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Aliases for TDP1 Gene

Aliases for TDP1 Gene

  • Tyrosyl-DNA Phosphodiesterase 1 2 3 3 5
  • Tyr-DNA Phosphodiesterase 1 3 4
  • EC 3.1.4.- 4

External Ids for TDP1 Gene

Previous GeneCards Identifiers for TDP1 Gene

  • GC14P087927
  • GC14P084237
  • GC14P088411
  • GC14P088412
  • GC14P089492
  • GC14P090422
  • GC14P070596

Summaries for TDP1 Gene

Entrez Gene Summary for TDP1 Gene

  • 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]

GeneCards Summary for TDP1 Gene

TDP1 (Tyrosyl-DNA Phosphodiesterase 1) is a Protein Coding gene. Diseases associated with TDP1 include Spinocerebellar Ataxia, Autosomal Recessive, With Axonal Neuropathy and Spinocerebellar Ataxia Type 1 With Axonal Neuropathy. Among its related pathways are DNA Double-Strand Break Repair and DNA Double Strand Break Response. Gene Ontology (GO) annotations related to this gene include double-stranded DNA binding and phosphoric diester hydrolase activity.

UniProtKB/Swiss-Prot for TDP1 Gene

  • DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3-phosphodiester bond, giving rise to DNA with a free 3 phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3-phosphoglycolates on protruding 3 ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3exonuclease activity and can remove a single nucleoside from the 3end of DNA and RNA molecules with 3hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3phosphate.

Gene Wiki entry for TDP1 Gene

Additional gene information for TDP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TDP1 Gene

Genomics for TDP1 Gene

GeneHancer (GH) Regulatory Elements for TDP1 Gene

Promoters and enhancers for TDP1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J089953 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 662 +1.0 1005 4.7 HDGF PKNOX1 FOXA2 MLX ARID4B NEUROD1 SIN3A DMAP1 ZNF2 YY1 TDP1 EFCAB11 ENSG00000259053 NRDE2 KCNK13 GC14M092412
GH14J089613 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.9 -337.3 -337338 8.8 PKNOX1 FOXA2 ARNT ARID4B SIN3A ZNF48 YY1 ETS1 GLIS2 ZNF143 FOXN3 LOC105370617 ENSG00000252655 TDP1 GC14P089623 RN7SKP107 GC14P089586 ENSG00000259053
GH14J089414 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.7 -537.8 -537815 4.7 HDGF PKNOX1 FOXA2 SMAD1 ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF207 FOXN3 FOXN3-AS1 NRDE2 ZC3H14 ENSG00000252655 RPL21P11 TDP1 LOC105370614 ENSG00000258380 ENSG00000259053
GH14J089909 Enhancer 1.4 FANTOM5 Ensembl ENCODE 7.6 -43.3 -43267 4.1 PKNOX1 FOXA2 ZNF2 ZNF213 ATF7 FOS NFKBIZ RXRA TSHZ1 REST NRDE2 RPL21P11 TDP1 EFCAB11 FOXN3 KCNK13 RAB42P1 ENSG00000259053
GH14J090060 Promoter/Enhancer 1.4 Ensembl ENCODE 4.8 +105.6 105608 0.3 SIN3A ZNF2 ZBTB7B YY1 GLIS2 KLF13 SP3 REST ZNF610 GMEB1 KCNK13 TDP1 PIR51411
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around TDP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TDP1 gene promoter:
  • Nkx2-5
  • MyoD
  • CUTL1
  • HSF1 (long)
  • AML1a
  • HSF1short
  • CBF-C
  • CBF-A
  • CBF(2)

Genomic Locations for TDP1 Gene

Genomic Locations for TDP1 Gene
chr14:89,954,935-90,044,768
(GRCh38/hg38)
Size:
89,834 bases
Orientation:
Plus strand
chr14:90,421,283-90,511,108
(GRCh37/hg19)
Size:
89,826 bases
Orientation:
Plus strand

Genomic View for TDP1 Gene

Genes around TDP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TDP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TDP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TDP1 Gene

Proteins for TDP1 Gene

  • Protein details for TDP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUW8-TYDP1_HUMAN
    Recommended name:
    Tyrosyl-DNA phosphodiesterase 1
    Protein Accession:
    Q9NUW8
    Secondary Accessions:
    • Q2HXX4
    • Q86TV8
    • Q96BK7
    • Q9NZM7
    • Q9NZM8

    Protein attributes for TDP1 Gene

    Size:
    608 amino acids
    Molecular mass:
    68420 Da
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for TDP1 Gene

    Alternative splice isoforms for TDP1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TDP1 Gene

