FB2025_05 , released December 11, 2025
Gene: Dmel\caly
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General Information
Symbol
Dmel\caly
Species
D. melanogaster
Name
calypso
Annotation Symbol
CG8445
Feature Type
protein_coding_gene
FlyBase ID
FBgn0262166
Gene Model Status
Current
Stock Availability
10 publicly available
Enzyme Name (EC)
ubiquitinyl hydrolase 1 (3.4.19.12)
Gene Summary
Catalytic component of the polycomb repressive deubiquitinase (PR-DUB) complex, a complex that specifically mediates deubiquitination of histone H2A monoubiquitinated at 'Lys-119' (H2AK118ub1) (PubMed:20436459, PubMed:30258054, PubMed:30639226, PubMed:36180891). Mediates bisymmetric organization of the PR-DUB complex and is involved in association with nucleosomes to mediate deubiquitination (PubMed:30258054). Does not deubiquitinate monoubiquitinated histone H2B (PubMed:20436459). Required to maintain the transcriptionally repressive state of homeotic genes throughout development (PubMed:20436459). The PR-DUB complex has weak or no activity toward 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains (PubMed:20436459). Polycomb group (PcG) protein (PubMed:17717194). (UniProt, Q7K5N4)
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
52F7-52F7
Sequence location
Recombination map
2-78
RefSeq locus
NT_033778 REGION:16194062..16196333
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
Gene Ontology (GO) Annotations (10 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
enables chromatin binding
inferred from direct assay
(Scheuermann et al., 2010)
enables cysteine-type deubiquitinase activity
inferred from direct assay
(Scheuermann et al., 2010)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables cysteine-type deubiquitinase activity
inferred from electronic annotation with InterPro:IPR001578, InterPro:IPR036959
(InterPro Project Members, 2004-)
inferred from biological aspect of ancestor with PANTHER:PTN000063280
(GO Reference Genome Project, 2011-)
Biological Process (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in epigenetic regulation of gene expression
inferred from direct assay
(Scheuermann et al., 2010)
involved_in heterochromatin formation
inferred from mutant phenotype
(Scheuermann et al., 2010)
involved_in specification of segmental identity, abdomen
inferred from mutant phenotype
(de Ayala Alonso et al., 2007)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in heterochromatin formation
inferred from biological aspect of ancestor with PANTHER:PTN000834067
(GO Reference Genome Project, 2011-)
involved_in ubiquitin-dependent protein catabolic process
inferred from electronic annotation with InterPro:IPR001578, InterPro:IPR036959
(InterPro Project Members, 2004-)
Cellular Component (4 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
located_in chromatin
inferred from direct assay
(Scheuermann et al., 2010)
located_in nucleus
inferred from direct assay
(Scheuermann et al., 2010)
part_of PR-DUB complex
inferred from direct assay
(Scheuermann et al., 2010)
inferred from physical interaction with FLYBASE:Asx; FB:FBgn0261823
(Scheuermann et al., 2010)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in cytoplasm
inferred from biological aspect of ancestor with PANTHER:PTN000063280
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the peptidase C12 family. BAP1 subfamily. (Q7K5N4)
Protein Signatures (InterPro)
Catalytic Activity (EC/Rhea)
cysteine-type deubiquitinase activity
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal) (3.4.19.12)
Summaries
Gene Group (FlyBase)
UCH DEUBIQUITINASES -
The ubiquitin C-terminal hydrolase (UCH) sub-family of deubiquitinases are cysteine proteases and that catalyze the removal of ubiquitin from ubiquitin chains and ubiquitinated proteins. UCH deubiquitinases belong to MEROPS family C12. (Adapted from PMID:19626045).
POLYCOMB REPRESSIVE DEUBIQUITINASE COMPLEX -
The Polycomb repressive deubiquitinase (PR-DUB) removes monoubiquitin from histone H2A. (Adapted from FBrf0210760).
Protein Function (UniProtKB)
Catalytic component of the polycomb repressive deubiquitinase (PR-DUB) complex, a complex that specifically mediates deubiquitination of histone H2A monoubiquitinated at 'Lys-119' (H2AK118ub1) (PubMed:20436459, PubMed:30258054, PubMed:30639226, PubMed:36180891). Mediates bisymmetric organization of the PR-DUB complex and is involved in association with nucleosomes to mediate deubiquitination (PubMed:30258054). Does not deubiquitinate monoubiquitinated histone H2B (PubMed:20436459). Required to maintain the transcriptionally repressive state of homeotic genes throughout development (PubMed:20436459). The PR-DUB complex has weak or no activity toward 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains (PubMed:20436459). Polycomb group (PcG) protein (PubMed:17717194).
(UniProt, Q7K5N4)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\caly 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 Q7K5N4)

