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    PDE12 phosphodiesterase 12 [ Homo sapiens (human) ]

    Gene ID: 201626, updated on 5-Mar-2024

    Summary

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    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 3'-5'-exoribonuclease activity. Involved in several processes, including RNA metabolic process; cellular response to cytokine stimulus; and regulation of mitochondrial mRNA stability. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in adrenal (RPKM 3.9), thyroid (RPKM 3.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDE12 in Genome Data Viewer
    Location:
    3p14.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (57556274..57656495)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (57596636..57696867)
    105.20220307 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 ADP ribosylation factor 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

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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. PDE12 in type 1 diabetes. Tekin H, et al. Sci Rep, 2022 Oct 28. PMID 36307540, Free PMC Article
    2. The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors. Wood ER, et al. J Biol Chem, 2015 Aug 7. PMID 26055709, Free PMC Article
    3. Crystallization and preliminary X-ray crystallographic analysis of human phosphodiesterase 12. Kohno T, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2010 May 1. PMID 20445249, Free PMC Article
    4. PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria. Rorbach J, et al. Nucleic Acids Res, 2011 Sep 1. PMID 21666256, Free PMC Article
    5. Identification of 2'-phosphodiesterase, which plays a role in the 2-5A system regulated by interferon. Kubota K, et al. J Biol Chem, 2004 Sep 3. PMID 15231837

    See all (60) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PDE12 disrupts mitochondrial oxidative phosphorylation and mediates mitochondrial dysfunction to induce oral mucosal epithelial barrier damage in oral submucous fibrosis.
      Title: PDE12 disrupts mitochondrial oxidative phosphorylation and mediates mitochondrial dysfunction to induce oral mucosal epithelial barrier damage in oral submucous fibrosis.
    2. PDE12 in type 1 diabetes.
      Title: PDE12 in type 1 diabetes.
    3. PDE12 is a negative regulator of the antiviral innate immune response.
      Title: The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors.
    4. 2'-phosphodiesterase is a mitochondrial protein that specifically removes poly(A) extensions from mitochondrial mRNAs both in vitro and in mitochondria of cultured cells.
      Title: PDE12 removes mitochondrial RNA poly(A) tails and controls translation in human mitochondria.
    5. 2'-PDE locates to the mitochondrial matrix of human cells, and comprise an active 3'-5' exoribonuclease exhibiting a preference for oligo-adenosine RNA like canonical cytoplasmic deadenylases.
      Title: Human 2'-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    7. crystals of phosphodiesterase 12 belonged to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 111.3, c = 192.4 A, and diffracted to 2.5 A resolution.
      Title: Crystallization and preliminary X-ray crystallographic analysis of human phosphodiesterase 12.
    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

    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'-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 
    Process Evidence Code Pubs
    involved_in antiviral innate immune response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to dsRNA IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cellular response to interferon-alpha IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to type II interferon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in defense response to virus TAS
    Traceable Author Statement
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitochondrial mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nucleic acid metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of viral genome replication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of mitochondrial mRNA stability 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 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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

    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.

    mRNA and Protein(s)

    1. NM_001322176.2 → NP_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
      Conserved Domains (1) summary
      cl00490
      Location:299 → 462
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    2. NM_001322177.2 → NP_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:299 → 462
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    3. NM_177966.7 → NP_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:299 → 608
      EEP; Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily

    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_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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6L8Q7.2 GenPept UniProtKB/Swiss-Prot:Q6L8Q7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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