Post-translational modifications for TDP1 Gene

  • Phosphorylated on serine and/or threonine residues, but not on tyrosine residues.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TDP1 Gene

Domains & Families for TDP1 Gene

Gene Families for TDP1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for TDP1 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TDP1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NUW8

UniProtKB/Swiss-Prot:

TYDP1_HUMAN :
  • Belongs to the tyrosyl-DNA phosphodiesterase family.
Family:
  • Belongs to the tyrosyl-DNA phosphodiesterase family.
genes like me logo Genes that share domains with TDP1: view

Function for TDP1 Gene

Molecular function for TDP1 Gene

UniProtKB/Swiss-Prot Function:
DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3-phosphodiester bond, giving rise to DNA with a free 3 phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomerase I active site tyrosine residue. Hydrolyzes 3-phosphoglycolates on protruding 3 ends on DNA double-strand breaks due to DNA damage by radiation and free radicals. Acts on blunt-ended double-strand DNA breaks and on single-stranded DNA. Has low 3exonuclease activity and can remove a single nucleoside from the 3end of DNA and RNA molecules with 3hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3phosphate.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.08 uM for 14-mer single-stranded oligo with a 3- phosphotyrosine {ECO:0000269 PubMed:22822062}; Note=kcat is 7 sec(-1) with single-stranded 5-tyrosyl DNA as substrate.;

Enzyme Numbers (IUBMB) for TDP1 Gene

Phenotypes From GWAS Catalog for TDP1 Gene

Gene Ontology (GO) - Molecular Function for TDP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003690 double-stranded DNA binding IDA 15811850
GO:0003697 single-stranded DNA binding IDA 15811850
GO:0004518 nuclease activity IEA --
GO:0004527 exonuclease activity IEA --
GO:0005515 protein binding IPI 15744309
genes like me logo Genes that share ontologies with TDP1: view
genes like me logo Genes that share phenotypes with TDP1: view

Human Phenotype Ontology for TDP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for TDP1

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for TDP1 Gene

Localization for TDP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TDP1 Gene

Nucleus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TDP1 gene
Compartment Confidence
nucleus 5
plasma membrane 4
mitochondrion 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleus (3)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TDP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA --
GO:0005737 cytoplasm IDA,IEA 17948061
GO:0005886 plasma membrane IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with TDP1: view

Pathways & Interactions for TDP1 Gene

genes like me logo Genes that share pathways with TDP1: view

Pathways by source for TDP1 Gene

1 Cell Signaling Technology pathway for TDP1 Gene

SIGNOR curated interactions for TDP1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for TDP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000012 single strand break repair IMP 17600775
GO:0006281 DNA repair IEA,IDA 17948061
GO:0006302 double-strand break repair IDA 12023295
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
genes like me logo Genes that share ontologies with TDP1: view

Drugs & Compounds for TDP1 Gene

(2) Drugs for TDP1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(5) Additional Compounds for TDP1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with TDP1: view

Transcripts for TDP1 Gene

Unigene Clusters for TDP1 Gene

Tyrosyl-DNA phosphodiesterase 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TDP1 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19 ^
SP1: - - - - - - - -
SP2: - - -
SP3: - - - - - - - -
SP4: - - - - - - - - -
SP5: - - - - -
SP6: -
SP7: - - - - -
SP8: - - -
SP9: -
SP10:

ExUns: 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b
SP1: -
SP2: - -
SP3: - -
SP4: - -
SP5: - -
SP6: -
SP7:
SP8:
SP9:
SP10:

Relevant External Links for TDP1 Gene

GeneLoc Exon Structure for
TDP1
ECgene alternative splicing isoforms for
TDP1

Expression for TDP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TDP1 Gene

Protein differential expression in normal tissues from HIPED for TDP1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (39.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TDP1 Gene



Protein tissue co-expression partners for TDP1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TDP1 Gene:

TDP1

SOURCE GeneReport for Unigene cluster for TDP1 Gene:

Hs.209945

mRNA Expression by UniProt/SwissProt for TDP1 Gene:

Q9NUW8-TYDP1_HUMAN
Tissue specificity: Ubiquitously expressed. Similar expression throughout the central nervous system (whole brain, amygdala, caudate nucleus, cerebellum, cerebral cortex, frontal lobe, hippocampus, medulla oblongata, occipital lobe, putamen, substantia nigra, temporal lobe, thalamus, nucleus accumbens and spinal cord) and increased expression in testis and thymus.

