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

Gene ID: 55775, updated on 8-Dec-2018

Summary

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
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

Genomic context

See TDP1 in Genome Data Viewer
Location:
14q32.11
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (89954923..90044768)
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

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11090, MGC104252

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-tyrosyl-DNA phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
3'-tyrosyl-DNA phosphodiesterase activity IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
tyrosyl-DNA phosphodiesterase 1
Names
tyr-DNA phosphodiesterase 1
NP_001008744.1
NP_001317134.1
NP_060789.2
XP_005267905.1
XP_006720260.1
XP_011535244.1
XP_011535246.1
XP_016876928.1
XP_016876929.1
XP_024305417.1
XP_024305418.1
XP_024305419.1
XP_024305420.1
XP_024305421.1
XP_024305422.1
XP_024305423.1
XP_024305424.1
XP_024305425.1
XP_024305426.1
XP_024305427.1

NCBI Reference Sequences (RefSeq)

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, ENST00000393454.6
    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, ENST00000335725.8
    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 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    89954923..90044768
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536942.3XP_011535244.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    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
  2. XM_024449655.1XP_024305423.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    Conserved Domains (1) summary
    pfam06087
    Location:166624
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  3. XM_024449650.1XP_024305418.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    Conserved Domains (1) summary
    pfam06087
    Location:166624
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  4. XM_017021439.2XP_016876928.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    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
  5. XM_011536944.2XP_011535246.1  tyrosyl-DNA phosphodiesterase 1 isoform X3

    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_024449649.1XP_024305417.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    Conserved Domains (1) summary
    pfam06087
    Location:166624
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  7. XM_017021440.2XP_016876929.1  tyrosyl-DNA phosphodiesterase 1 isoform X3

    UniProtKB/TrEMBL
    G3V2F4
    Related
    ENSP00000450628.1, ENST00000555880.5
    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
  8. XM_024449652.1XP_024305420.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    Conserved Domains (1) summary
    pfam06087
    Location:166624
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  9. XM_024449657.1XP_024305425.1  tyrosyl-DNA phosphodiesterase 1 isoform X4

    Conserved Domains (1) summary
    pfam06087
    Location:26343
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  10. XM_024449658.1XP_024305426.1  tyrosyl-DNA phosphodiesterase 1 isoform X4

    Conserved Domains (1) summary
    pfam06087
    Location:26343
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  11. XM_006720197.4XP_006720260.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    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
  12. XM_024449659.1XP_024305427.1  tyrosyl-DNA phosphodiesterase 1 isoform X5

    Conserved Domains (1) summary
    pfam06087
    Location:26317
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  13. XM_024449653.1XP_024305421.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    Conserved Domains (1) summary
    pfam06087
    Location:166624
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  14. XM_005267848.3XP_005267905.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    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
  15. XM_024449651.1XP_024305419.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    Conserved Domains (1) summary
    pfam06087
    Location:166624
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  16. XM_024449656.1XP_024305424.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    Conserved Domains (1) summary
    pfam06087
    Location:166624
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase
  17. XM_024449654.1XP_024305422.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    Conserved Domains (1) summary
    pfam06087
    Location:166624
    Tyr-DNA_phospho; Tyrosyl-DNA phosphodiesterase

RNA

  1. XR_943492.3 RNA Sequence

  2. XR_001750427.2 RNA Sequence

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