Human Gene PDE1B (uc009znq.3)
  Description: Homo sapiens phosphodiesterase 1B, calmodulin-dependent (PDE1B), transcript variant 2, mRNA.
RefSeq Summary (NM_001165975): The protein encoded by this gene belongs to the cyclic nucleotide phosphodiesterase (PDE) family, and PDE1 subfamily. Members of the PDE1 family are calmodulin-dependent PDEs that are stimulated by a calcium-calmodulin complex. This PDE has dual-specificity for the second messengers, cAMP and cGMP, with a preference for cGMP as a substrate. cAMP and cGMP function as key regulators of many important physiological processes. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011].
Transcript (Including UTRs)
   Position: hg19 chr12:54,955,228-54,973,023 Size: 17,796 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr12:54,966,403-54,971,112 Size: 4,710 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:54,955,228-54,973,023)mRNA (may differ from genome)Protein (332 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsH-INV
HGNCLynxMGIneXtProtPubMedReactome
TreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PDE1B_HUMAN
DESCRIPTION: RecName: Full=Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B; Short=Cam-PDE 1B; EC=3.1.4.17; AltName: Full=63 kDa Cam-PDE;
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 preference for cGMP as a substrate.
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: Type I PDE are activated by the binding of calmodulin in the presence of Ca(2+).
SUBUNIT: Homodimer (By similarity).
SUBCELLULAR LOCATION: Cytoplasm.
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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PDE1B
CDC HuGE Published Literature: PDE1B

-  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: 131.63 RPKM in Brain - Caudate (basal ganglia)
Total median expression: 674.72 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 -167.07443-0.377 Picture PostScript Text
3' UTR -607.021397-0.435 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

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1LXR - Model 1TAZ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q01064
FrontTopSide
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004112 cyclic-nucleotide phosphodiesterase activity
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:0005515 protein binding
GO:0005516 calmodulin binding
GO:0008081 phosphoric diester hydrolase activity
GO:0016787 hydrolase activity
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:0001505 regulation of neurotransmitter levels
GO:0001975 response to amphetamine
GO:0006198 cAMP catabolic process
GO:0006915 apoptotic process
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007626 locomotory behavior
GO:0008542 visual learning
GO:0030224 monocyte differentiation
GO:0036006 cellular response to macrophage colony-stimulating factor stimulus
GO:0042053 regulation of dopamine metabolic process
GO:0042428 serotonin metabolic process
GO:0046069 cGMP catabolic process
GO:0097011 cellular response to granulocyte macrophage colony-stimulating factor stimulus

