calmodulin-dependent (PDE1A) gene, encodes complete protein.
DQ896694 - Synthetic construct Homo sapiens clone IMAGE:100011154; FLH196726.01L; RZPDo839H06155D phosphodiesterase 1A, calmodulin-dependent (PDE1A) gene, encodes complete protein.
AB384753 - Synthetic construct DNA, clone: pF1KB3114, Homo sapiens PDE1A gene for calmodulin-dependent phosphodiesterase 1A, complete cds, without stop codon, in Flexi system.
AL110263 - Homo sapiens mRNA; cDNA DKFZp586G0221 (from clone DKFZp586G0221).
AJ401610 - Homo sapiens mRNA for 3'5' cyclic nucleotide phosphodiesterase (PDE1A5 gene).
U40370 - Human 3',5' cyclic nucleotide phosphodiesterase (HSPDE1A3A) mRNA, complete cds.
AF110235 - Homo sapiens clone L34 calcium/calmodulin-stimulated cyclic nucleotide phosphodiesterase (PDE1A) mRNA, partial cds.
AF110237 - Homo sapiens clone C1 calcium/calmodulin-stimulated cyclic nucleotide phosphodiesterase (PDE1A) mRNA, partial cds.
AF110236 - Homo sapiens clone L42 calcium/calmodulin-stimulated cyclic nucleotide phosphodiesterase (PDE1A) mRNA, partial cds.
BC047057 - Homo sapiens phosphodiesterase 1A, calmodulin-dependent, mRNA (cDNA clone IMAGE:5275668), with apparent retained intron.
AF110238 - Homo sapiens clone H8-3 calcium/calmodulin-stimulated cyclic nucleotide phosphodiesterase (PDE1A) mRNA, partial cds.
JD039715 - Sequence 20739 from Patent EP1572962.
JD404295 - Sequence 385319 from Patent EP1572962.
AK301720 - Homo sapiens cDNA FLJ54988 complete cds, highly similar to Calcium/calmodulin-dependent 3',5'-cyclicnucleotide phosphodiesterase 1A (EC 3.1.4.17).
AB038227 - Homo sapiens HSPDE1A mRNA for calmodulin-dependent phosphodiesterase, partial cds, C-terminal splice variant.
AB038228 - Homo sapiens HSPDE1A mRNA for calmodulin-dependent phosphodiesterase, partial cds, N-terminal variant.

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

Protein P54750 (Reactome details) participates in the following event(s):

R-HSA-111956 Calmodulin activates Cam-PDE 1
R-HSA-418456 cGMP is degraded by PDEs
R-HSA-418553 cAMP degradation by Phosphodiesterases
R-HSA-111955 cAMP hydrolysis by Cam-PDE 1
R-HSA-111957 Cam-PDE 1 activation
R-HSA-111933 Calmodulin induced events
R-HSA-418457 cGMP effects
R-HSA-418555 G alpha (s) signalling events
R-HSA-111997 CaM pathway
R-HSA-392154 Nitric oxide stimulates guanylate cyclase
R-HSA-388396 GPCR downstream signalling
R-HSA-111996 Ca-dependent events
R-HSA-1489509 DAG and IP3 signaling
R-HSA-418346 Platelet homeostasis
R-HSA-372790 Signaling by GPCR
R-HSA-112043 PLC beta mediated events
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-109582 Hemostasis
R-HSA-162582 Signal Transduction
R-HSA-112040 G-protein mediated events
R-HSA-111885 Opioid Signalling
R-HSA-418594 G alpha (i) signalling events

-  Other Names for This Gene
  Alternate Gene Symbols: D3DPG5, ENST00000409365.1, ENST00000409365.2, ENST00000409365.3, ENST00000409365.4, ENST00000409365.5, NM_001363871, P54750, PDE1A , PDE1A_HUMAN, Q86VZ0, Q9C0K8, Q9C0K9, Q9C0L0, Q9C0L1, Q9C0L2, Q9C0L3, Q9C0L4, Q9UFX3, uc319fpy.1, uc319fpy.2
UCSC ID: ENST00000409365.6_11
RefSeq Accession: NM_001363871.4
Protein: P54750 (aka PDE1A_HUMAN or CN1A_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.