FB2025_02 , released April 17, 2025
Gene: Dmel\Atx2
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General Information
Symbol
Dmel\Atx2
Species
D. melanogaster
Name
Ataxin-2
Annotation Symbol
CG5166
Feature Type
FlyBase ID
FBgn0041188
Gene Model Status
Stock Availability
Gene Summary
Ataxin-2 (Atx2) encodes the ortholog of human gene ATXN2, which is implicated in spinocerebellar ataxia 2. It contributes to eye development, circadian behaviour, and microRNA function. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
Also Known As

dAtx2, l(3)06490, Atx-2, dSCA2, ATXN2

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
3-57
RefSeq locus
NT_033777 REGION:15408423..15417277
Sequence
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
Gene Ontology (GO) Annotations (21 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
inferred from physical interaction with FLYBASE:tyf; FB:FBgn0026083
enables RNA binding
inferred from direct assay
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables mRNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000304339
enables RNA binding
inferred from electronic annotation with InterPro:IPR045117, InterPro:IPR047575
Biological Process (15 terms)
Terms Based on Experimental Evidence (14 terms)
CV Term
Evidence
References
involved_in chaeta development
inferred from mutant phenotype
inferred from genetic interaction with FLYBASE:per; FB:FBgn0003068
inferred from genetic interaction with FLYBASE:tyf; FB:FBgn0026083
inferred from mutant phenotype
inferred from physical interaction with FLYBASE:tyf; FB:FBgn0026083
inferred from mutant phenotype
inferred from mutant phenotype
involved_in habituation
inferred from mutant phenotype
involved_in locomotor rhythm
inferred from mutant phenotype
involved_in long-term memory
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
NOT involved_in short-term memory
inferred from mutant phenotype
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000304339
Cellular Component (3 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
inferred from direct assay
located_in cytoplasm
inferred from direct assay
inferred from high throughput direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000304339
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the ataxin-2 family. (Q8SWR8)
Summaries
Gene Snapshot
Ataxin-2 (Atx2) encodes the ortholog of human gene ATXN2, which is implicated in spinocerebellar ataxia 2. It contributes to eye development, circadian behaviour, and microRNA function. [Date last reviewed: 2019-03-07]
Protein Function (UniProtKB)
RNA binding protein that regulates various processes including circadian behaviors, actin filament formation, eye development and oocyte formation (PubMed:12524342, PubMed:28388438). Forms a complex with tyf and pAbp which functions in adult circadian pacemaker neurons to sustain circadian rhythms likely by switching between activator and repressor modes of post-transcriptional regulation via interaction with Lsm12a or me31B (PubMed:28388438). Forms an activator complex (Atx2-tyf activator complex) via association with Lsm12a and activates the TYF-dependent translation of per to maintain 24 hour periodicity in circadian locomotor behaviors (PubMed:28388438). Forms a repressor complex (Atx2-Not1 repressor complex) via the me31B-dependent association with Not1 to promote Not1-dependent post-transcriptional gene silencing and support high-amplitude circadian rhythms in a per-independent manner (PubMed:28388438). Regulates actin filament formation, though it does not directly assemble with actin filaments (PubMed:12524342). Required for oocyte specification and oocyte positioning in the female germline (PubMed:12524342). Also required for normal eye development and bristle morphology (PubMed:12524342).
(UniProt, Q8SWR8)
Summary (Interactive Fly)

multi-functional protein that binds DEAD box helicases of the Me31B family that associated with Argonaute and microRNA function - required for microRNA function and synapse-specific long-term olfactory habituation - assembles with polyribosomes and poly(A)-binding protein, a key regulator of mRNA translation

Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Atx2 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 Q8SWR8)

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 5.53

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0083099
4533
1084
FBtr0083100
4999
1023
FBtr0344377
4935
1023
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
FBpp0082555
117.6
1084
9.25
FBpp0082556
111.4
1023
8.15
Polypeptides with Identical Sequences

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

1023 aa isoforms: Atx2-PC, Atx2-PD
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Homodimer (PubMed:28388438). In the circadian pacemaker neurons, core component of the Atx2-tyf activator complex composed of at least Atx2, tyf, pAbp, Lsm12a (PubMed:28388438). In the circadian pacemaker neurons, also a core component of the Atx2-Not1 repressor complex composed of at least Atx2, tyf, pAbp, me31B (PubMed:28388438). Interacts (via PAM2 motif) with pAbp (PubMed:28388438). Interacts (via N-terminus) with tyf independently of pAbp (PubMed:28388438). Forms a subcomplex composed of Atx2 and pAbP which can associate with the 5' cap of pre-mRNAs independently of tyf, Lsm12a or me31B (PubMed:28388438). Interacts with Lsm12a and me31B (PubMed:28388438).

(UniProt, Q8SWR8)
Domain

The PAM2 motif, and therefore interaction with pAbp, is essential for binding to the 5' cap of pre-mRNAs.

(UniProt, Q8SWR8)
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\Atx2 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).

