FlyBase Gene Report: Dmel\AGO3

General Information

Symbol

Dmel\AGO3

Species

D. melanogaster

Name

Argonaute 3

Annotation Symbol

CG40300

Feature Type

protein_coding_gene

FlyBase ID

FBgn0250816

Gene Model Status

Current

Stock Availability

6 publicly available

Gene Summary

Argonaute 3 (AGO3) encodes a germline-specific Argonaute/Piwi family protein, which interacts with Piwi-interacting RNAs (piRNAs) to form effector complexes. It exhibits piRNA-guided RNA cleavage activity required for both piRNA amplification and transposon silencing, thereby securing germline development. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

Ago-3, BEST:LD15785

Key Links

Genomic Location

Cytogenetic map

80F9-80F9

Sequence location

3L:23,554,593..23,689,640 [+]

Recombination map

3-47

RefSeq locus

NT_037436 REGION:23554593..23689640

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse

Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

Gene Ontology (GO) Annotations (16 terms)

Molecular Function (5 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

enables piRNA binding

inferred from direct assay

(Webster et al., 2015, Huang et al., 2014, Nagao et al., 2010, Brennecke et al., 2007)

enables RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism

inferred from direct assay

(Gunawardane et al., 2007)

enables RNA endonuclease activity

inferred from direct assay

(Huang et al., 2014)

Terms Based on Predictions or Assertions (5 terms)

CV Term

Evidence

References

enables nucleic acid binding

inferred from electronic annotation with InterPro:IPR003165, InterPro:IPR036397

(InterPro Project Members, 2004-)

enables piRNA binding

inferred from biological aspect of ancestor with PANTHER:PTN007716312

(GO Reference Genome Project, 2011-)

enables RNA binding

inferred from electronic annotation with InterPro:IPR003100

(InterPro Project Members, 2004-)

enables RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism

non-traceable author statement

(Chen et al., 2025)

enables RNA endonuclease activity

inferred from sequence or structural similarity with UniProtKB:A8D8P8

(Gene Ontology Curators, 2002-)

inferred from biological aspect of ancestor with PANTHER:PTN008584027

(GO Reference Genome Project, 2011-)

Biological Process (6 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in piRNA-mediated gene silencing by mRNA destabilization

inferred from mutant phenotype

(Rouget et al., 2010)

involved_in secondary piRNA processing

inferred from direct assay

(Gunawardane et al., 2007)

inferred from physical interaction with FLYBASE:krimp; FB:FBgn0034098,FLYBASE:AGO3; FB:FBgn0250816

(Huang et al., 2021)

inferred from genetic interaction with FLYBASE:aub; FB:FBgn0000146

(Vrettos et al., 2021)

inferred from mutant phenotype

(Huang et al., 2014)

involved_in transposable element silencing by piRNA-mediated mRNA destabilization

inferred from mutant phenotype

(Huang et al., 2014)

Terms Based on Predictions or Assertions (4 terms)

CV Term

Evidence

References

involved_in piRNA processing

inferred from biological aspect of ancestor with PANTHER:PTN002339693

(GO Reference Genome Project, 2011-)

involved_in piRNA-mediated gene silencing by mRNA destabilization

non-traceable author statement

(Chen et al., 2025)

involved_in regulatory ncRNA-mediated gene silencing

inferred from biological aspect of ancestor with PANTHER:PTN001875625

(GO Reference Genome Project, 2011-)

involved_in spermatogenesis

inferred from biological aspect of ancestor with PANTHER:PTN002339693

(GO Reference Genome Project, 2011-)

Cellular Component (5 terms)

Terms Based on Experimental Evidence (4 terms)

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Gunawardane et al., 2007)

located_in cytosol

inferred from direct assay

(Tindell et al., 2020)

is_active_in extrinsic component of mitochondrial outer membrane

inferred from direct assay

(Huang et al., 2014)

is_active_in P granule

inferred from direct assay

(Lim et al., 2022, Vrettos et al., 2021, Munafò et al., 2019, Huang et al., 2014, Klattenhoff et al., 2009, Lim et al., 2009, Brennecke et al., 2007)

located_in P granule

inferred from direct assay

(Tindell et al., 2020, Ge et al., 2019, Webster et al., 2015, Liu et al., 2011, Nagao et al., 2010, Patil and Kai, 2010)

inferred from direct assay

(Nagao et al., 2011)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

is_active_in nucleus

inferred from biological aspect of ancestor with PANTHER:PTN001875625

(GO Reference Genome Project, 2011-)

is_active_in P granule

inferred from biological aspect of ancestor with PANTHER:PTN007716312

(GO Reference Genome Project, 2011-)

