FB2025_05 , released December 11, 2025
Gene: Dmel\Aptx
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General Information
Symbol
Dmel\Aptx
Species
D. melanogaster
Name
aprataxin
Annotation Symbol
CG5316
Feature Type
protein_coding_gene
FlyBase ID
FBgn0038704
Gene Model Status
Current
Stock Availability
10 publicly available
Enzyme Name (EC)
adenosine-5'-diphospho-5'-[DNA] diphosphatase (3.6.1.71)
DNA-3'-diphospho-5'-guanosine diphosphatase (3.6.1.72)
Gene Summary
DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair and base excision repair. Resolves abortive DNA ligation intermediates formed either at base excision sites, or when DNA ligases attempt to repair non-ligatable breaks induced by reactive oxygen species. Catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined (By similarity). (UniProt, Q8MSG8)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
92A3-92A3
Sequence location
Recombination map
3-66
RefSeq locus
NT_033777 REGION:19403455..19406294
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 (12 terms)
Molecular Function (8 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (8 terms)
CV Term
Evidence
References
enables catalytic activity
inferred from electronic annotation with InterPro:IPR011146
(InterPro Project Members, 2004-)
enables damaged DNA binding
inferred from sequence or structural similarity with UniProtKB:Q7Z2E3
(Gene Ontology Curators, 2002-)
enables DNA 5'-adenosine monophosphate hydrolase activity
inferred from biological aspect of ancestor with PANTHER:PTN000281062
(GO Reference Genome Project, 2011-)
enables DNA-3'-diphospho-5'-guanosine diphosphatase activity
inferred from sequence or structural similarity with UniProtKB:O74859
(Gene Ontology Curators, 2002-)
enables double-stranded RNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000281062
(GO Reference Genome Project, 2011-)
enables mismatched DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000281062
(GO Reference Genome Project, 2011-)
enables single-strand break-containing DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000281062
(GO Reference Genome Project, 2011-)
enables single-stranded DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000281062
(GO Reference Genome Project, 2011-)
Biological Process (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in mRNA splicing, via spliceosome
inferred by curator from GO:0071011
(Herold et al., 2009)
involved_in single strand break repair
inferred from sequence or structural similarity with UniProtKB:Q7Z2E3-1
(Gene Ontology Curators, 2002-)
inferred from biological aspect of ancestor with PANTHER:PTN000281062
(GO Reference Genome Project, 2011-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
part_of precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN000281062
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
DNA-3'-diphospho-5'-guanosine diphosphatase activity
a 3'-end 2'-deoxyribonucleotide-3'-diphospho-5'-guanosine-DNA + H2O = a 3'-end 2'-deoxyribonucleotide 3'-phosphate-DNA + GMP + 2 H(+) (3.6.1.72)
RHEA 52140: DNA 5'-adenosine monophosphate hydrolase activity
(1) a 5'-end adenosine-5'-diphospho-5'-2'-deoxyribonucleoside-DNA + H2O = a 5'-end 5'-phospho-2'-deoxyribonucleoside-DNA + AMP + 2 H(+) (3.6.1.71)
(2) a 5'-end adenosine-5'-diphospho-5'-ribonucleoside- 2'-deoxyribonucleotide-DNA + H2O = a 5'-end 5'-phospho-ribonucleoside- 2'-deoxyribonucleotide-DNA + AMP + 2 H(+) (3.6.1.71)
Summaries
Gene Group (FlyBase)
UNCLASSIFIED ACID ANHYDRIDE HYDROLASES -
This group comprises acid anhydride hydrolases that do not classify under other groups in FlyBase.
Protein Function (UniProtKB)
DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair and base excision repair. Resolves abortive DNA ligation intermediates formed either at base excision sites, or when DNA ligases attempt to repair non-ligatable breaks induced by reactive oxygen species. Catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined (By similarity).
(UniProt, Q8MSG8)
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\Aptx 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 Q8MSG8)

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

Low-frequency RNA-Seq exon junction(s) not annotated.

Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.

Gene model reviewed during 5.49

Gene model includes transcripts encoding non-overlapping portions of the full CDS.

NOTE: This locus appears to be dicistronic in other Drosophila species. The longest protein isoform may be specific to D. melanogaster; in all other sequenced species there is a stop codon in a position corresponding to amino acid 191 (see, for example, Dsim\GD19289 and Dsec\GM26840). SNP data indicate that all Dmel strains are lacking this stop codon. The short 139-aa protein isoform annotated in Dmel is truncated relative this gene in other species, but it may serve a similar function. The 443-aa protein isoform corresponds to the second gene within the dicistronic loci of othe species.

Gene model reviewed during 6.10

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Aptx-RA
FBtr0083759
NM_169859
2610
139
Aptx-RB
FBtr0083760
NM_142548
2483
662
Aptx-RC
FBtr0083758
NM_169858
2376
662
Aptx-RE
FBtr0445726
NM_001260266
2553
443
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
Aptx-PA
FBpp0083173
16.0
139
10.53
NP_732422
AAF55667
Aptx-PB
FBpp0083174
76.5
662
9.97
Q8MSG8
NP_650805
AAF55666
Aptx-PC
FBpp0083172
76.5
662
9.97
Q8MSG8
NP_732421
AAN13800
Aptx-PE
FBpp0401601
51.2
443
10.21
NP_001247195
API64938
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

662 aa isoforms: Aptx-PB, Aptx-PC
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Domain

The HIT domain is required for enzymatic activity.

