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Aliases for PDE1B Gene

Aliases for PDE1B Gene

  • Phosphodiesterase 1B 2 3 5
  • Phosphodiesterase 1B, Calmodulin-Dependent 2 3
  • 63 KDa Cam-PDE 3 4
  • Cam-PDE 1B 3 4
  • PDES1B 3 4
  • PDE1B1 3 4
  • Presumed 63kDa Form Of The Type 1 Cyclic Nucleotide Phosphodiesterase Family Known As PDE1B 3
  • Calcium/Calmodulin-Dependent 3,5-Cyclic Nucleotide Phosphodiesterase 1B 3
  • Calcium/Calmodulin-Stimulated Cyclic Nucleotide Phosphodiesterase 3
  • Epididymis Secretory Sperm Binding Protein Li 79p 3
  • Calmodulin-Stimulated Phosphodiesterase PDE1B1 3
  • EC 3.1.4.17 4
  • HEL-S-79p 3

External Ids for PDE1B Gene

Previous HGNC Symbols for PDE1B Gene

  • PDES1B

Previous GeneCards Identifiers for PDE1B Gene

  • GC12P055070
  • GC12P054660
  • GC12P053229
  • GC12P054943
  • GC12P051981

Summaries for PDE1B Gene

Entrez Gene Summary for PDE1B Gene

  • 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]

GeneCards Summary for PDE1B Gene

PDE1B (Phosphodiesterase 1B) is a Protein Coding gene. Among its related pathways are G-Beta Gamma Signaling and Pyrimidine metabolism (KEGG). Gene Ontology (GO) annotations related to this gene include calmodulin binding and 3,5-cyclic-AMP phosphodiesterase activity. An important paralog of this gene is PDE1C.

UniProtKB/Swiss-Prot for PDE1B Gene

  • 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.

Tocris Summary for PDE1B Gene

  • Phosphodiesterases (PDEs) are a family of phosphohydrolyases that catalyze the hydrolysis of 3' cyclic phosphate bonds in adenosine and/or guanine 3',5' cyclic monophosphate (cAMP and/or cGMP). PDEs regulate the second messengers by controlling their degradation.

Gene Wiki entry for PDE1B Gene

Additional gene information for PDE1B Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDE1B Gene

Genomics for PDE1B Gene

GeneHancer (GH) Regulatory Elements for PDE1B Gene

Promoters and enhancers for PDE1B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J054559 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 664.5 +11.9 11924 2.7 HDGF PKNOX1 ATF1 GTF2E2 IRF3 RFX5 FOXK2 POLR2A NFYB FOS PDE1B PPP1R1A
GH12J054549 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 655.2 +0.4 449 1.6 HDGF FOXA2 SIN3A ZNF2 GLIS2 ZNF213 FOS RUNX3 SP3 REST PDE1B ENSG00000258344 ATF7 PPP1R1A HNRNPA1 ENSG00000257596 GTSF1
GH12J054548 Enhancer 0.2 FANTOM5 666.9 -1.2 -1225 0.2 PDE1B ENSG00000257824 NCKAP1L
GH12J054527 Enhancer 0.6 ENCODE 11.7 -22.0 -22048 0.2 SCRT1 CTCF ZNF654 NFATC3 MAX TRIM22 SIN3A REST RAD21 ZNF585B PHC1P1 PDE1B NCKAP1L CBX5 PPP1R1A ENSG00000257824
GH12J054571 Enhancer 0.5 ENCODE 11.2 +22.4 22362 0.2 SP1 RFX1 MYNN MAX BMI1 PDE1B NCKAP1L PPP1R1A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDE1B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDE1B gene promoter:
  • AREB6
  • FOXF2
  • MZF-1
  • SREBP-1a
  • CRE-BP1
  • ATF-2
  • Pax-2a
  • Pax-2
  • SREBP-1b

Genomic Locations for PDE1B Gene

Genomic Locations for PDE1B Gene
chr12:54,549,350-54,579,239
(GRCh38/hg38)
Size:
29,890 bases
Orientation:
Plus strand
chr12:54,943,134-54,973,023
(GRCh37/hg19)
Size:
29,890 bases
Orientation:
Plus strand

Genomic View for PDE1B Gene

Genes around PDE1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDE1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDE1B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDE1B Gene