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
Comments on Gene Model

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

Gene model reviewed during 5.50

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
caly-RA
FBtr0087245
NM_137252
2147
471
caly-RB
FBtr0087246
NM_176194
2117
471
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
caly-PA
FBpp0086383
51.5
471
9.25
Q7K5N4
NP_611096
AAF58046
caly-PB
FBpp0086384
51.5
471
9.25
Q7K5N4
NP_788374
AAO41384
Polypeptides with Identical Sequences

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

471 aa isoforms: caly-PA, caly-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Catalytic component of the polycomb repressive deubiquitinase (PR-DUB) complex, at least composed of caly/calypso, Asx and sba (MBD5/6 homolog) (PubMed:20436459, PubMed:36180891). The PR-DUB complex associates with nucleosomes to mediate deubiquitination of histone H2AK118ub1 substrates; the association requires the positively charged C-terminal tail of caly, probably due to direct binding of DNA (PubMed:30258054, PubMed:30639226). Interacts (via ULD domain) with Asx (via DEUBAD domain); the interaction produces a stable heterodimer with a composite binding site for ubiquitin (PubMed:30258054, PubMed:30639226). Homodimerizes (via coiled-coil hinge-region between the UCH and ULD domains) to mediate assembly of 2 copies of the caly-Asx heterodimer into a bisymmetric tetramer; dimerization enhances PR-DUB association with nucleosomes (PubMed:30258054).

(UniProt, Q7K5N4)
Crossreferences
InterPro - A database of protein families, domains and functional sites
PDB - An information portal to biological macromolecular structures
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\caly 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).

1.11

Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in chromatin
inferred from direct assay
(Scheuermann et al., 2010)
located_in nucleus
inferred from direct assay
(Scheuermann et al., 2010)
part_of PR-DUB complex
inferred from direct assay
(Scheuermann et al., 2010)
inferred from physical interaction with FLYBASE:Asx; FB:FBgn0261823
(Scheuermann et al., 2010)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\caly 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
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 5 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 13 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of caly
Transgenic constructs containing regulatory region of caly
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(2R)Exel6063
(Ryder, 2004.4.26)
Inferred from location ( 7 )
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) (4)
Hsap\BAP1
13 of 14
Yes
Yes
2  
Hsap\UCHL5
3 of 14
No
No
1  
Hsap\UCHL1
1 of 14
No
No
1  
Hsap\UCHL3
1 of 14
No
No
1  
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) (4)
Rnor\Bap1
12 of 14
Yes
Yes
Rnor\Uchl5
2 of 14
No
No
Rnor\Uchl1
1 of 14
No
No
Rnor\Uchl3
1 of 14
No
No
Mus musculus (laboratory mouse) (5)
Mmus\Bap1
13 of 14
Yes
Yes
Mmus\Uchl5
2 of 14
No
No
Mmus\Uchl1
1 of 14
No
No
Mmus\Uchl3
1 of 14
No
No
Mmus\Uchl4
1 of 14
No
No
Xenopus tropicalis (Western clawed frog) (5)
Xtro\bap1
10 of 13
Yes
Yes
Xtro\rab11b.2
2 of 13
No
No
Xtro\uchl5
2 of 13
No
No
Xtro\rad23b
1 of 13
No
No
Xtro\uchl1
1 of 13
No
No
Danio rerio (Zebrafish) (4)
Drer\bap1
12 of 14
Yes
Yes
Drer\uchl5
2 of 14
No
No
Drer\uchl1
1 of 14
No
No
Drer\uchl3
1 of 14
No
No
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\ubh-4
3 of 14
Yes
No
Cele\ubh-1
2 of 14
No
No
Cele\ubh-2
2 of 14
No
No
Cele\ubh-3
2 of 14
No
No
Anopheles gambiae (African malaria mosquito) (2)
Agam\AgaP_AGAP005540
3 of 12
Yes
No
Agam\AgaP_AGAP012113
1 of 12
No
No
Arabidopsis thaliana (thale-cress) (3)
Atha\UCH1
4 of 13
Yes
No
Atha\UCH2
4 of 13
Yes
No
Atha\UCH3
1 of 13
No
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\YUH1
1 of 13
Yes
No
Schizosaccharomyces pombe (Fission yeast) (2)
Spom\uch2
3 of 12
Yes
No
Spom\uch1
1 of 12
No
No
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:caly. 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) (3)
Uch-L5R
5 of 13
Uch-L5
5 of 13
Uch
3 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 ( 1 )
    Human Ortholog
    Disease
    Evidence
    References
    BAP1; BRCA1 associated deubiquitinase 1
    model of  uveal melanoma
    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?
    BAP1; BRCA1 associated deubiquitinase 1
    13 of 14
    603089
     