Gene Group (FlyBase)

ARGONAUTE ENDORIBONUCLEASES

Protein Family (UniProt)

Belongs to the argonaute family. Piwi subfamily. (Q7PLK0)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

Gene Group (FlyBase)

ARGONAUTE ENDORIBONUCLEASES -: Argonaute (AGO) proteins play an important role in small-RNA-mediated (miRNA, siRNA and piRNA) gene-silencing events and form the core constituent of the RNA-induced silencing complex (RISC). The PIWI domain of AGO proteins resembles RNase-H and accounts for their endonuclease activity that cleaves target mRNA complementary to the bound small RNA. (Adapted from PMID: 29447113).

Protein Function (UniProtKB)

Component of the perinuclear meiotic nuage, a germline-specific subcellular membraneless ribonucleoprotein compartment involved in production of transposable element-repressing Piwi-interacting RNA (piRNA)-induced silencing complexes (piRISCs), which are essential for maintaining germline integrity during oogenesis (PubMed:22303351, PubMed:26295961). Acts via the Piwi-interacting RNA (piRNA) metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons (PubMed:17322028, PubMed:17346786, PubMed:19395009, PubMed:20980675). Piwi protein that directly binds piRNAs, a class of 24 to 30 nucleotide RNAs that are generated by a Dicer-independent mechanism and are primarily derived from transposons and other repeated sequence elements (PubMed:17322028, PubMed:17346786, PubMed:26212455, PubMed:26295961). Associates predominantly with sense piRNAs that contain adenine at nucleotide 10, but shows no preference for uridine at the 5' end (PubMed:17322028, PubMed:17346786, PubMed:26212455). Shows RNA cleavage or slicer activity (PubMed:17322028). Together with Piwi protein aub recruited to subregions of the perinuclear nuage by krimp, which coordinates their activity in the ping-pong amplification step of secondary piRNA biogenesis (PubMed:26295961, PubMed:34210982). Krimp recruits piRNA bound aub and unbound AGO3, bringing them into close proximity to facilitate the loading onto AGO3 of freshly cut piRNAs generated by aub cleavage of target sequences; krimp recognizes the piRNA loading state of the Piwi proteins via symmetrically dimethylated arginine modification in their N-terminus (PubMed:34210982). Important for asymmetric ping-pong amplification to bias production towards antisense piRNAs capable of silencing transposable elements (PubMed:19395009, PubMed:26212455). In testis, associates with Su(Ste) and AT-chX-1 piRNAs mostly produced from antisense precursors (PubMed:20980675). In the germline, acts to amplify pools of antisense piRNAs, among others Su(Ste), AT-chX-1 and roo, and to limit sense piRNA accumulation (PubMed:20980675). Forms a complex with smg, twin, aub and specific piRNAs that targets nos mRNA (and probably other maternal mRNAS) for deadenylation promoting its decay during early embryogenesis (PubMed:20953170). Involved in transposon silencing in the adult brain (PubMed:23559253).

(UniProt, Q7PLK0)

Summary (Interactive Fly)

cleaves transposon derived piwi-interacting RNAs to form an adaptive system for transposon control

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\AGO3 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 Q7PLK0)