-0.58

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
organism

Comment: maternally deposited

RT-PCR
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

Two isoforms of Atx2 are differentially expressed. Atx2-RB is expressed at a low level throughout development. Levels of Atx2 increase about 8 times from the third instar larval to adult stages.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
western blot
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

An antibody directed against the N-terminal part of Atx2-PB detects protein at all stages confirming that the upstream ATG is used. Levels are significantly higher in embryos and first instar larvae than in second instar larvae, third instar larvae, pupae, and adults. An antibody that detects both forms detects similar levels at all stages. Atx2 protein levels are higher in extracts from ovaries than in imaginal disc, CNS, fat body, or testis extracts.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
located_in cytoplasm
inferred from direct assay
inferred from high throughput direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Atx2 in JBrowse
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 16 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 32 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Atx2
Transgenic constructs containing regulatory region of Atx2
Aberrations (Deficiencies and Duplications) ( 4 )
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
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
adult thorax & chaeta, with Atx2UAS.cSa
adult thorax & chaeta, with Atx2X1
nurse cell & actin filament | germ-line clone
nurse cell & nucleus | germ-line clone
Orthologs
Human Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Homo sapiens (Human) (2)
10 of 14
Yes
Yes
6 of 14
No
Yes
12  
Model Organism Orthologs (via DIOPT v9.1)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
Rattus norvegicus (Norway rat) (2)
10 of 14
Yes
Yes
6 of 14
No
Yes
Mus musculus (laboratory mouse) (2)
10 of 14
Yes
Yes
7 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (3)
6 of 13
Yes
Yes
5 of 13
No
Yes
1 of 13
No
Yes
Danio rerio (Zebrafish) (2)
10 of 14
Yes
Yes
7 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
7 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
9 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (4)
6 of 13
Yes
Yes
6 of 13
Yes
Yes
1 of 13
No
Yes
1 of 13
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
5 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
4 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Atx2. Refer to their site for version information.
Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 7 )
Potential Models Based on Orthology ( 2 )
Human Ortholog
Disease
Evidence
References
Modifiers Based on Experimental Evidence ( 15 )
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.
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

Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
RNA-protein
Physical Interaction
Assay
References
Summary of Genetic Interactions
Interaction Browsers

Please look at the allele data for full details of the genetic interactions
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
External Data
Subunit Structure (UniProtKB)
Homodimer (PubMed:28388438). In the circadian pacemaker neurons, core component of the Atx2-tyf activator complex composed of at least Atx2, tyf, pAbp, Lsm12a (PubMed:28388438). In the circadian pacemaker neurons, also a core component of the Atx2-Not1 repressor complex composed of at least Atx2, tyf, pAbp, me31B (PubMed:28388438). Interacts (via PAM2 motif) with pAbp (PubMed:28388438). Interacts (via N-terminus) with tyf independently of pAbp (PubMed:28388438). Forms a subcomplex composed of Atx2 and pAbP which can associate with the 5' cap of pre-mRNAs independently of tyf, Lsm12a or me31B (PubMed:28388438). Interacts with Lsm12a and me31B (PubMed:28388438).
(UniProt, Q8SWR8 )
Linkouts
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
MIST (genetic) - An integrated Molecular Interaction Database
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)
3R
Recombination map
3-57
Cytogenetic map
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
88F4-88F4
Limits computationally determined from genome sequence between P{lacW}MRG15j6A3 and P{PZ}l(3)0653606536
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
88F-89A1
(determined by in situ hybridisation)
88F7-88F8
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (13)
Genomic Clones (11)
 

Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

cDNA Clones (59)
 

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)
    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

        S2 cells treated with dsRNA generated against this gene show reduced phagocytosis of Candida albicans compared to untreated cells.

        RNAi generated by PCR using primers directed to this gene causes a cell growth and viability phenotype when assayed in Kc167 and S2R+ cells.

        Area matching Drosophila EST AI062939.

        Relationship to Other Genes
        Source for database merge of

        Source for merge of: Atx2 l(3)06490 BEST:GH27029

        Source for merge of: Atx2 CG5166

        Source for merge of: Atx2 anon-WO0118547.351 anon-WO0140519.1

        Source for merge of: Atx2 anon- EST:fe2E1

        Additional comments

        Source for merge of Atx2 CG5166 was a shared cDNA ( date:030206 ).

        Source for merge of Atx2 anon-WO0118547.351 anon-WO0140519.1 was sequence comparison ( date:051113 ).

        Source for merge of Atx2 anon- EST:fe2E1 was sequence comparison ( date:030620 ).

        Nomenclature History
        Source for database identify of
        Nomenclature comments
        Etymology
        Synonyms and Secondary IDs (30)
        Reported As
        Symbol Synonym
        BEST:GH27029
        anon-EST:fe2E1
        anon-WO0118547.351
        anon-WO0140519.1
        Secondary FlyBase IDs
        • FBgn0010892
        • FBgn0025221
        • FBgn0038338
        • FBgn0044786
        • FBgn0062074
        • FBgn0063367
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        Study result (0)
        Result
        Result Type
        Title
        External Crossreferences and Linkouts ( 72 )
        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 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.
        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
        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)
        Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        MIST (genetic) - An integrated Molecular Interaction Database
        MIST (protein-protein) - An integrated Molecular Interaction Database
        References (159)