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    TDP1 tyrosyl-DNA phosphodiesterase 1 [ Homo sapiens (human) ]

    Gene ID: 55775, updated on 5-Nov-2017
    Official Symbol
    TDP1provided by HGNC
    Official Full Name
    tyrosyl-DNA phosphodiesterase 1provided by HGNC
    Primary source
    HGNC:HGNC:18884
    See related
    Ensembl:ENSG00000042088 MIM:607198; Vega:OTTHUMG00000171016
    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
    Summary
    The protein encoded by this gene is involved in repairing stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3-prime phosphate of DNA. This protein may also remove glycolate from single-stranded DNA containing 3-prime phosphoglycolate, suggesting a role in repair of free-radical mediated DNA double-strand breaks. This gene is a member of the phospholipase D family and contains two PLD phosphodiesterase domains. Mutations in this gene are associated with the disease spinocerebellar ataxia with axonal neuropathy (SCAN1). [provided by RefSeq, Aug 2016]
    Expression
    Broad expression in testis (RPKM 7.3), lymph node (RPKM 4.5) and 24 other tissues See more
    Orthologs
    Location:
    14q32.11
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 14 NC_000014.9 (89954935..90044764)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (90421944..90511108)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene cysteine and histidine rich domain containing 2, pseudogene Neighboring gene EF-hand calcium binding domain 11 Neighboring gene RAB42, member RAS oncogene family, pseudogene 1 Neighboring gene potassium two pore domain channel subfamily K member 13 Neighboring gene glutaredoxin pseudogene 2 Neighboring gene proteasome 26S subunit, ATPase 1

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    • DNA Double-Strand Break Repair, organism-specific biosystem (from REACTOME)
      DNA Double-Strand Break Repair, organism-specific biosystemNumerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-s...
    • DNA Repair, organism-specific biosystem (from REACTOME)
      DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
    • Nonhomologous End-Joining (NHEJ), organism-specific biosystem (from REACTOME)
      Nonhomologous End-Joining (NHEJ), organism-specific biosystemThe nonhomologous end joining (NHEJ) pathway is initiated in response to the formation of DNA double-strand breaks (DSBs) induced by DNA-damaging agents, such as ionizing radiation. DNA DSBs are reco...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • FLJ11090, MGC104252

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    3'-tyrosyl-DNA phosphodiesterase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    double-strand break repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleic acid phosphodiester bond hydrolysis IEA
    Inferred from Electronic Annotation
    more info
     
    single strand break repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    single strand break repair IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    Preferred Names
    tyrosyl-DNA phosphodiesterase 1
    Names
    tyr-DNA phosphodiesterase 1
    NP_001008744.1
    NP_060789.2
    XP_005267904.1
    XP_005267905.1
    XP_006720260.1
    XP_006720261.1
    XP_006720262.1
    XP_011535244.1
    XP_011535245.1
    XP_011535246.1
    XP_016876928.1
    XP_016876929.1
    XP_016876930.1
    XP_016876931.1
    XP_016876932.1
    XP_016876933.1
    XP_016876934.1
    XP_016876935.1

    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_009164.1 RefSeqGene

      Range
      5001..93863
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001008744.1NP_001008744.1  tyrosyl-DNA phosphodiesterase 1 isoform a

      See identical proteins and their annotated locations for NP_001008744.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).
      Source sequence(s)
      AK001952, AK023514, AL137128, BC015474, BM661793, BU849335
      Consensus CDS
      CCDS9888.1
      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5, B3KN41
      Related
      ENSP00000377099.2, OTTHUMP00000244883, ENST00000393454.6, OTTHUMT00000411237
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    2. NM_001330205.1NP_001317134.1  tyrosyl-DNA phosphodiesterase 1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' and 3' UTRs, and lacks an alternate exon in the 3' coding region resulting in a frameshift and a novel 3' coding region, compared to variant 1. The encoded isoform (b) is shorter, and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AL137128, BM661793
      Consensus CDS
      CCDS81836.1
      UniProtKB/TrEMBL
      G3V2F4
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166550
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    3. NM_018319.3NP_060789.2  tyrosyl-DNA phosphodiesterase 1 isoform a