Proteins for PDE1B Gene

  • Protein details for PDE1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q01064-PDE1B_HUMAN
    Recommended name:
    Calcium/calmodulin-dependent 3,5-cyclic nucleotide phosphodiesterase 1B
    Protein Accession:
    Q01064
    Secondary Accessions:
    • Q92825
    • Q96KP3

    Protein attributes for PDE1B Gene

    Size:
    536 amino acids
    Molecular mass:
    61380 Da
    Cofactor:
    Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PDE1B Gene

    Alternative splice isoforms for PDE1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDE1B Gene

Post-translational modifications for PDE1B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDE1B Gene

Domains & Families for PDE1B Gene

Gene Families for PDE1B Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PDE1B Gene

Graphical View of Domain Structure for InterPro Entry

Q01064

UniProtKB/Swiss-Prot:

PDE1B_HUMAN :
  • Belongs to the cyclic nucleotide phosphodiesterase family. PDE1 subfamily.
Family:
  • Belongs to the cyclic nucleotide phosphodiesterase family. PDE1 subfamily.
genes like me logo Genes that share domains with PDE1B: view

Function for PDE1B Gene

Molecular function for PDE1B Gene

UniProtKB/Swiss-Prot 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.
UniProtKB/Swiss-Prot CatalyticActivity:
Nucleoside 3,5-cyclic phosphate + H(2)O = nucleoside 5-phosphate.
UniProtKB/Swiss-Prot EnzymeRegulation:
Type I PDE are activated by the binding of calmodulin in the presence of Ca(2+).

Enzyme Numbers (IUBMB) for PDE1B Gene

Phenotypes From GWAS Catalog for PDE1B Gene

Gene Ontology (GO) - Molecular Function for PDE1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004112 cyclic-nucleotide phosphodiesterase activity IEA --
GO:0004114 3,5-cyclic-nucleotide phosphodiesterase activity IEA --
GO:0004115 3,5-cyclic-AMP phosphodiesterase activity TAS --
GO:0004117 calmodulin-dependent cyclic-nucleotide phosphodiesterase activity TAS --
GO:0005515 protein binding IPI 21044950
genes like me logo Genes that share ontologies with PDE1B: view
genes like me logo Genes that share phenotypes with PDE1B: view

Animal Models for PDE1B Gene

MGI Knock Outs for PDE1B:

Animal Model Products

  • Taconic Biosciences Mouse Models for PDE1B

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDE1B Gene

Localization for PDE1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDE1B Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDE1B gene
Compartment Confidence
cytosol 5
nucleus 4

Gene Ontology (GO) - Cellular Components for PDE1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0043025 neuronal cell body IEA --
genes like me logo Genes that share ontologies with PDE1B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDE1B Gene

Pathways & Interactions for PDE1B Gene

genes like me logo Genes that share pathways with PDE1B: view

Gene Ontology (GO) - Biological Process for PDE1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001975 response to amphetamine IEA --
GO:0006198 cAMP catabolic process IDA 14687666
GO:0006915 apoptotic process TAS 8855339
GO:0007165 signal transduction IEA --
GO:0007186 G-protein coupled receptor signaling pathway TAS --
genes like me logo Genes that share ontologies with PDE1B: view

No data available for SIGNOR curated interactions for PDE1B Gene

Drugs & Compounds for PDE1B Gene

(17) Drugs for PDE1B Gene - From: DrugBank, DGIdb, FDA Approved Drugs, IUPHAR, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Bepridil Approved, Withdrawn Pharma Pore Blocker, Target, inhibitor 0
Felodipine Approved, Investigational Pharma Potentiation, Activator, Target, inhibitor 22
Nicardipine Approved, Investigational Pharma Antagonist, Target, inhibitor 33
Trapidil Approved Pharma Target, inhibitor 1
Caffeine Approved Nutra Antagonist, Activator, Target, inhibitor 434

(5) Additional Compounds for PDE1B Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Eggmanone
505068-32-6
Etazolate hydrochloride
35838-58-5
IBMX
Antagonist 28822-58-4
MY-5445
78351-75-4
Ro 20-1724
29925-17-5

(5) Tocris Compounds for PDE1B Gene

Compound Action Cas Number
Eggmanone Potent and selective PDE4 inhibitor; suppresses hedgehog signaling 505068-32-6
Etazolate hydrochloride PDE4 inhibitor 35838-58-5
IBMX PDE inhibitor (non-selective) 28822-58-4
MY-5445 PDE5 inhibitor 78351-75-4
Ro 20-1724 PDE4 inhibitor 29925-17-5
genes like me logo Genes that share compounds with PDE1B: view

