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PDE1B phosphodiesterase 1B [ Homo sapiens (human) ]

Gene ID: 5153, updated on 5-Mar-2024

Summary

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Official Symbol
PDE1Bprovided by HGNC
Official Full Name
phosphodiesterase 1Bprovided by HGNC
Primary source
HGNC:HGNC:8775
See related
Ensembl:ENSG00000123360 MIM:171891; AllianceGenome:HGNC:8775
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PDE1B1; PDES1B; HEL-S-79p
Summary
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]
Expression
Broad expression in brain (RPKM 8.5), fat (RPKM 6.8) and 19 other tissues See more
Orthologs
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Genomic context

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Location:
12q13.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54549601..54579239)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (54516175..54545790)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54943385..54973023)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene GPR84, ZNF385A, ITGA5 and GTSF1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54867463-54867989 Neighboring gene gametocyte specific factor 1 Neighboring gene MPRA-validated peak1739 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6445 Neighboring gene NCK associated protein 1 like Neighboring gene NANOG hESC enhancer GRCh37_chr12:54940243-54940787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54943935-54944563 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:54957859-54958550 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:54958551-54959240 Neighboring gene Sharpr-MPRA regulatory region 444 Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 1A Neighboring gene glycosylation dependent cell adhesion molecule 1 (pseudogene)

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Phosphodiesterases in neurodegenerative disorders. Bollen E, et al. IUBMB Life, 2012 Dec. PMID 23129425
  2. Quantitative comparison of phosphodiesterase mRNA distribution in human brain and peripheral tissues. Lakics V, et al. Neuropharmacology, 2010 Nov. PMID 20493887
  3. PDE1B2 regulates cGMP and a subset of the phenotypic characteristics acquired upon macrophage differentiation from a monocyte. Bender AT, et al. Proc Natl Acad Sci U S A, 2006 Jan 10. PMID 16407168, Free PMC Article
  4. Selective up-regulation of PDE1B2 upon monocyte-to-macrophage differentiation. Bender AT, et al. Proc Natl Acad Sci U S A, 2005 Jan 11. PMID 15625104, Free PMC Article
  5. Identification and characterisation of a human calmodulin-stimulated phosphodiesterase PDE1B1. Yu J, et al. Cell Signal, 1997 Nov. PMID 9419816

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The c.1618G>A, p.Gly540Ser substitution in CNGA3 was identified as the causative mutation for a novel form of ACHM in Awassi sheep. Gene augmentation therapy restored vision in the affected sheep. This novel mutation provides a large-animal model that is valid for most human CNGA3 ACHM patients; the majority of them carry missense rather than premature-termination mutations.
    Title: Gene Augmentation Therapy for a Missense Substitution in the cGMP-Binding Domain of Ovine CNGA3 Gene Restores Vision in Day-Blind Sheep.
  2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  4. Selective up-regulation of PDE1B2 upon monocyte-to-macrophage differentiation.
    Title: Selective up-regulation of PDE1B2 upon monocyte-to-macrophage differentiation.
  5. PDE1B2 regulates a subset of phenotypic changes that occur upon phorbol-12-myristate-13-acetate-induced differentiation and likely also plays a role in differentiated macrophages by regulating agonist-stimulated cGMP levels
    Title: PDE1B2 regulates cGMP and a subset of the phenotypic characteristics acquired upon macrophage differentiation from a monocyte.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat decreases the intracellular levels of cAMP and CREB ser-133 phosphorylation through a signal transduction pathway involving sequential activation of phosphatidylinositol 3-kinase, AKT, and cyclic nucleoside phosphodiesterases PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3',5'-cyclic-AMP phosphodiesterase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 3',5'-cyclic-AMP phosphodiesterase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables 3',5'-cyclic-GMP phosphodiesterase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables calmodulin binding IEA
Inferred from Electronic Annotation
more info
  
enables calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cAMP-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cellular response to granulocyte macrophage colony-stimulating factor stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to macrophage colony-stimulating factor stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in dopamine catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in locomotory behavior IEA
Inferred from Electronic Annotation
more info
  
involved_in monocyte differentiation IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in response to amphetamine IEA
Inferred from Electronic Annotation
more info
  
involved_in serotonin metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in visual learning IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
Names
63 kDa Cam-PDE
calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B
calcium/calmodulin-stimulated cyclic nucleotide phosphodiesterase
calmodulin-stimulated phosphodiesterase PDE1B1
cam-PDE 1B
epididymis secretory sperm binding protein Li 79p
phosphodiesterase 1B, calmodulin-dependent
presumed 63kDa form of the type 1 cyclic nucleotide phosphodiesterase family known as PDE1B
NP_000915.1
NP_001159447.1
NP_001275697.1
NP_001275698.1
NP_001302463.1
NP_001302464.1
XP_016874921.1
XP_016874922.1
XP_047284926.1
XP_054228193.1
XP_054228194.1
XP_054228195.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029621.1 RefSeqGene

