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    Tdp1 tyrosyl-DNA phosphodiesterase 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 314380, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Tdp1provided by RGD
    Official Full Name
    tyrosyl-DNA phosphodiesterase 1provided by RGD
    Primary source
    RGD:1309618
    See related
    EnsemblRapid:ENSRNOG00000003831 AllianceGenome:RGD:1309618
    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
    Summary
    Predicted to enable 3'-tyrosyl-DNA phosphodiesterase activity; double-stranded DNA binding activity; and single-stranded DNA binding activity. Predicted to be involved in double-strand break repair. Predicted to act upstream of or within single strand break repair. Predicted to be located in cytoplasm; nucleoplasm; and plasma membrane. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in spinocerebellar ataxia with axonal neuropathy 1. Orthologous to human TDP1 (tyrosyl-DNA phosphodiesterase 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 34.1), Testes (RPKM 26.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tdp1 in Genome Data Viewer
    Location:
    6q32
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (124892821..124960646)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (119163192..119231029)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (123895860..123963688)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108351290 Neighboring gene EF-hand calcium binding domain 11 Neighboring gene uncharacterized LOC120103598 Neighboring gene potassium two pore domain channel subfamily K member 13 Neighboring gene uncharacterized LOC120103599 Neighboring gene malate dehydrogenase 1, pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. TDP1 facilitates chromosomal single-strand break repair in neurons and is neuroprotective in vivo. Katyal S, et al. EMBO J, 2007 Nov 14. PMID 17914460, Free PMC Article
    2. TDP1 facilitates repair of ionizing radiation-induced DNA single-strand breaks. El-Khamisy SF, et al. DNA Repair (Amst), 2007 Oct 1. PMID 17600775
    3. Novel high-throughput electrochemiluminescent assay for identification of human tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors and characterization of furamidine (NSC 305831) as an inhibitor of Tdp1. Antony S, et al. Nucleic Acids Res, 2007. PMID 17576665, Free PMC Article
    4. Increased expression and activity of repair genes TDP1 and XPF in non-small cell lung cancer. Liu C, et al. Lung Cancer, 2007 Mar. PMID 17118488, Free PMC Article
    5. Substrate specificity of tyrosyl-DNA phosphodiesterase I (Tdp1). Raymond AC, et al. J Biol Chem, 2005 Jun 10. PMID 15811850

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC112732

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 3'-tyrosyl-DNA phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 3'-tyrosyl-DNA phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables 3'-tyrosyl-DNA phosphodiesterase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables 3'-tyrosyl-DNA phosphodiesterase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoric diester hydrolase 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
    		  
    Process Evidence Code Pubs
    involved_in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in biological_process ND
    No biological Data available
    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 single strand break repair IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within single strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in single strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    NOT located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    tyrosyl-DNA phosphodiesterase 1
    Names
    tyr-DNA phosphodiesterase 1
    NP_001026827.1
    XP_006240494.1
    XP_038968275.1
    XP_038968277.1

    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_001031657.1 → NP_001026827.1  tyrosyl-DNA phosphodiesterase 1

      See identical proteins and their annotated locations for NP_001026827.1

      Status: PROVISIONAL

      Source sequence(s)
      BC098739
      UniProtKB/Swiss-Prot
      Q4G056
      UniProtKB/TrEMBL
      A0A8I6AVZ5, A6JEG4
      Related
      ENSRNOP00000110852.1, ENSRNOT00000157506.1
      Conserved Domains (1) summary
      pfam06087
      Location:167 → 580
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase

    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_086024.1 Reference GRCr8

      Range
      124892821..124960646
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039112347.2 → XP_038968275.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AVZ5
      Related
      ENSRNOP00000093319.2, ENSRNOT00000115515.2
      Conserved Domains (1) summary
      pfam06087
      Location:172 → 585
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase

    2. XM_006240432.5 → XP_006240494.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

      UniProtKB/TrEMBL
      A0A0H2UHC3, A0A8I6AFL5
      Related
      ENSRNOP00000005167.6, ENSRNOT00000005167.8
      Conserved Domains (3) summary
      cd09193
      Location:179 → 347
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:369 → 562
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:183 → 599
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase

    3. XM_039112349.2 → XP_038968277.1  tyrosyl-DNA phosphodiesterase 1 isoform X3

      Conserved Domains (1) summary
      pfam06087
      Location:1 → 314
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4G056.1 GenPept UniProtKB/Swiss-Prot:Q4G056

    Gene LinkOut

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