FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\CSN3
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General Information
Symbol
Dmel\CSN3
Species
D. melanogaster
Name
COP9 signalosome subunit 3
Annotation Symbol
CG18332
Feature Type
protein_coding_gene
FlyBase ID
FBgn0027055
Gene Model Status
Current
Stock Availability
7 publicly available
Gene Summary
COP9 signalosome subunit 3 (CSN3) encodes the subunit 3 of the COP9 signalosome (CSN) and is essential for the stability of the complex. The CSN plays a central role in the regulation of E3-cullin RING ubiquitin ligases. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
All Summaries
Also Known As

COP9 complex homolog subunit 3, Dch3

Key Links
Genomic Location
Cytogenetic map
77F1-77F1
Sequence location
Recombination map
3-47
RefSeq locus
NT_037436 REGION:20839096..20841576
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 (8 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (7 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
involved_in female germ-line stem cell population maintenance
inferred from mutant phenotype
(Pan et al., 2014)
involved_in germ cell development
inferred from mutant phenotype
(Qian et al., 2015)
involved_in germarium-derived cystoblast division
inferred from mutant phenotype
(Pan et al., 2014)
involved_in male germ-line cyst encapsulation
inferred from mutant phenotype
(Qian et al., 2015)
involved_in protein stabilization
inferred from mutant phenotype
(Ullah et al., 2007)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in protein deneddylation
inferred from sequence or structural similarity with UniProtKB:Q9UNS2
(Gene Ontology Curators, 2002-)
involved_in ubiquitin-dependent protein catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000079485
(GO Reference Genome Project, 2011-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of COP9 signalosome
inferred from sequence or structural similarity with MGI:MGI:1349409
(Freilich et al., 1999)
inferred from biological aspect of ancestor with PANTHER:PTN000079486
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the CSN3 family. (Q8SYG2)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
COP9 signalosome subunit 3 (CSN3) encodes the subunit 3 of the COP9 signalosome (CSN) and is essential for the stability of the complex. The CSN plays a central role in the regulation of E3-cullin RING ubiquitin ligases. [Date last reviewed: 2019-03-07]
Gene Group (FlyBase)
COP9 SIGNALOSOME -
The COP9 signalosome is an eight-subunit complex that is structurally and evolutionarily related to the 19S lid of the 26S proteasome. The COP9 signalosome plays a central role in the regulation of the E3-cullin RING ubiquitin ligases, deNEDDylating the cullin subunit via the isopeptidase activity of the CNS5 subunit. (Adapted from FBrf0225508 and FBrf0225509).
COP9 SIGNALOSOME COMPLEX - TESTIS-SPECIFIC VARIANT -
The COP9 signalosome is an eight-subunit complex that is structurally and evolutionarily related to the 19S lid of the 26S proteasome. The COP9 signalosome plays a central role in the regulation of the E3-cullin RING ubiquitin ligases, deNEDDylating the cullin subunit via the isopeptidase activity of the CNS5 subunit. (Adapted from FBrf0225508 and FBrf0225509).
Protein Function (UniProtKB)
Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of the SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. The CSN complex plays an essential role in oogenesis and embryogenesis and is required for proper photoreceptor R cell differentiation and promote lamina glial cell migration or axon targeting. It also promotes Ubl-dependent degradation of cyclin E (CycE) during early oogenesis.
(UniProt, Q8SYG2)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\CSN3 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 Q8SYG2)

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.

Gene model reviewed during 5.45

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
CSN3-RA
FBtr0078269
NM_079466
1679
445
Additional Transcript Data and Comments
Reported size (kB)

1.675 (longest cDNA)

(Freilich et al., 1999)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
CSN3-PA
FBpp0077927
50.7
445
6.19
Q8SYG2
NP_524190
AAF51652
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)

445 (aa)

(Freilich et al., 1999)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the CSN complex, probably composed of CSN1b, alien/CSN2, CSN3, CSN4, CSN5, CSN6, CSN7 and CSN8.

(UniProt, Q8SYG2)
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\CSN3 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).

0.72

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\CSN3 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 ( 2 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 9 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of CSN3
Transgenic constructs containing regulatory region of CSN3
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 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\COPS3
13 of 14
Yes
Yes
Hsap\PSMD3
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) (2)
Rnor\Cops3
12 of 14
Yes
Yes
Rnor\Psmd3
1 of 14
No
No
Mus musculus (laboratory mouse) (2)
Mmus\Cops3
12 of 14
Yes
Yes
Mmus\Psmd3
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (1)
Xtro\cops3
11 of 13
Yes
Yes
Danio rerio (Zebrafish) (2)
Drer\cops3
11 of 14
Yes
Yes
Drer\psmd3
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
Cele\csn-3
7 of 14
Yes
Yes
Cele\rpn-3
2 of 14
No
No
Anopheles gambiae (African malaria mosquito) (3)
Agam\AgaP_AGAP006445
12 of 12
Yes
Yes
Agam\AgaP_AGAP008498
1 of 12
No
No
Agam\PSMD3_ANOGA
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (4)
Atha\COP13
12 of 13
Yes
Yes
Atha\AT1G75990
1 of 13
No
No
Atha\EER5
1 of 13
No
No
Atha\EMB2719
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\RPN3
2 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\csn3
3 of 12
Yes
Yes
Spom\rpn3
1 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:CSN3. 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) (2)
Rpn3
3 of 13
PCID2
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 ( 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?
    COPS3; COP9 signalosome subunit 3
    13 of 14
    604665
        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
        Subunit Structure (UniProtKB)
        Component of the CSN complex, probably composed of CSN1b, alien/CSN2, CSN3, CSN4, CSN5, CSN6, CSN7 and CSN8.
        (UniProt, Q8SYG2 )
        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
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        3L
        Recombination map
        3-47
        Cytogenetic map
        77F1-77F1
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        77F1-77F1
        Limits computationally determined from genome sequence between P{EP}trblEP3519 and P{EP}fngEP3082&P{lacW}skdL7062
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        3-47

        (FlyBase, 2016)

        3-43.7

        (Comeron et al., 2012)
        Left of (cM)
        Right of (cM)
        Notes
        Stocks and Reagents
        Stocks (7)
        Genomic Clones (14)
         

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

        cDNA Clones (53)
         

        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

            Expression is enriched in embryonic gonads.

            (Shigenobu et al., 2006)

            COP9 signalosome is essential for development.

            (Freilich et al., 1999)
            Relationship to Other Genes
            Source for database merge of
            Additional comments
            Nomenclature History
            Source for database identify of
            Nomenclature comments
            Etymology
            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
            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
            FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            References (74)