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    TDP2 tyrosyl-DNA phosphodiesterase 2 [ Homo sapiens (human) ]

    Gene ID: 51567, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TDP2provided by HGNC
    Official Full Name
    tyrosyl-DNA phosphodiesterase 2provided by HGNC
    Primary source
    HGNC:HGNC:17768
    See related
    Ensembl:ENSG00000111802 MIM:605764; AllianceGenome:HGNC:17768
    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
    EAP2; AD022; EAPII; TTRAP; hTDP2; dJ30M3.3
    Summary
    This gene encodes a member of a superfamily of divalent cation-dependent phosphodiesterases. The encoded protein associates with CD40, tumor necrosis factor (TNF) receptor-75 and TNF receptor associated factors (TRAFs), and inhibits nuclear factor-kappa-B activation. This protein has sequence and structural similarities with APE1 endonuclease, which is involved in both DNA repair and the activation of transcription factors. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in small intestine (RPKM 97.5), colon (RPKM 87.6) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TDP2 in Genome Data Viewer
    Location:
    6p22.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (24649979..24666899, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (24520363..24537292, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (24650207..24667127, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene aldehyde dehydrogenase 5 family member A1 Neighboring gene uncharacterized LOC124901277 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:24538795-24539994 Neighboring gene NANOG hESC enhancer GRCh37_chr6:24547459-24547981 Neighboring gene KIAA0319 Neighboring gene MPRA-validated peak5735 silencer Neighboring gene keratin 8 pseudogene 43 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16993 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:24666173-24666845 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:24666846-24667517 Neighboring gene uncharacterized LOC124901279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24682160-24682927 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:24682928-24683696 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:24683697-24684463 Neighboring gene acyl-CoA thioesterase 13 Neighboring gene uncharacterized LOC124901278

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. A novel non-sense mutation in TDP2 causes spinocerebellar ataxia autosomal recessive 23 accompanied by bilateral upward gaze; report of a case and review of the literature. Zoghi S, et al. Eur J Med Genet, 2021 Dec. PMID 34606976
    2. The PML nuclear bodies-associated protein TTRAP regulates ribosome biogenesis in nucleolar cavities upon proteasome inhibition. Vilotti S, et al. Cell Death Differ, 2012 Mar. PMID 21921940, Free PMC Article
    3. Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2. Schellenberg MJ, et al. Nucleic Acids Res, 2020 Jun 19. PMID 32356875, Free PMC Article
    4. Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase 1 DNA-protein crosslinks and 3'-blocking lesions in the absence of tyrosyl-DNA phosphodiesterase 1 (TDP1). Tsuda M, et al. DNA Repair (Amst), 2020 Jul-Aug. PMID 32460231
    5. Characterization of a novel loss-of-function variant in TDP2 in two adult patients with spinocerebellar ataxia autosomal recessive 23 (SCAR23). Errichiello E, et al. J Hum Genet, 2020 Dec. PMID 32651480

    See all (86) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exploring the removal of Spo11 and topoisomerases from DNA breaks in S. cerevisiae by human Tyrosyl DNA Phosphodiesterase 2.
      Title: Exploring the removal of Spo11 and topoisomerases from DNA breaks in S. cerevisiae by human Tyrosyl DNA Phosphodiesterase 2.
    2. Inactivating TDP2 missense mutation in siblings with congenital abnormalities reminiscent of fanconi anemia.
      Title: Inactivating TDP2 missense mutation in siblings with congenital abnormalities reminiscent of fanconi anemia.
    3. A novel non-sense mutation in TDP2 causes spinocerebellar ataxia autosomal recessive 23 accompanied by bilateral upward gaze; report of a case and review of the literature.
      Title: A novel non-sense mutation in TDP2 causes spinocerebellar ataxia autosomal recessive 23 accompanied by bilateral upward gaze; report of a case and review of the literature.
    4. DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks.
      Title: DNA and RNA Cleavage Complexes and Repair Pathway for TOP3B RNA- and DNA-Protein Crosslinks.
    5. Characterization of a novel loss-of-function variant in TDP2 in two adult patients with spinocerebellar ataxia autosomal recessive 23 (SCAR23).
      Title: Characterization of a novel loss-of-function variant in TDP2 in two adult patients with spinocerebellar ataxia autosomal recessive 23 (SCAR23).
    6. Untangling trapped topoisomerases with tyrosyl-DNA phosphodiesterases.
      Title: Untangling trapped topoisomerases with tyrosyl-DNA phosphodiesterases.
    7. Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase 1 DNA-protein crosslinks and 3'-blocking lesions in the absence of tyrosyl-DNA phosphodiesterase 1 (TDP1).
      Title: Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase 1 DNA-protein crosslinks and 3'-blocking lesions in the absence of tyrosyl-DNA phosphodiesterase 1 (TDP1).
    8. Effects of TDP2/VPg Unlinkase Activity on Picornavirus Infections Downstream of Virus Translation.
      Title: Effects of TDP2/VPg Unlinkase Activity on Picornavirus Infections Downstream of Virus Translation.
    9. TDP2 suppresses genomic instability induced by androgens in the epithelial cells of prostate glands.
      Title: TDP2 suppresses genomic instability induced by androgens in the epithelial cells of prostate glands.
    10. Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.
      Title: Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.
    Submit: New GeneRIF Correction See all GeneRIFs (39)

    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

    Associated conditions

    Description Tests
    Spinocerebellar ataxia, autosomal recessive 23
    MedGen: C4750914 OMIM: 616949 GeneReviews: Not available
    		Compare labs

    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
    integrase gag-pol TTRAP and HIV-1 IN interact in vivo and in vitro. The interaction involves the first 180 amino acids of TTRAP 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

    Clone Names

    • MGC9099, MGC111021

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-tyrosyl-DNA phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5'-tyrosyl-DNA phosphodiesterase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 5'-tyrosyl-DNA phosphodiesterase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables manganese ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription corepressor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables tyrosyl-RNA phosphodiesterase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in double-strand break repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in double-strand break repair IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in PML body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in aggresome IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tyrosyl-DNA phosphodiesterase 2
    Names
    5'-Tyr-DNA phosphodiesterase
    5'-tyrosyl-DNA phosphodiesterase
    ETS1-associated protein 2
    ETS1-associated protein II
    TRAF and TNF receptor-associated protein
    VPg unlinkase
    epididymis secretory sperm binding protein
    tyr-DNA phosphodiesterase 2
    tyrosyl-RNA phosphodiesterase
    NP_057698.2

    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_052787.1 RefSeqGene

      Range
      4989..21909
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_016614.3 → NP_057698.2  tyrosyl-DNA phosphodiesterase 2

      See identical proteins and their annotated locations for NP_057698.2

      Status: REVIEWED

      Source sequence(s)
      AL031775
      Consensus CDS
      CCDS4557.1
      UniProtKB/Swiss-Prot
      B4DKL8, B4DQ95, O95551, Q2TBE2, Q5JYM0, Q7Z6U5, Q9NUK5, Q9NYY9
      UniProtKB/TrEMBL
      A0A384MDM5
      Related
      ENSP00000367440.4, ENST00000378198.9
      Conserved Domains (2) summary
      cd09080
      Location:114 → 358
      TDP2; Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains
      cd14344
      Location:27 → 63
      UBA_TYDP2; UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      24649979..24666899 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      24520363..24537292 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95551.1 GenPept UniProtKB/Swiss-Prot:O95551

    Gene LinkOut

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

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