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    PDE1B phosphodiesterase 1B [ Homo sapiens (human) ]

    Gene ID: 5153, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See PDE1B in Genome Data Viewer
    Location:
    12q13.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54549601..54579239)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (54516175..54545790)
    RS_2024_09 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

    Bibliography

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    Related articles in PubMed

    1. 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
    2. Phosphodiesterases in neurodegenerative disorders. Bollen E, et al. IUBMB Life, 2012 Dec. PMID 23129425
    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. Inhibition of calmodulin-dependent phosphodiesterase induces apoptosis in human leukemic cells. Jiang X, et al. Proc Natl Acad Sci U S A, 1996 Oct 1. PMID 8855339, Free PMC Article
    5. Quantitative comparison of phosphodiesterase mRNA distribution in human brain and peripheral tissues. Lakics V, et al. Neuropharmacology, 2010 Nov. PMID 20493887

    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)

    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'-cGMP-inhibited cyclic-nucleotide phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables 3',5'-cGMP-stimulated cyclic-nucleotide phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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_2024_08

    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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