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

    Gene ID: 51567, updated on 17-Jun-2024

    Summary

    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
    NEW
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    Genomic context

    See TDP2 in Genome Data Viewer
    Location:
    6p22.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (24649979..24666899, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (24520363..24537292, complement)
    105.20220307 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

    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?

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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.

    Genomic

    1. NG_052787.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_016614.3NP_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:114358
      TDP2; Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains
      cd14344
      Location:2763
      UBA_TYDP2; UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins

    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_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)