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    Tdp2 tyrosyl-DNA phosphodiesterase 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 498749, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Tdp2provided by RGD
    Official Full Name
    tyrosyl-DNA phosphodiesterase 2provided by RGD
    Primary source
    RGD:1560342
    See related
    EnsemblRapid:ENSRNOG00000018246 AllianceGenome:RGD:1560342
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Ttrap
    Summary
    Predicted to enable metal ion binding activity; phosphoric diester hydrolase activity; and single-stranded DNA binding activity. Predicted to be involved in double-strand break repair and neuron development. Predicted to be located in aggresome and nuclear body. Predicted to be active in PML body and cytoplasm. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 23. Orthologous to human TDP2 (tyrosyl-DNA phosphodiesterase 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 166.9), Adrenal (RPKM 160.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tdp2 in Genome Data Viewer
    Location:
    17p11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (40656969..40668362, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (40228943..40240337, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (42229667..42241025, complement)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene glycosylphosphatidylinositol specific phospholipase D1 Neighboring gene aldehyde dehydrogenase 5 family, member A1 Neighboring gene KIAA0319 homolog Neighboring gene ribosomal protein L37, pseudogene 1 Neighboring gene acyl-CoA thioesterase 13 Neighboring gene similar to human chromosome 6 open reading frame 62

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. An RNA virus hijacks an incognito function of a DNA repair enzyme. Virgen-Slane R, et al. Proc Natl Acad Sci U S A, 2012 Sep 4. PMID 22908287, Free PMC Article
    2. Characterization of magnesium requirement of human 5'-tyrosyl DNA phosphodiesterase mediated reaction. Adhikari S, et al. BMC Res Notes, 2012 Mar 9. PMID 22405347, Free PMC Article
    3. TDP2/TTRAP is the major 5'-tyrosyl DNA phosphodiesterase activity in vertebrate cells and is critical for cellular resistance to topoisomerase II-induced DNA damage. Zeng Z, et al. J Biol Chem, 2011 Jan 7. PMID 21030584, Free PMC Article
    4. A human 5'-tyrosyl DNA phosphodiesterase that repairs topoisomerase-mediated DNA damage. Cortes Ledesma F, et al. Nature, 2009 Oct 1. PMID 19794497
    5. Biochemical characterization of human tyrosyl-DNA phosphodiesterase 2 (TDP2/TTRAP): a Mg(2+)/Mn(2+)-dependent phosphodiesterase specific for the repair of topoisomerase cleavage complexes. Gao R, et al. J Biol Chem, 2012 Aug 31. PMID 22822062, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC124734

    Gene Ontology Provided by RGD

    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables 5'-tyrosyl-DNA phosphodiesterase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables 5'-tyrosyl-DNA phosphodiesterase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables magnesium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables magnesium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables manganese ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables manganese ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables manganese ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables nuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables single-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables tyrosyl-RNA phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables tyrosyl-RNA phosphodiesterase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in double-strand break repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neuron development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in PML body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in PML body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in PML body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in PML body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in aggresome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in aggresome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    tyrosyl-DNA phosphodiesterase 2
    Names
    5'-Tyr-DNA phosphodiesterase
    5'-tyrosyl-DNA phosphodiesterase
    TRAF and TNF receptor-associated protein
    Traf and Tnf receptor associated protein
    tyr-DNA phosphodiesterase 2
    NP_001030119.1
    XP_063132761.1
    XP_063132762.1

    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_001034947.1 → NP_001030119.1  tyrosyl-DNA phosphodiesterase 2

      See identical proteins and their annotated locations for NP_001030119.1

      Status: PROVISIONAL

      Source sequence(s)
      BC101920
      UniProtKB/Swiss-Prot
      Q3T1H5
      UniProtKB/TrEMBL
      A6KLF1, G3V9Q6
      Related
      ENSRNOP00000056326.2, ENSRNOT00000059570.5
      Conserved Domains (2) summary
      cd09080
      Location:120 → 362
      TDP2; Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains
      cl21463
      Location:39 → 70
      UBA_like_SF; UBA domain-like superfamily

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086035.1 Reference GRCr8

      Range
      40656969..40668362 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063276692.1 → XP_063132762.1  tyrosyl-DNA phosphodiesterase 2 isoform X2

    2. XM_063276691.1 → XP_063132761.1  tyrosyl-DNA phosphodiesterase 2 isoform X1

    RNA

    1. XR_005495319.2 RNA Sequence

    2. XR_005495318.2 RNA Sequence

    3. XR_010058920.1 RNA Sequence

    4. XR_010058919.1 RNA Sequence

    5. XR_010058918.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q3T1H5.1 GenPept UniProtKB/Swiss-Prot:Q3T1H5

    Gene LinkOut

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

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