Evidence on tissue expression from TISSUES for TDP1 Gene

  • Pancreas(4.1)
  • Nervous system(2.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TDP1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • head
Limb:
  • foot
  • hand
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with TDP1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for TDP1 Gene

Orthologs for TDP1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TDP1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TDP1 34 33
  • 99.34 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TDP1 34 33
  • 87.55 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TDP1 34 33
  • 84.07 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tdp1 33
  • 82.24 (n)
mouse
(Mus musculus)
Mammalia Tdp1 16 34 33
  • 81.25 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TDP1 34
  • 75 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TDP1 34
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves TDP1 34 33
  • 68.94 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TDP1 34
  • 64 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tdp1 33
  • 66.44 (n)
Str.15945 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.16878 33
zebrafish
(Danio rerio)
Actinopterygii tdp1 34 33
  • 61.71 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta gkt 34 33
  • 48.05 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010577 33
  • 47.97 (n)
worm
(Caenorhabditis elegans)
Secernentea F52C12.1 34 35 33
  • 46.93 (n)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TDP1 36
thale cress
(Arabidopsis thaliana)
eudicotyledons TDP1 33
  • 48.85 (n)
rice
(Oryza sativa)
Liliopsida Os07g0530100 33
  • 47.96 (n)
Os.9987 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
OneToOne
Cin.1071 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.1071 33
Species where no ortholog for TDP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TDP1 Gene

ENSEMBL:
Gene Tree for TDP1 (if available)
TreeFam:
Gene Tree for TDP1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TDP1: view image

Paralogs for TDP1 Gene

No data available for Paralogs for TDP1 Gene

Variants for TDP1 Gene

Sequence variations from dbSNP and Humsavar for TDP1 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs10151377 likely-benign, Autosomal recessive cerebellar ataxia 89,985,186(+) T/C coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs119467003 pathogenic, Spinocerebellar ataxia autosomal recessive with axonal neuropathy, Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy (SCAN1) [MIM:607250] 89,993,420(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs141725364 uncertain-significance, Autosomal recessive cerebellar ataxia, not specified 89,989,741(+) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs144746398 uncertain-significance, Autosomal recessive cerebellar ataxia 89,989,742(+) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs17126522 likely-benign, Autosomal recessive cerebellar ataxia 89,985,156(+) A/G coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for TDP1 Gene

Variant ID Type Subtype PubMed ID
nsv832854 CNV gain 17160897
nsv832853 CNV gain 17160897
nsv521779 CNV loss 19592680
nsv1392 CNV deletion 18451855
nsv1045864 CNV loss 25217958
esv3635305 CNV loss 21293372

Variation tolerance for TDP1 Gene

Residual Variation Intolerance Score: 47.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.27; 40.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TDP1 Gene

Human Gene Mutation Database (HGMD)
TDP1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TDP1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TDP1 Gene

Disorders for TDP1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for TDP1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search TDP1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

TYDP1_HUMAN
  • Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy (SCAN1) [MIM:607250]: Spinocerebellar ataxia is a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAN1 is an autosomal recessive cerebellar ataxia (ARCA) associated with peripheral axonal motor and sensory neuropathy, distal muscular atrophy, pes cavus and steppage gait as seen in Charcot-Marie-Tooth neuropathy. All affected individuals have normal intelligence. {ECO:0000269 PubMed:12244316, ECO:0000269 PubMed:15647511, ECO:0000269 PubMed:15920477, ECO:0000269 PubMed:16141202, ECO:0000269 PubMed:17948061}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TDP1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TDP1: view

No data available for Genatlas for TDP1 Gene

Publications for TDP1 Gene

  1. The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1. (PMID: 11839309) Davies DR … Hol WG (Structure (London, England : 1993) 2002) 2 3 4 22 58
  2. Irinotecan pharmacogenetics: influence of pharmacodynamic genes. (PMID: 18347181) Hoskins JM … Baiget M (Clinical cancer research : an official journal of the American Association for Cancer Research 2008) 3 22 44 58
  3. Deficiency in 3'-phosphoglycolate processing in human cells with a hereditary mutation in tyrosyl-DNA phosphodiesterase (TDP1). (PMID: 15647511) Zhou T … Povirk LF (Nucleic acids research 2005) 3 4 22 58
  4. Substrate specificity of tyrosyl-DNA phosphodiesterase I (Tdp1). (PMID: 15811850) Raymond AC … Burgin AB (The Journal of biological chemistry 2005) 3 4 22 58
  5. SCAN1 mutant Tdp1 accumulates the enzyme--DNA intermediate and causes camptothecin hypersensitivity. (PMID: 15920477) Interthal H … Champoux JJ (The EMBO journal 2005) 3 4 22 58

Products for TDP1 Gene

Sources for TDP1 Gene

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