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

PDB - An information portal to biological macromolecular structures

7CFC

Comments on Gene Model

Gene model reviewed during 5.55

Gene model reviewed during 5.45

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

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

AGO3-RD

FBtr0299880

NM_001043162

2800

867

AGO3-RE

FBtr0299881

NM_001043164

2974

867

AGO3-RF

FBtr0299882

NM_001043163

2773

867

AGO3-RG

FBtr0301725

NM_001170027

2728

866

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

AGO3-PD

FBpp0289158

99.1

867

9.04

FBpp0289159

99.1

867

9.04

FBpp0289160

99.1

867

9.04

FBpp0290939

99.1

866

9.05

NP_001163498

ACZ94769

Polypeptides with Identical Sequences

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

867 aa isoforms: AGO3-PD, AGO3-PE, AGO3-PF

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Component of the ping-pong piRNA processing (4P) complex consisting of krimp, aub and AGO3 (PubMed:19959991, PubMed:26295961, PubMed:34210982). Interacts (via N-terminus when not methylated on arginine residues) with krimp (via non-canonical tudor domain); this interaction leads to symmetrical dimethylation on AGO3 arginine residues and its subsequent dissociation from krimp (PubMed:26212455, PubMed:26295961, PubMed:34210982). Krimp associated AGO3 is mostly free of piRNA binding and the interaction plays an important role in the loading of AGO3 with piRNAs; piRNA binding may stimulate dissociation of the two proteins (PubMed:26212455, PubMed:26295961). May form part of a piRNA processing complex consisting of tud, aub and AGO3 (PubMed:19959991). Interacts (when symmetrically dimethylated on arginine residues) with tud (PubMed:19959991, PubMed:26212455). Forms a complex with smg, twin, aub, nos mRNA and piRNAs that target the nos 3'-untranslated region, in early embryos (PubMed:20953170). Interacts (via the N-terminal region when symmetrically methylated on arginine residues) with papi (via C-terminus); this interaction is RNA-independent and may be required for AGO3 localization to the nuage (PubMed:21447556). Interacts with TER94 and tral (PubMed:21447556).

(UniProt, Q7PLK0)

Post Translational Modification

Symmetrically dimethylated on Arg-4, Arg-68 and Arg-70, most likely by csul/PRMT5/DART5 (PubMed:19377467, PubMed:19959991, PubMed:26212455). Methylation state probably functions as an indicator of its piRNA binding state (PubMed:34210982).

(UniProt, Q7PLK0)

Crossreferences

InterPro - A database of protein families, domains and functional sites

PDB - An information portal to biological macromolecular structures

7CFC

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q7PLK0

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\AGO3 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).

-0.11

Transcript Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 1 -- 4

organism

(Liu et al., 2011)

adult stage | male

male germline stem cell

(Nagao et al., 2010)

spermatogonium

(Nagao et al., 2010)

primary gonial cell

(Nagao et al., 2010)

adult stage | female

egg chamber

Comment: postgermarial

(Liu et al., 2011)

oogenesis & adult stage | female

female germline cell of germarium

(Minakhina et al., 2014)

adult stage | female & oogenesis

female germline cell

• P granule

(Nagao et al., 2011)

adult stage | male & spermatogenesis

male germline cell

• P granule

(Nagao et al., 2011)

oogenesis

female germline stem cell

(Liu et al., 2011)

female germline cyst

(Liu et al., 2011)

nurse cell

(Liu et al., 2011)

mass spectroscopy

Stage

Tissue/Position (including subcellular localization)

Reference

day 5 of adulthood | male -- day 7 of adulthood | male

spermatozoon

(Wasbrough et al., 2010)

Additional Descriptive Data

Colocalization of AGO3 and papi was seen, particularly in the cytoplasm of germline stem cells, differentiating cysts, and postgermarial egg chambers. It is particularly pronounced in the nuage of nurse cells. In early embryos, they colocalize in the cytoplasm.

(Liu et al., 2011)

AGO3 protein is present in the cytoplasm of germline stem cells, gonialblasts, and spermatogonia.

(Nagao et al., 2010)

Marker for

Subcellular Localization

CV Term

Evidence

References

located_in cytoplasm

inferred from direct assay

(Gunawardane et al., 2007)

located_in cytosol

inferred from direct assay

(Tindell et al., 2020)

is_active_in extrinsic component of mitochondrial outer membrane

inferred from direct assay

(Huang et al., 2014)

is_active_in P granule

inferred from direct assay

(Lim et al., 2022, Vrettos et al., 2021, Munafò et al., 2019, Huang et al., 2014, Klattenhoff et al., 2009, Lim et al., 2009, Brennecke et al., 2007)

located_in P granule

inferred from direct assay

(Tindell et al., 2020, Ge et al., 2019, Webster et al., 2015, Liu et al., 2011, Nagao et al., 2010, Patil and Kai, 2010)

inferred from direct assay

(Nagao et al., 2011)

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\AGO3 in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\AGO3

View exonic expression by tissue for Dmel\AGO3

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

3355150/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0250816

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0250816

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0250816

Flygut - An atlas of the Drosophila adult midgut

FBgn0250816

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 16 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 22 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of AGO3

