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    PDE12 phosphodiesterase 12 [ Homo sapiens (human) ]

    Gene ID: 201626, updated on 9-Dec-2024

    Summary

    Official Symbol
    PDE12provided by HGNC
    Official Full Name
    phosphodiesterase 12provided by HGNC
    Primary source
    HGNC:HGNC:25386
    See related
    Ensembl:ENSG00000174840 MIM:616519; AllianceGenome:HGNC:25386
    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
    2-PDE; 2'-PDE
    Summary
    Enables poly(A)-specific ribonuclease activity. Involved in several processes, including cellular response to interferon-alpha; innate immune response; and mRNA catabolic process. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in adrenal (RPKM 3.9), thyroid (RPKM 3.9) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PDE12 in Genome Data Viewer
    Location:
    3p14.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (57556274..57656495)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (57596636..57696867)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (57542001..57642222)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 12 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:57529659-57530209 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:57543831-57544463 Neighboring gene RNA, U6 small nuclear 108, pseudogene Neighboring gene RNA, U6 small nuclear 483, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19989 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:57582608-57583807 Neighboring gene RNA, U6atac small nuclear 26, pseudogene Neighboring gene ARF4 antisense RNA 1 Neighboring gene ARF GTPase 4 Neighboring gene DENN domain containing 6A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14481 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:57678132-57678632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14483 Neighboring gene DENND6A divergent transcript Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:57737311-57738510 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr3:57741142-57742044 and GRCh37_chr3:57742045-57742946 Neighboring gene MPRA-validated peak4671 silencer Neighboring gene sarcolemma associated protein Neighboring gene PDHA1 pseudogene 1

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3'-5'-RNA exonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables 3'-5'-RNA exonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables exonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables oligoribonucleotidase activity TAS
    Traceable Author Statement
    more info
     
    enables poly(A)-specific ribonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in mitochondrial matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in mitochondrial matrix IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    2',5'-phosphodiesterase 12
    Names
    2'-phosphodiesterase
    mitochondrial deadenylase
    NP_001309105.1
    NP_001309106.1
    NP_808881.3

    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_001322176.2NP_001309105.1  2',5'-phosphodiesterase 12 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. These differences result in a shorter protein (isoform 2) with a distinct C-terminus, compared to isoform 1. Isoform 2 may lack phospodiesterase or deadenylase activty.
      Source sequence(s)
      AC092418, AC114480, BM713922
      Related
      ENSP00000520545.1, ENST00000715954.1
      Conserved Domains (1) summary
      cl00490
      Location:299462
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
    2. NM_001322177.2NP_001309106.1  2',5'-phosphodiesterase 12 isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. These differences result in a shorter protein (isoform 3) with a distinct C-terminus, compared to isoform 1. Isoform 3 may lack phospodiesterase or deadenylase activty.
      Source sequence(s)
      AC092418, BC034978, U79276
      Consensus CDS
      CCDS82792.1
      UniProtKB/TrEMBL
      F6T1Q0
      Related
      ENSP00000420626.1, ENST00000487257.1
      Conserved Domains (1) summary
      cl00490
      Location:299462
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily
    3. NM_177966.7NP_808881.3  2',5'-phosphodiesterase 12 isoform 1 precursor

      See identical proteins and their annotated locations for NP_808881.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript and encodes the canonical protein (isoform 1).
      Source sequence(s)
      AC092418, AL831824, U79276
      Consensus CDS
      CCDS33772.1
      UniProtKB/Swiss-Prot
      B4DTU8, Q6L8Q7, Q8IYU3, Q8NDU2, Q8TE78
      Related
      ENSP00000309142.7, ENST00000311180.9
      Conserved Domains (1) summary
      cl00490
      Location:299608
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      57556274..57656495
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      57596636..57696867
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)