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

Gene ID: 55775, updated on 3-Apr-2024

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; AllianceGenome:HGNC:18884
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
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Genomic context

See TDP1 in Genome Data Viewer
Location:
14q32.11
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (89954968..90044764)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (84179088..84268965)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (90422271..90511108)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene EF-hand calcium binding domain 11 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:90359151-90359706 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:90377489-90378106 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:90378107-90378722 Neighboring gene Sharpr-MPRA regulatory region 15055 Neighboring gene uncharacterized LOC124903358 Neighboring gene RAB42, member RAS oncogene family, pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:90420803-90421303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90424329-90424837 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:90429220-90430419 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:90473008-90473175 Neighboring gene uncharacterized LOC124903406 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90527279-90527780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90527781-90528280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90555766-90556266 Neighboring gene potassium two pore domain channel subfamily K member 13 Neighboring gene glutaredoxin pseudogene 2

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ11090, MGC104252

Gene Ontology Provided by GOA

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 IDA
Inferred from Direct Assay
more info
PubMed 
enables double-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables exonuclease 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 
Process Evidence Code Pubs
involved_in DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in DNA repair IDA
Inferred from Direct Assay
more info
PubMed 
involved_in double-strand break repair IDA
Inferred from Direct Assay
more info
PubMed 
involved_in single strand break repair IDA
Inferred from Direct Assay
more info
PubMed 
involved_in single strand break repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in 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_016876929.1
XP_047287524.1
XP_047287525.1
XP_047287526.1
XP_047287528.1
XP_047287529.1
XP_047287530.1
XP_047287531.1
XP_047287532.1
XP_047287533.1
XP_047287534.1
XP_047287535.1
XP_054232334.1
XP_054232335.1
XP_054232336.1
XP_054232337.1
XP_054232338.1
XP_054232339.1
XP_054232340.1
XP_054232341.1
XP_054232342.1
XP_054232343.1
XP_054232344.1

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_009164.1 RefSeqGene

    Range
    5026..93863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001008744.2NP_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
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
    UniProtKB/TrEMBL
    B2RDI0
    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_001330205.2NP_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
    E7EPD8, 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_018319.4NP_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
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
    UniProtKB/TrEMBL
    B2RDI0
    Related
    ENSP00000337353.4, ENST00000335725.9
    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: 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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    89954968..90044764
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431570.1XP_047287526.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  2. XM_011536942.4XP_011535244.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    See identical proteins and their annotated locations for XP_011535244.1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
    UniProtKB/TrEMBL
    B2RDI0
    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_047431568.1XP_047287524.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  4. XM_047431576.1XP_047287532.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    UniProtKB/TrEMBL
    G3V2F4
  5. XM_047431569.1XP_047287525.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  6. XM_006720197.5XP_006720260.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    See identical proteins and their annotated locations for XP_006720260.1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
    UniProtKB/TrEMBL
    B2RDI0
    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
  7. XM_047431577.1XP_047287533.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    UniProtKB/TrEMBL
    G3V2F4
  8. XM_047431573.1XP_047287529.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  9. XM_005267848.4XP_005267905.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    See identical proteins and their annotated locations for XP_005267905.1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
    UniProtKB/TrEMBL
    B2RDI0
    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_047431572.1XP_047287528.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  11. XM_017021440.3XP_016876929.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    UniProtKB/TrEMBL
    E7EPD8, 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
  12. XM_047431579.1XP_047287535.1  tyrosyl-DNA phosphodiesterase 1 isoform X4

  13. XM_047431578.1XP_047287534.1  tyrosyl-DNA phosphodiesterase 1 isoform X3

  14. XM_047431574.1XP_047287530.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  15. XM_047431575.1XP_047287531.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8

RNA

  1. XR_007064032.1 RNA Sequence

  2. XR_007064034.1 RNA Sequence

  3. XR_007064035.1 RNA Sequence

  4. XR_007064033.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    84179088..84268965
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376362.1XP_054232337.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  2. XM_054376361.1XP_054232336.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  3. XM_054376360.1XP_054232335.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  4. XM_054376367.1XP_054232342.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    UniProtKB/TrEMBL
    G3V2F4
  5. XM_054376363.1XP_054232338.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  6. XM_054376359.1XP_054232334.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  7. XM_054376366.1XP_054232341.1  tyrosyl-DNA phosphodiesterase 1 isoform X2

    UniProtKB/TrEMBL
    G3V2F4
  8. XM_054376369.1XP_054232344.1  tyrosyl-DNA phosphodiesterase 1 isoform X4

  9. XM_054376368.1XP_054232343.1  tyrosyl-DNA phosphodiesterase 1 isoform X3

  10. XM_054376364.1XP_054232339.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8
  11. XM_054376365.1XP_054232340.1  tyrosyl-DNA phosphodiesterase 1 isoform X1

    UniProtKB/Swiss-Prot
    Q2HXX4, Q86TV8, Q96BK7, Q9NUW8, Q9NZM7, Q9NZM8

RNA

  1. XR_008488883.1 RNA Sequence