Transgenic constructs containing regulatory region of AGO3

Aberrations (Deficiencies and Duplications) ( 5 )

Inferred from experimentation ( 5 )

Gene disrupted in

Df(3L)4A-1677

(Syrzycka et al., 2019)

Df(3L)18A-1677

(Syrzycka et al., 2019)

Df(3L)TTT

(Syrzycka et al., 2019, Li et al., 2009)

Gene not disrupted in

Df(3L)1-16

(Cook, 2016.2.8)

Df(3L)γ-28

(Syrzycka et al., 2019)

Inferred from location ( 2 )

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

viable

AGO3^t3

viable (with AGO3^t1)

viable (with AGO3^t2)

viable (with AGO3^t3)

viable (with Df(3L)TTT)

Sterility

Allele

female sterile, with Scer\GAL4^nanos.PG

female sterile (with AGO3¹⁷⁷⁷)

AGO3⁵⁰²⁷

female sterile (with AGO3⁵⁰²⁷)

AGO3¹⁷⁷⁷

female sterile (with AGO3^t2)

AGO3^t3

female sterile (with AGO3^t3)

AGO3^t2

male semi-sterile (with AGO3^t2)

AGO3^t3

male semi-sterile (with AGO3^t3)

AGO3^t2

Phenotype manifest in

Allele

dorsal appendage | maternal effect (with AGO3^t2)

AGO3^t3

dorsal appendage | maternal effect (with AGO3^t3)

AGO3^t2

egg | maternal effect (with AGO3^t2)

AGO3^t3

egg | maternal effect (with AGO3^t3)

AGO3^t2

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (8)

Hsap\PIWIL1

13 of 14

Yes

Hsap\PIWIL3

12 of 14

Yes

Hsap\PIWIL4

11 of 14

Yes

Hsap\PIWIL2

9 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (7)

Rnor\Piwil1

13 of 14

Yes

Rnor\Piwil2

11 of 14

Yes

Rnor\Piwil4

11 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Mus musculus (laboratory mouse) (7)

Mmus\Piwil1

12 of 14

Yes

Mmus\Piwil2

11 of 14

Yes

Mmus\Piwil4

10 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (8)

Xtro\piwil3

10 of 13

Yes

Xtro\piwil2

8 of 13

Yes

Xtro\piwil4

8 of 13

Yes

3 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Danio rerio (Zebrafish) (7)

Drer\piwil1

13 of 14

Yes

Drer\piwil2

10 of 14

Yes

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (21)

Cele\prg-1

11 of 14

Yes

Cele\csr-1

2 of 14

Yes

Cele\ppw-1

2 of 14

Yes

Cele\sago-2

2 of 14

Yes

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (5)

Agam\AgaP_AGAP008862

12 of 12

Yes

6 of 12

5 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (10)

Atha\AGO3

3 of 13

Yes

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Saccharomyces cerevisiae (Brewer's yeast) (0)

Schizosaccharomyces pombe (Fission yeast) (1)

Spom\ago1

1 of 12

Yes

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:AGO3. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (4)

aub

10 of 13

piwi

10 of 13

AGO1

1 of 13

AGO2

1 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

Disease Ontology (DO) Annotations

Models Based on Experimental Evidence ( 0 )

Allele

Disease

Evidence

References

Potential Models Based on Orthology ( 0 )

Human Ortholog

Disease

Evidence

References

Modifiers Based on Experimental Evidence ( 4 )

Allele

Disease

Interaction

References

AGO3^GL00117

ameliorates Alzheimer's disease

modeled by Hsap\MAPT^R406W.UAS

(Frost et al., 2014)

AGO3^HMS00125

ameliorates Alzheimer's disease

modeled by Hsap\MAPT^R406W.UAS

(Frost et al., 2014)

AGO3^t2

ameliorates amyotrophic lateral sclerosis type 6

modeled by caz^RNAi.UAS.cUa

(Wakisaka et al., 2019)

modeled by caz^HMS00790

(Wakisaka et al., 2019)

AGO3^t3

ameliorates amyotrophic lateral sclerosis type 6

modeled by caz^RNAi.UAS.cUa

(Wakisaka et al., 2019)

modeled by caz^HMS00790

(Wakisaka et al., 2019)

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?

