FB2026_02 , released June 18, 2026
Gene: Dmel\Tdp1
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General Information
Symbol
Dmel\Tdp1
Species
D. melanogaster
Name
Tyrosyl-DNA phosphodiesterase 1
Annotation Symbol
CG8825
Feature Type
protein_coding_gene
FlyBase ID
FBgn0260817
Gene Model Status
Current
Stock Availability
11 publicly available
Gene Summary
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) encodes a member of the phospholipase D superfamily. It is essential for the formation of epithelial polarity and nervous system development. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
All Summaries
Also Known As

gkt, glaikit, anon-23Db, c22

Key Links
Genomic Location
Cytogenetic map
23D3-23D4
Sequence location
Recombination map
2-8
RefSeq locus
NT_033779 REGION:3159950..3162399
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (5 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables 3'-tyrosyl-DNA phosphodiesterase activity
inferred from mutant phenotype
(Guo et al., 2014)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
enables 3'-tyrosyl-DNA phosphodiesterase activity
inferred from sequence or structural similarity with UniProtKB:P38319
(Gene Ontology Curators, 2002-)
enables 5'-tyrosyl-DNA phosphodiesterase activity
inferred from sequence or structural similarity with UniProtKB:P38319
(Gene Ontology Curators, 2002-)
enables double-stranded DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000275870
(GO Reference Genome Project, 2011-)
enables phosphoric diester hydrolase activity
inferred from electronic annotation with InterPro:IPR010347
(InterPro Project Members, 2004-)
enables single-stranded DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000275870
(GO Reference Genome Project, 2011-)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in central nervous system development
inferred from mutant phenotype
(Dunlop et al., 2004)
involved_in establishment or maintenance of epithelial cell apical/basal polarity
inferred from mutant phenotype
(Dunlop et al., 2004)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in DNA repair
inferred from electronic annotation with InterPro:IPR010347
(InterPro Project Members, 2004-)
inferred from sequence or structural similarity with UniProtKB:P38319
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000275870
(GO Reference Genome Project, 2011-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
located_in cytoplasm
inferred from experiment
(Dunlop et al., 2004)
located_in nucleus
inferred from sequence or structural similarity with UniProtKB:P38319
(Gene Ontology Curators, 2002-)
inferred from sequence or structural similarity with UniProtKB:Q9NUW8
(Gene Ontology Curators, 2002-)
inferred from electronic annotation with InterPro:IPR010347
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the tyrosyl-DNA phosphodiesterase family. (Q9VQM4)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) encodes a member of the phospholipase D superfamily. It is essential for the formation of epithelial polarity and nervous system development. [Date last reviewed: 2019-03-07]
Gene Group (FlyBase)
UNCLASSIFIED PHOSPHORIC DIESTER HYDROLASES -
This group comprises phosphoric diester hydrolases that do not classify under other groups in FlyBase.
Protein Function (UniProtKB)
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 (PubMed:25331878). 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. May have low 3'exonuclease activity and may be able to remove a single nucleoside from the 3'end of DNA and RNA molecules with 3'hydroxyl groups. Has no exonuclease activity towards DNA or RNA with a 3'phosphate (By similarity). Required for normal polarization of epidermal cells, correct subcellular location of the Crb complex to the apical lateral membrane, and for normal neuronal development during embryonic development (PubMed:15556867). Contributes to maintenance of epithelial cells in response to topoisomerase-1-mediated and oxidative DNA damage (PubMed:25331878). Required for precise axonal bifurcation in mushroom body neurons (PubMed:28465232). Required for maintenance of normal neuronal function (PubMed:25331878).
(UniProt, Q9VQM4)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Tdp1 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VQM4)

If you don't see a structure in the viewer, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Experimentally Determined Structures
Crossreferences
Comments on Gene Model

Gene model reviewed during 5.39

Gene model reviewed during 5.45

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Tdp1-RA
FBtr0077574
NM_078741
2221
580
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Tdp1-PA
FBpp0077263
64.2
580
7.90
Q9VQM4
NP_523465
AAF51141
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Tdp1 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