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


-  Descriptions from all associated GenBank mRNAs
  BC032226 - Homo sapiens phosphodiesterase 1B, calmodulin-dependent, mRNA (cDNA clone MGC:34576 IMAGE:5200139), complete cds.
AB209200 - Homo sapiens mRNA for phosphodiesterase 1B, calmodulin-dependent variant protein.
EU668337 - Homo sapiens epididymis secretory sperm binding protein Li 79p (HEL-S-79p) mRNA, complete cds.
AK302899 - Homo sapiens cDNA FLJ54120 complete cds, highly similar to Calcium/calmodulin-dependent 3',5'-cyclicnucleotide phosphodiesterase 1B (EC 3.1.4.17).
U86078 - Homo sapiens calmodulin-stimulated phosphodiesterase PDE1B1 mRNA, complete cds.
U56976 - Human calmodulin dependent phosphodiesterase PDE1B1 mRNA, complete cds.
AB590318 - Synthetic construct DNA, clone: pFN21AE1429, Homo sapiens PDE1B gene for phosphodiesterase 1B, calmodulin-dependent, without stop codon, in Flexi system.
DQ894859 - Synthetic construct Homo sapiens clone IMAGE:100009319; FLH179165.01L; RZPDo839D07129D phosphodiesterase 1B, calmodulin-dependent (PDE1B) gene, encodes complete protein.
DQ891673 - Synthetic construct clone IMAGE:100004303; FLH179169.01X; RZPDo839D07130D phosphodiesterase 1B, calmodulin-dependent (PDE1B) gene, encodes complete protein.
AK296422 - Homo sapiens cDNA FLJ53347 complete cds, highly similar to Calcium/calmodulin-dependent 3',5'-cyclicnucleotide phosphodiesterase 1B (EC 3.1.4.17).
BX538092 - Homo sapiens mRNA; cDNA DKFZp686L23131 (from clone DKFZp686L23131).
AK302931 - Homo sapiens cDNA FLJ53684 complete cds, highly similar to Calcium/calmodulin-dependent 3',5'-cyclicnucleotide phosphodiesterase 1B (EC 3.1.4.17).
AK126899 - Homo sapiens cDNA FLJ44951 fis, clone BRAWH2002333, highly similar to Calcium/calmodulin-dependent 3',5'-cyclicnucleotide phosphodiesterase 1B (EC 3.1.4.17).
AJ401609 - Homo sapiens mRNA for 3'5' cyclic nucleotide phosphodiesterase 1B2 (PDE1B2 gene).
U40584 - Human calcium/calmodulin stimulated cyclic nucleotide phosphodiesterase (PDE1B) mRNA, partial cds.
M94539 - Homo sapiens cyclic nucleotide phosphodiesterase (CaM-PDE) mRNA, partial cds.
JD526682 - Sequence 507706 from Patent EP1572962.
JD135177 - Sequence 116201 from Patent EP1572962.
JD514812 - Sequence 495836 from Patent EP1572962.
JD372824 - Sequence 353848 from Patent EP1572962.
JD464001 - Sequence 445025 from Patent EP1572962.
JD487932 - Sequence 468956 from Patent EP1572962.
JD565776 - Sequence 546800 from Patent EP1572962.
JD060721 - Sequence 41745 from Patent EP1572962.
JD230360 - Sequence 211384 from Patent EP1572962.
JD105231 - Sequence 86255 from Patent EP1572962.
JD193409 - Sequence 174433 from Patent EP1572962.
JD455525 - Sequence 436549 from Patent EP1572962.
JD393290 - Sequence 374314 from Patent EP1572962.
JD488393 - Sequence 469417 from Patent EP1572962.
JD494140 - Sequence 475164 from Patent EP1572962.
JD146112 - Sequence 127136 from Patent EP1572962.
JD341222 - Sequence 322246 from Patent EP1572962.
JD206987 - Sequence 188011 from Patent EP1572962.
JD063473 - Sequence 44497 from Patent EP1572962.
JD406409 - Sequence 387433 from Patent EP1572962.
JD536802 - Sequence 517826 from Patent EP1572962.
JD164025 - Sequence 145049 from Patent EP1572962.
JD548410 - Sequence 529434 from Patent EP1572962.
JD502061 - Sequence 483085 from Patent EP1572962.
JD464683 - Sequence 445707 from Patent EP1572962.
JD390809 - Sequence 371833 from Patent EP1572962.
JD217984 - Sequence 199008 from Patent EP1572962.
JD147712 - Sequence 128736 from Patent EP1572962.
JD479952 - Sequence 460976 from Patent EP1572962.
JD133154 - Sequence 114178 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00230 - Purine metabolism
hsa04020 - Calcium signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein Q01064 (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: AK126899, PDE1B1, PDE1B_HUMAN, PDES1B, Q01064, Q92825, Q96KP3
UCSC ID: uc009znq.3
RefSeq Accession: NM_001165975
Protein: Q01064 (aka PDE1B_HUMAN or CN1B_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK126899.1
exon count: 13CDS single in 3' UTR: no RNA size: 2782
ORF size: 999CDS single in intron: no Alignment % ID: 99.78
txCdsPredict score: 1882.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.