The C2H2-type zinc finger mediates DNA-binding.

(UniProt, Q8MSG8)
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\Aptx 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).

0.29

Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of precatalytic spliceosome
inferred from high throughput direct assay
(Herold et al., 2009)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Aptx 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
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 ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Aptx
Transgenic constructs containing regulatory region of Aptx
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 7 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal | female limited, with Scer\GAL4dome-PG14
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
fertile
Other Phenotypes
Allele
visible, with Scer\GAL4nub-AC-62
Phenotype manifest in
Allele
wing, with Scer\GAL4nub-AC-62
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) (5)
Hsap\APTX
10 of 14
Yes
Yes
Hsap\HINT1
1 of 14
No
No
1  
Hsap\HINT2
1 of 14
No
No
1  
Hsap\HINT3
1 of 14
No
No
Hsap\PNKP
1 of 14
No
No
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) (6)
Rnor\Aptx
10 of 14
Yes
Yes
Rnor\Hint1-ps1
1 of 14
No
No
Rnor\Hint1
1 of 14
No
No
Rnor\Hint2
1 of 14
No
No
Rnor\Hint3
1 of 14
No
No
Rnor\Pnkp
1 of 14
No
No
Mus musculus (laboratory mouse) (5)
Mmus\Aptx
9 of 14
Yes
Yes
Mmus\Hint1
1 of 14
No
No
Mmus\Hint2
1 of 14
No
No
Mmus\Hint3
1 of 14
No
No
Mmus\Pnkp
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (4)
Xtro\aptx
7 of 13
Yes
Yes
Xtro\hint1
1 of 13
No
No
Xtro\hint3
1 of 13
No
No
Xtro\pnkp
1 of 13
No
No
Danio rerio (Zebrafish) (6)
Drer\aptx
10 of 14
Yes
Yes
Drer\hint1
1 of 14
No
No
Drer\hint2
1 of 14
No
No
Drer\hint3
1 of 14
No
No
Drer\pnkp
1 of 14
No
No
Drer\si:dkey-187j14.4
1 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (3)
Cele\dcs-1
1 of 14
Yes
No
Cele\hint-1
1 of 14
Yes
No
Cele\hint-3
1 of 14
Yes
No
Anopheles gambiae (African malaria mosquito) (7)
Agam\AgaP_AGAP012563
9 of 12
Yes
Yes
Agam\AgaP_AGAP004084
8 of 12
No
Yes
Agam\AgaP_AGAP004307
8 of 12
No
Yes
Agam\AgaP_AGAP012174
2 of 12
No
No
Agam\AgaP_AGAP006353
1 of 12
No
No
Agam\AgaP_AGAP007577
1 of 12
No
No
Agam\AgaP_AGAP007702
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (5)
Atha\APTX
7 of 13
Yes
Yes
Atha\HINT 2
1 of 13
No
No
Atha\HINT3
1 of 13
No
No
Atha\HINT4
1 of 13
No
No
Atha\HIT3
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (2)
Scer\HNT3
8 of 13
Yes
Yes
Scer\HNT1
1 of 13
No
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\SPCC18.09c
6 of 12
Yes
Yes
Spom\SPCC1442.14c
1 of 12
No
No
Escherichia coli (enterobacterium) (1)
Ecol\hinT
1 of 11
Yes
No
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Aptx. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Gene Symbol
Score
Source
Compara
Domainoid
eggNOG
Homologene
Inparanoid
OMA
OrthoDB
OrthoFinder
OrthoInspector
orthoMCL
Panther
Phylome
SonicParanoid
Alignment
Drosophila melanogaster (Fruit fly) (4)
CG15362
3 of 13
CG34015
3 of 13
HINT1
1 of 13
PNKP
1 of 13
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 1 )
Allele
Disease
Evidence
References
AptxKK108374
model of  ataxia with oculomotor apraxia type 1
CEA
(Eidhof et al., 2023)
Potential Models Based on Orthology ( 1 )
Human Ortholog
Disease
Evidence
References
APTX; aprataxin
model of  ataxia with oculomotor apraxia type 1
IEA
(FlyBase, 2019-)
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?
APTX; aprataxin
10 of 14
606350
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
Interaction Browsers
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.
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)
3R
Recombination map
3-66
Cytogenetic map
92A3-92A3
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
92A3-92A3
Limits computationally determined from genome sequence between P{EP}EP650 and P{PZ}l(3)1058510585
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

3-66

(FlyBase, 2016)

3-68.0

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (10)
Genomic Clones (31)
cDNA Clones (96)
 

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
     
    Commercially Available Antibodies
     
    Cell Line Information
    Publicly Available Cell Lines
     
      Other Stable Cell Lines
       
        Other Comments
        Relationship to Other Genes
        Source for database merge of
        Additional comments
        Nomenclature History
        Source for database identify of

        Source for identity of: Aptx CG5316

        (Eidhof et al., 2023)
        Nomenclature comments
        Etymology

        The gene is named 'Aptx' based on the closest human ortholog.

        (Eidhof et al., 2023)
        Synonyms and Secondary IDs (3)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 49 )
        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
        UniProt/TrEMBL - Automatically annotated and unreviewed 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.
        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
        FlyMine - An integrated database for Drosophila genomics
        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.
        References (43)