      See identical proteins and their annotated locations for NP_060789.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AK023514, AL137128, BC015474, BM661793, BU849335
      Consensus CDS
      CCDS9888.1
      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5, B3KN41
      Related
      ENSP00000337353.4, OTTHUMP00000244885, ENST00000335725.8, OTTHUMT00000411239
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p7 Primary Assembly

      Range
      89954935..90044764
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005267847.2XP_005267904.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

      See identical proteins and their annotated locations for XP_005267904.1

      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    2. XM_011536942.2XP_011535244.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

      See identical proteins and their annotated locations for XP_011535244.1

      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    3. XM_017021439.1XP_016876928.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    4. XM_017021440.1XP_016876929.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

      UniProtKB/TrEMBL
      G3V2F4
      Related
      ENSP00000450628.1, OTTHUMP00000244892, ENST00000555880.5, OTTHUMT00000411248
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166550
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    5. XM_011536944.1XP_011535246.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

      UniProtKB/TrEMBL
      G3V2F4
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166550
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    6. XM_017021444.1XP_016876933.1  tyrosyl-DNA phosphodiesterase 1 isoform X3

      UniProtKB/Swiss-Prot
      Q9NUW8
      Conserved Domains (3) summary
      cd09195
      Location:113306
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:26343
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
      cl15239
      Location:2691
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins
    7. XM_006720199.1XP_006720262.1  tyrosyl-DNA phosphodiesterase 1 isoform X4

      See identical proteins and their annotated locations for XP_006720262.1

      Conserved Domains (3) summary
      cd09195
      Location:87280
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:1317
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
      cl15239
      Location:165
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins
    8. XM_006720197.3XP_006720260.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

      See identical proteins and their annotated locations for XP_006720260.1

      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    9. XM_005267848.2XP_005267905.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

      See identical proteins and their annotated locations for XP_005267905.1

      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    10. XM_017021446.1XP_016876935.1  tyrosyl-DNA phosphodiesterase 1 isoform X4

      Conserved Domains (3) summary
      cd09195
      Location:87280
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:1317
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
      cl15239
      Location:165
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins
    11. XM_017021441.1XP_016876930.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166550
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    12. XM_017021443.1XP_016876932.1  tyrosyl-DNA phosphodiesterase 1 isoform X3

      UniProtKB/Swiss-Prot
      Q9NUW8
      Conserved Domains (3) summary
      cd09195
      Location:113306
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:26343
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
      cl15239
      Location:2691
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins
    13. XM_011536943.2XP_011535245.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

      See identical proteins and their annotated locations for XP_011535245.1

      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    14. XM_006720198.3XP_006720261.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

      See identical proteins and their annotated locations for XP_006720261.1

      UniProtKB/Swiss-Prot
      Q9NUW8
      UniProtKB/TrEMBL
      A0A024R6L5
      Conserved Domains (3) summary
      cd09193
      Location:162330
      PLDc_mTdp1_1; Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase
      cd09195
      Location:352545
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:166582
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
    15. XM_017021442.1XP_016876931.1  tyrosyl-DNA phosphodiesterase 1 isoform X3

      UniProtKB/Swiss-Prot
      Q9NUW8
      Conserved Domains (3) summary
      cd09195
      Location:113306
      PLDc_mTdp1_2; Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase
      pfam06087
      Location:26343
      Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
      cl15239
      Location:2691
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins
    16. XM_017021445.1XP_016876934.1  tyrosyl-DNA phosphodiesterase 1 isoform X5

    RNA

    1. XR_001750427.1 RNA Sequence

    2. XR_943492.2 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018925.2 Alternate CHM1_1.1

      Range
      90360149..90448932
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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