2.89

Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Tdp1 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 6 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Tdp1
Transgenic constructs containing regulatory region of Tdp1
Aberrations (Deficiencies and Duplications) ( 2 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (2)
Hsap\TDP1
14 of 14
Yes
Yes
Hsap\LOC107984974
1 of 14
No
Yes
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Source
Compara
Domainoid
eggNOG
Hieranoid
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (1)
Rnor\Tdp1
14 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Tdp1
13 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (3)
Xtro\tdp1
10 of 13
Yes
Yes
Xtro\kcnk12
1 of 13
No
Yes
Xtro\tyw3
1 of 13
No
Yes
Danio rerio (Zebrafish) (1)
Drer\tdp1
14 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\tdpo-1
13 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP010577
11 of 12
Yes
Yes
Agam\AgaP_AGAP010578
4 of 12
No
Yes
Agam\AgaP_AGAP010579
3 of 12
No
Yes
Arabidopsis thaliana (thale-cress) (2)
Atha\TDP1
13 of 13
Yes
Yes
Atha\AT5G07400
1 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\TDP1
11 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\tdp1
11 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Tdp1. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 1 )
Allele
Disease
Evidence
References
Tdp1KK100809
model of  spinocerebellar ataxia with axonal neuropathy 1
CEA
(Eidhof et al., 2023)
Potential Models Based on Orthology ( 1 )
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
Disease Associations of Human Orthologs (via DIOPT v9.1 and OMIM)
Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
Homo sapiens (Human)
Gene name
Score
OMIM
OMIM Phenotype
DO term
Complementation?
Transgene?
TDP1; tyrosyl-DNA phosphodiesterase 1
14 of 14
607198
Functional Complementation Data
Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
Interactions
Summary of Physical Interactions
Summary of Genetic Interactions
Interaction Browsers
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Linkouts
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
FlyBase
External Links
External Data
Linkouts
KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
Class of Gene
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map
2-8
Cytogenetic map
23D3-23D4
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
23D3-23D4
Limits computationally determined from genome sequence between P{lacW}Madk00237 and P{lacW}Pdswk10101; Left limit from molecular mapping relative to Mad (FBrf0080380) Right limit from molecular mapping relative to Mad (FBrf0100048)
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
23D-23D
(Wiersdorff et al., 1996)
Experimentally Determined Recombination Data
Location

2-8

(FlyBase, 2016)

2-7.4

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (11)
Genomic Clones (22)
cDNA Clones (41)
 

Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced
BDGP DGC clones
Other clones
Drosophila Genomics Resource Center cDNA clones

For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones
RNAi and Array Information
Linkouts
DRSC - Results frm RNAi screens
Antibody Information
Laboratory Generated Antibodies
 

polyclonal

(Guo et al., 2014)
Commercially Available Antibodies
 
Cell Line Information
Publicly Available Cell Lines
 
    Other Stable Cell Lines
     
      Other Comments

      gkt is essential for the formation of epithelial polarity and for neuronal development during embryogenesis.

      (Dunlop et al., 2004)
      Relationship to Other Genes
      Source for database merge of

      Source for merge of: gkt anon-23Db

      (Wisotzkey et al., 2003)
      Additional comments

      Source for identity of glaikit CG8826 was sequence comparison ( date:000414 ).

      (FlyBase, 1996-)
      Nomenclature History
      Source for database identify of

      Source for identity of: glaikit CG8826

      (FlyBase, 1996-)

      Source for identity of: Tdp1 gkt

      (FlyBoard ad hoc nomenclature committee, 2024.7.14)
      Nomenclature comments

      The original gene name "glaikit" (gkt) was changed to "Tyrosyl-DNA phosphodiesterase 1" (Tdp1) to reflect its homology to the human gene and eliminate its potentially offensive association with human mental disability.

      (FlyBoard ad hoc nomenclature committee, 2024.7.14)
      Etymology

      The word "glaikit" signifies thoughtless or stupid in the Scottish language.

      (Dunlop et al., 2000)
      Synonyms and Secondary IDs (12)
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      Study result (0)
      Result
      Result Type
      Title
      External Crossreferences and Linkouts ( 40 )
      Sequence Crossreferences
      NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
      GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
      GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
      RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
      UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
      UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
      Other crossreferences
      AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
      EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
      FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      References (49)