PIWIL1; piwi like RNA-mediated gene silencing 1

13 of 14

605571

PIWIL3; piwi like RNA-mediated gene silencing 3

12 of 14

610314

PIWIL4; piwi like RNA-mediated gene silencing 4

11 of 14

610315

PIWIL2; piwi like RNA-mediated gene silencing 2

9 of 14

610312

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

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

AGO3 - CG14036

anti tag coimmunoprecipitation, western blot

(Kina et al., 2025)

AGO3 - Fkbp59

anti bait coimmunoprecipitation, western blot

(Cappucci et al., 2019)

AGO3 - Hsc70-4

anti bait coimmunoprecipitation, western blot

(Cappucci et al., 2019)

AGO3 - Hsp70

anti bait coimmunoprecipitation, western blot

(Cappucci et al., 2019)

AGO3 - Hsp83

anti bait coimmunoprecipitation, western blot

(Cappucci et al., 2019)

AGO3 - Klp10A

coimmunoprecipitation, Identification by mass spectrometry, anti bait coimmunoprecipitation, western blot

(Venkei et al., 2020)

AGO3 - Kots

anti tag coimmunoprecipitation, western blot

(Lim et al., 2022)

AGO3 - Stip1

anti bait coimmunoprecipitation, western blot

(Cappucci et al., 2019)

AGO3 - TER94

anti bait coimmunoprecipitation, western blot

(Liu et al., 2011)

AGO3 - armi

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation

(Huang et al., 2014)

AGO3 - aub

pull down, western blot, anti bait coimmunoprecipitation, cosedimentation, anti tag western blot

(Cappucci et al., 2019, Zhang et al., 2011, Rouget et al., 2010, Nishida et al., 2009)

AGO3 - krimp

anti tag coimmunoprecipitation, anti tag western blot, anti bait coimmunoprecipitation, western blot, pull down, x-ray crystallography, isothermal titration calorimetry, predetermined participant

(Huang et al., 2021, Sato et al., 2015, Webster et al., 2015)

AGO3 - papi

anti bait coimmunoprecipitation, western blot, two hybrid

(Liu et al., 2011)

AGO3 - smg

anti bait coimmunoprecipitation, western blot

(Rouget et al., 2010)

AGO3 - spn-E

anti tag coimmunoprecipitation, cross-linking study, western blot

(Lin et al., 2023)

AGO3 - tapas

anti bait coimmunoprecipitation, western blot, anti tag coimmunoprecipitation, anti tag western blot

(Patil et al., 2014)

AGO3 - tej

anti tag coimmunoprecipitation, cross-linking study, western blot

(Lin et al., 2023)

AGO3 - tral

anti bait coimmunoprecipitation, western blot

(Liu et al., 2011)

AGO3 - tud

anti bait coimmunoprecipitation, western blot, cosedimentation, pull down

(Sato et al., 2015, Nishida et al., 2009)

AGO3 - twin

anti tag coimmunoprecipitation, anti tag western blot

(Fu et al., 2015)

AGO3 - vas

anti tag coimmunoprecipitation, cross-linking study, western blot

(Lin et al., 2023)

AGO3 - vret

anti tag coimmunoprecipitation, western blot

(Zamparini et al., 2011)

AGO3 - zuc

anti tag coimmunoprecipitation, western blot

(Huang et al., 2014)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

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

ct|lncRNA:flam

suppressible

AGO2|AGO3

(Guida et al., 2016)

ct|lncRNA:flam

suppressible

AGO3

(Guida et al., 2016)

trabl

suppressible

AGO3

(Chen et al., 2025)

External Data

Subunit Structure (UniProtKB)

(UniProt, Q7PLK0 )

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0250816

MIST (protein-protein) - An integrated Molecular Interaction Database

3355150

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.

Dorso-ventral axis formation

Class of Gene

gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-47

Cytogenetic map

80F9-80F9

Sequence location

3L:23,554,593..23,689,640 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

80F9-80F9

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

80-80

h47

(Drosophila Heterochromatin Genome Project, 2004)

80B-80C

(determined by in situ hybridisation)

(Moshkin et al., 2002)

Experimentally Determined Recombination Data

Location

3-47

(FlyBase, 2016)

3-44.1

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (6)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

44543

y¹ v¹; P{TRiP.HMC02938}attP40

28270

bw¹; st¹ AGO3^t3/TM6B, Tb¹

35232

y¹ sc^* v¹ sev²¹; P{TRiP.GL00117}attP2

34815

y¹ sc^* v¹ sev²¹; P{TRiP.HMS00125}attP2

NIG-Fly

HMC02938

y¹ v¹; P{TRiP.HMC02938}attP40

GL00117

y¹ sc^* v¹ sev²¹; P{TRiP.GL00117}attP2

Genomic Clones (49)

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

cDNA Clones (33)

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

LD15865

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.

