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    PDE3B phosphodiesterase 3B [ Homo sapiens (human) ]

    Gene ID: 5140, updated on 26-Apr-2024

    Summary

    Official Symbol
    PDE3Bprovided by HGNC
    Official Full Name
    phosphodiesterase 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:8779
    See related
    Ensembl:ENSG00000152270 MIM:602047; AllianceGenome:HGNC:8779
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HcGIP1; cGIPDE1
    Summary
    Enables 3',5'-cyclic-nucleotide phosphodiesterase activity. Involved in negative regulation of angiogenesis; negative regulation of cell adhesion; and negative regulation of lipid catabolic process. Located in membrane. Part of guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in fat (RPKM 53.0), lymph node (RPKM 8.6) and 12 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PDE3B in Genome Data Viewer
    Location:
    11p15.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (14643804..14872044)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (14739099..14968415)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (14665350..14893590)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4474 Neighboring gene RNA, U7 small nuclear 49 pseudogene Neighboring gene COPI coat complex subunit beta 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:14541725-14542339 Neighboring gene proteasome 20S subunit alpha 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14654809-14655398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3173 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:14683201-14683380 Neighboring gene mortality factor 4 like 1 pseudogene 3 Neighboring gene uncharacterized LOC107984315 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14737137-14737723 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:14737724-14738309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:14748217-14748780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:14764591-14765090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14799188-14799688 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:14838787-14838962 Neighboring gene uncharacterized LOC124902639 Neighboring gene MPRA-validated peak1207 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14929307-14929806 Neighboring gene cytochrome P450 family 2 subfamily R member 1 Neighboring gene calcitonin pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:14993078-14993724 Neighboring gene calcitonin related polypeptide alpha

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
    EBI GWAS Catalog
    Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.
    EBI GWAS Catalog

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in Golgi apparatus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of guanyl-nucleotide exchange factor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B
    Names
    CGI-PDE B
    CGIP1
    cGMP-inhibited 3',5'-cyclic phosphodiesterase B
    cyclic GMP-inhibited phosphodiesterase B
    cyclic nucleotide phosphodiesterase
    phosphodiesterase 3B, cGMP-inhibited
    NP_000913.2
    NP_001350498.1
    NP_001350499.1
    XP_006718312.1
    XP_047283071.1
    XP_054225082.1
    XP_054225083.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_000922.4NP_000913.2  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 2

      See identical proteins and their annotated locations for NP_000913.2

      Status: VALIDATED

      Source sequence(s)
      AC090835, BC136565, BC150307
      Consensus CDS
      CCDS7817.1
      UniProtKB/Swiss-Prot
      B7ZM37, O00639, Q13370, Q14408, Q6SEI4
      UniProtKB/TrEMBL
      A7E2E5
      Related
      ENSP00000282096.4, ENST00000282096.9
      Conserved Domains (2) summary
      pfam00233
      Location:7361010
      PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
      pfam06532
      Location:136282
      DUF1109; Protein of unknown function (DUF1109)
    2. NM_001363569.2NP_001350498.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC018795, AC087207, AC090835
      Consensus CDS
      CCDS91445.1
      UniProtKB/TrEMBL
      A7E2E5
      Related
      ENSP00000388644.2, ENST00000455098.2
      Conserved Domains (2) summary
      pfam00233
      Location:685959
      PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
      pfam06532
      Location:136282
      DUF1109; Protein of unknown function (DUF1109)
    3. NM_001363570.2NP_001350499.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC018795, AC087207, AC090835
      UniProtKB/TrEMBL
      A7E2E5
      Conserved Domains (2) summary
      pfam00233
      Location:8141088
      PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
      pfam06532
      Location:136282
      DUF1109; Protein of unknown function (DUF1109)
    4. NM_001429699.1NP_001416628.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC018795, AC087207, AC090835
    5. NM_001429700.1NP_001416629.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC018795, AC087207, AC090835

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      14643804..14872044
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    2. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      14887823..14899321
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006718249.4XP_006718312.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X1

      Conserved Domains (1) summary
      pfam06532
      Location:136282
      DUF1109; Protein of unknown function (DUF1109)
    2. XM_047427115.1XP_047283071.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      14739099..14968415
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    2. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      14984289..14995688
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369107.1XP_054225082.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X1

    2. XM_054369108.1XP_054225083.1  cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B isoform X2