    Range
    5209..34847
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000924.4 → NP_000915.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 1

    See identical proteins and their annotated locations for NP_000915.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC079310, BC032226, DA254686
    Consensus CDS
    CCDS8882.1
    UniProtKB/Swiss-Prot
    Q01064, Q92825, Q96KP3
    Related
    ENSP00000243052.3, ENST00000243052.8
    Conserved Domains (2) summary
    pfam00233
    Location:222 → 449
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
    pfam08499
    Location:81 → 137
    PDEase_I_N; 3'5'-cyclic nucleotide phosphodiesterase N-terminal

  2. NM_001165975.3 → NP_001159447.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 2

    See identical proteins and their annotated locations for NP_001159447.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains a distinct 5' UTR, lacks part of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    BC032226, BP342896, BX538092
    Consensus CDS
    CCDS53800.1
    UniProtKB/Swiss-Prot
    Q01064
    UniProtKB/TrEMBL
    Q7Z364
    Related
    ENSP00000448519.1, ENST00000550620.1
    Conserved Domains (2) summary
    pfam00233
    Location:202 → 429
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
    pfam08499
    Location:61 → 117
    PDEase_I_N; 3'5'-cyclic nucleotide phosphodiesterase N-terminal

  3. NM_001288768.2 → NP_001275697.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 3

    See identical proteins and their annotated locations for NP_001275697.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in its 5' UTR and uses a downstream start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Variants 3 and 5 both encode the same isoform (3).
    Source sequence(s)
    AK302899, BC032226, BX538092, DA254686
    UniProtKB/TrEMBL
    Q7Z364
    Conserved Domains (1) summary
    pfam00233
    Location:85 → 312
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  4. NM_001288769.2 → NP_001275698.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 4

    See identical proteins and their annotated locations for NP_001275698.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains a distinct 5' UTR, lacks part of the 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK296422, BC032226, BX538092
    Consensus CDS
    CCDS73477.1
    UniProtKB/TrEMBL
    B4DK72
    Related
    ENSP00000442559.1, ENST00000538346.5
    Conserved Domains (2) summary
    pfam00233
    Location:181 → 408
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
    pfam08499
    Location:40 → 96
    PDEase_I_N; 3'5'-cyclic nucleotide phosphodiesterase N-terminal

  5. NM_001315534.2 → NP_001302463.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains a distinct 5' UTR, lacks part of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus compared to isoform 1. Variants 3 and 5 both encode the same isoform (3).
    Source sequence(s)
    AC068789, BC032226, BX538092
    UniProtKB/TrEMBL
    Q7Z364
    Related
    ENST00000394277.7
    Conserved Domains (1) summary
    pfam00233
    Location:85 → 312
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  6. NM_001315535.2 → NP_001302464.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains a distinct 5' UTR, lacks part of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (5) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC068789, AC079310, AK126899, BC032226, BX538092
    UniProtKB/TrEMBL
    B3KX78
    Related
    ENST00000542335.5
    Conserved Domains (1) summary
    pfam00233
    Location:18 → 245
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    54549601..54579239
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428970.1 → XP_047284926.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X1

  2. XM_017019433.2 → XP_016874922.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X3

    UniProtKB/TrEMBL
    B4DK72
    Conserved Domains (2) summary
    pfam00233
    Location:181 → 408
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
    pfam08499
    Location:40 → 96
    PDEase_I_N; 3'5'-cyclic nucleotide phosphodiesterase N-terminal

  3. XM_017019432.2 → XP_016874921.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    54516175..54545790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372218.1 → XP_054228193.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X1

  2. XM_054372220.1 → XP_054228195.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X3

    UniProtKB/TrEMBL
    B4DK72

  3. XM_054372219.1 → XP_054228194.1  dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q01064.2 GenPept UniProtKB/Swiss-Prot:Q01064

Gene LinkOut

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