FBgn0250816

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0250816

Antibody Information

Laboratory Generated Antibodies

polyclonal

(Lim et al., 2022, Sato et al., 2015, Huang et al., 2014, Klattenhoff et al., 2009, Lim et al., 2009, Nishida et al., 2009)

monoclonal

(Sato et al., 2015, Senti et al., 2015)

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

AGO3 acts to amplify piRNA pools and to enforce on them an antisense bias, increasing the number of piRNAs that can act to silence transposons.

(Li et al., 2009)

AGO3 protein binds sense-strand piRNAs.

(Brennecke et al., 2007)

AGO3 protein exhibits Slicer activity in vitro.

(Gunawardane et al., 2007)

New annotation (CG40300) in release 3 of the genome annotation.

(FlyBase Genome Annotators, 2002-2003)

Relationship to Other Genes

Source for database merge of

Source for merge of: AGO3 CG40300

(Gunawardane et al., 2007)

Source for merge of: AGO3 BEST:LD15785

(FlyBase, 1996-)

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (12)

Reported As

Symbol Synonym

AGO-3

(Soleimani et al., 2020)

AGO3

(Chen et al., 2025, Fitz-James et al., 2025, Hughes et al., 2024, Li et al., 2024, Kotov et al., 2022, Tarikere et al., 2022, Yang et al., 2022, Proshkina et al., 2021, Schneider and Imler, 2021, Adashev et al., 2020, Galagali and Kim, 2020, Gamez et al., 2020, Sato and Siomi, 2020, Shatskikh et al., 2020, Dou et al., 2019, Duc et al., 2019, Guan et al., 2019, Kolliopoulou et al., 2019, Luhur et al., 2019, Park et al., 2019, Story et al., 2019, Trcek and Lehmann, 2019, Wakisaka et al., 2019, Huang et al., 2018, Moon et al., 2018, Wang et al., 2018, Rogers et al., 2017, Sousa-Victor et al., 2017, Teixeira et al., 2017, Azlan et al., 2016, Guida et al., 2016, Lo et al., 2016, Luo et al., 2016, Na et al., 2016, Ryazansky et al., 2016, Malone et al., 2015, Mugat et al., 2015, Sato et al., 2015, Zhang et al., 2015, Hayashi et al., 2014, Huang et al., 2014, Jalvingh et al., 2014, Minakhina et al., 2014, Ross et al., 2014, Castel and Martienssen, 2013, Czech et al., 2013, Dönertas et al., 2013, Handler et al., 2013, Handler et al., 2013, Lasko, 2013, Saito, 2013, Seervai and Wessel, 2013, Sentmanat et al., 2013, Kibanov et al., 2012, Olivieri et al., 2012, Stefanov et al., 2012, Ishizu et al., 2011, Kolaczkowski et al., 2011, Liu et al., 2011, Qi et al., 2011, Sato et al., 2011, Zamparini et al., 2011, Janic et al., 2010, Lee and Langley, 2010, Moshkovich and Lei, 2010, Olivieri et al., 2010, Rigoutsos, 2010, Saito et al., 2010, Siomi et al., 2010, Wasbrough et al., 2010, Lau et al., 2009, Malone et al., 2009, Miyoshi et al., 2009, Nishida et al., 2009, Saito et al., 2009, Kawamura et al., 2008, Brower-Toland et al., 2007, Grewal and Elgin, 2007, Gunawardane et al., 2007, Gunawardane et al., 2007, Saito et al., 2007)

Ago-3

(Benoit et al., 2022, Kelleher et al., 2020, Dehghani and Lasko, 2017, Klenov, 2008, Klenov et al., 2007)