Transcripts for PDE1B Gene

Unigene Clusters for PDE1B Gene

Phosphodiesterase 1B, calmodulin-dependent:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDE1B Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17
SP1: - - - - - -
SP2: - - - -
SP3: - - -
SP4: - - - - - -
SP5: - - - -
SP6:
SP7: - - -
SP8: - - - - - - - - -

Relevant External Links for PDE1B Gene

GeneLoc Exon Structure for
PDE1B
ECgene alternative splicing isoforms for
PDE1B

Expression for PDE1B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDE1B Gene

mRNA differential expression in normal tissues according to GTEx for PDE1B Gene

This gene is overexpressed in Brain - Putamen (basal ganglia) (x10.8), Brain - Caudate (basal ganglia) (x9.0), and Brain - Nucleus accumbens (basal ganglia) (x8.0).

Protein differential expression in normal tissues from HIPED for PDE1B Gene

This gene is overexpressed in Urine (46.6) and Frontal cortex (9.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PDE1B Gene



Protein tissue co-expression partners for PDE1B Gene

NURSA nuclear receptor signaling pathways regulating expression of PDE1B Gene:

PDE1B

SOURCE GeneReport for Unigene cluster for PDE1B Gene:

Hs.530871

Evidence on tissue expression from TISSUES for PDE1B Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with PDE1B: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDE1B Gene

Orthologs for PDE1B Gene

This gene was present in the common ancestor of animals.

Orthologs for PDE1B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDE1B 34 33
  • 99.5 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PDE1B 34 33
  • 91.76 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pde1b 16 34 33
  • 90.78 (n)
rat
(Rattus norvegicus)
Mammalia Pde1b 33
  • 90.65 (n)
dog
(Canis familiaris)
Mammalia PDE1B 34 33
  • 88.91 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDE1B 34
  • 58 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDE1B 34
  • 83 (a)
OneToOne
LOC777528 33
  • 80.76 (n)
lizard
(Anolis carolinensis)
Reptilia PDE1B 34
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pde1b 33
  • 74.55 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG14940 35
  • 53 (a)
Pde1c 34
  • 21 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea T04D3.3 35
  • 54 (a)
pde-1 34
  • 36 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 47 (a)
OneToMany
Species where no ortholog for PDE1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for PDE1B Gene

ENSEMBL:
Gene Tree for PDE1B (if available)
TreeFam:
Gene Tree for PDE1B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDE1B: view image

Paralogs for PDE1B Gene

(11) SIMAP similar genes for PDE1B Gene using alignment to 3 proteins:

  • PDE1B_HUMAN
  • B4DK72_HUMAN
  • F8VZK3_HUMAN
genes like me logo Genes that share paralogs with PDE1B: view

Variants for PDE1B Gene

Sequence variations from dbSNP and Humsavar for PDE1B Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000041635 -- 54,566,279(+) A/T intron_variant
rs1000079146 -- 54,548,572(+) T/A upstream_transcript_variant
rs1000112718 -- 54,556,907(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000213696 -- 54,578,918(+) T/A 3_prime_UTR_variant
rs1000273760 -- 54,566,838(+) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PDE1B Gene

Variant ID Type Subtype PubMed ID
nsv832421 CNV gain 17160897

Variation tolerance for PDE1B Gene

Residual Variation Intolerance Score: 20.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.97; 20.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDE1B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDE1B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDE1B Gene

Disorders for PDE1B Gene

Additional Disease Information for PDE1B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PDE1B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDE1B Gene

Publications for PDE1B Gene

  1. Identification and characterisation of a human calmodulin-stimulated phosphodiesterase PDE1B1. (PMID: 9419816) Yu J … Gelinas R (Cellular signalling 1997) 2 3 4 22 58
  2. Inhibition of calmodulin-dependent phosphodiesterase induces apoptosis in human leukemic cells. (PMID: 8855339) Jiang X … Epstein PM (Proceedings of the National Academy of Sciences of the United States of America 1996) 2 3 4 22 58
  3. Isolation and differential tissue distribution of two human cDNAs encoding PDE1 splice variants. (PMID: 11747989) Fidock M … Lanfear J (Cellular signalling 2002) 3 4 22 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for PDE1B Gene

Sources for PDE1B Gene

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