    UCHL5; ubiquitin C-terminal hydrolase L5
    3 of 14
    610667
         
        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)
        Catalytic component of the polycomb repressive deubiquitinase (PR-DUB) complex, at least composed of caly/calypso, Asx and sba (MBD5/6 homolog) (PubMed:20436459, PubMed:36180891). The PR-DUB complex associates with nucleosomes to mediate deubiquitination of histone H2AK118ub1 substrates; the association requires the positively charged C-terminal tail of caly, probably due to direct binding of DNA (PubMed:30258054, PubMed:30639226). Interacts (via ULD domain) with Asx (via DEUBAD domain); the interaction produces a stable heterodimer with a composite binding site for ubiquitin (PubMed:30258054, PubMed:30639226). Homodimerizes (via coiled-coil hinge-region between the UCH and ULD domains) to mediate assembly of 2 copies of the caly-Asx heterodimer into a bisymmetric tetramer; dimerization enhances PR-DUB association with nucleosomes (PubMed:30258054).
        (UniProt, Q7K5N4 )
        Linkouts
        DroID - A comprehensive database of gene and protein interactions.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Pathways
        Signaling Pathways (FlyBase)
        Metabolic Pathways
        FlyBase
        External Links
        External Data
        Linkouts
        KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
        Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
        Class of Gene
        Genomic Location and Detailed Mapping Data
        Chromosome (arm)
        2R
        Recombination map
        2-78
        Cytogenetic map
        52F7-52F7
        Sequence location
        FlyBase Computed Cytological Location
        Cytogenetic map
        Evidence for location
        52F7-52F7
        Limits computationally determined from genome sequence between P{lacW}Lis-1k11702&P{EP}CG8443EP969 and P{lacW}l(2)k07824k07824&P{lacW}vegk03402
        Experimentally Determined Cytological Location
        Cytogenetic map
        Notes
        References
        Experimentally Determined Recombination Data
        Location

        2-78

        (FlyBase, 2016)

        2-81.1

        (Comeron et al., 2012)

        2-

        (de Ayala Alonso et al., 2007)
        Left of (cM)
        Right of (cM)
        Notes

        Maps to 2R.

        (de Ayala Alonso et al., 2007)
        Stocks and Reagents
        Stocks (10)
        Genomic Clones (19)
        cDNA Clones (11)
         

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

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

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

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

        polyclonal

        (Tsuboyama et al., 2022, Scheuermann et al., 2010)
        Commercially Available Antibodies
         
        Cell Line Information
        Publicly Available Cell Lines
         
          Other Stable Cell Lines
           
            Other Comments

            calypso is a Polycomb group gene and is required for long-term repression of HOX genes in embryos and larvae.

            (de Ayala Alonso et al., 2007)
            Relationship to Other Genes
            Source for database merge of

            Source for merge of: calypso CG8445

            (Scheuermann et al., 2010)
            Additional comments
            Nomenclature History
            Source for database identify of

            Source for identity of: caly calypso

            (Dardalhon-Cuménal et al., 2018)
            Nomenclature comments
            Etymology
            Synonyms and Secondary IDs (8)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            External Crossreferences and Linkouts ( 38 )
            Sequence Crossreferences
            NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
            GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
            GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
            RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
            UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
            UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
            Other crossreferences
            AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
            BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
            DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
            EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
            FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            MARRVEL_MODEL - MARRVEL (model organism gene)
            PDB - An information portal to biological macromolecular structures
            Linkouts
            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
            FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
            MIST (protein-protein) - An integrated Molecular Interaction Database
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            References (71)