Ago3

(Cacchione et al., 2025, Castelló-Sanjuán et al., 2025, Glineburg and Nguyen, 2025, Kina et al., 2025, Luan, 2025, Pritam and Signor, 2025, Suyama and Kai, 2025, Vedanayagam, 2025, Ho et al., 2024, Patel et al., 2024, Yushkova, 2024, Santos et al., 2023, Arkov, 2022, Brosh et al., 2022, He et al., 2022, Lim et al., 2022, Huang and Wong, 2021, Huang et al., 2021, Lawlor et al., 2021, Onishi et al., 2021, Rayford et al., 2021, Vrettos et al., 2021, Wang and Lin, 2021, Cacchione et al., 2020, Mérel et al., 2020, Sankaranarayanan and Weil, 2020, Tindell et al., 2020, Ge et al., 2019, Hirakata and Siomi, 2019, Kneuss et al., 2019, Munafò et al., 2019, Saha and Mishra, 2019, Specchia et al., 2019, Jankovics et al., 2018, Rojas-Ríos and Simonelig, 2018, van den Beek et al., 2018, Yamashiro and Siomi, 2018, Huang et al., 2017, Hyun, 2017, Karam et al., 2017, Luo and Lu, 2017, Pandey et al., 2017, Rashpa et al., 2017, Ryazansky et al., 2017, Vrettos et al., 2017, Yang and Xi, 2017, Andress et al., 2016, Frost et al., 2016, Hayashi et al., 2016, Hirakata and Siomi, 2016, Kelleher, 2016, Lewis et al., 2016, Wang et al., 2016, Bouleau and Tricoire, 2015, Fu et al., 2015, Meller et al., 2015, Molla-Herman et al., 2015, Sun and Chen, 2015, Wang et al., 2015, Webster et al., 2015, Yang et al., 2015, Frost et al., 2014, Larracuente, 2014, Mani et al., 2014, Patil et al., 2014, Wang et al., 2014, Zhang et al., 2014, Barckmann and Simonelig, 2013, Gomes et al., 2013, Guzzardo et al., 2013, Mani and Juliano, 2013, Olovnikov and Kalmykova, 2013, Rozhkov et al., 2013, Simkin et al., 2013, Vagin et al., 2013, Bozzetti et al., 2012, Kelleher et al., 2012, McCue and Slotkin, 2012, Preall et al., 2012, Vazquez-Pianzola and Suter, 2012, Zhang et al., 2012, Handler et al., 2011, Khurana et al., 2011, Pane et al., 2011, Patil and Kai, 2010, Rouget et al., 2010, Kirino et al., 2009, Olson et al., 2008, Brennecke et al., 2007, Lin, 2007, Zamore, 2007, Zaratiegui, 2007)

BEST:LD15785

CG40300

(Meadows, 2019.11.20, Çiçek et al., 2016, Na et al., 2016, Ni et al., 2011.7.19, Ni et al., 2010.12.1, Gunawardane et al., 2007)

dAgo3

(Denli and Hannon, 2003)

Name Synonyms

AGO3

Argonaute 3

(Hirakata and Siomi, 2016, Wang et al., 2015, Temme et al., 2014, Gomes et al., 2013, Wood and Helfand, 2013, Kibanov et al., 2012, Handler et al., 2011, Liu et al., 2011, Zamparini et al., 2011, Rigoutsos, 2010, Saito et al., 2009)

Argonaute-3

(Kelleher et al., 2020, Olson et al., 2008)

Argonaute3

(Pek and Kai, 2011, Patil and Kai, 2010, Zamore, 2007)

BEST:LD15785

CG40300

argonaute3

(Seervai and Wessel, 2013)

Secondary FlyBase IDs

FBgn0086780
FBgn0066316
FBgn0058300
FBan0040300
FBgn0069062

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 41 )

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.

3355150

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.

Q7PLK0

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

Q7PLK0

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.

Q7PLK0

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

3355150/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0250816

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0250816

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG40300

MARRVEL_MODEL - MARRVEL (model organism gene)

3355150

PDB - An information portal to biological macromolecular structures

7CFC

Linkouts

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0250816

DroID - A comprehensive database of gene and protein interactions.

FBgn0250816

DRSC - Results frm RNAi screens

FBgn0250816

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0250816

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0250816

Flygut - An atlas of the Drosophila adult midgut

FBgn0250816

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

TC008511

Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution

Interactive Fly

KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.

Dorso-ventral axis formation

MIST (protein-protein) - An integrated Molecular Interaction Database

3355150

References (276)

The following external sites may use different assemblies or annotations than FlyBase.

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