FB2026_02 , released June 18, 2026
FB2026_02 , released June 18, 2026
Gene: Dmel\Chchd3
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General Information
Symbol
Dmel\Chchd3
Species
D. melanogaster
Name
Coiled-coil-helix-coiled-coil-helix domain containing 3
Annotation Symbol
CG1715
Feature Type
protein_coding_gene
FlyBase ID
FBgn0010808
Gene Model Status
Current
Stock Availability
9 publicly available
Gene Summary
Coiled-coil-helix-coiled-coil-helix domain containing 3 (Chchd3) encodes a mitochondrial inner membrane protein that is required for mitochondrial fusion. Loss of Chchd3 leads to inactivation of Hippo activity, decreased tissue growth, cell proliferation defects, oxidative stress and JNK pathway activation. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
All Summaries
Also Known As

l(3)03670, l(3)S127408, anon-l, lethal (3) 03670

Key Links
Genomic Location
Cytogenetic map
100B1-100B1
Sequence location
Recombination map
3-102
RefSeq locus
NT_033777 REGION:31052616..31053915
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 (5 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
involved_in cristae formation
inferred from mutant phenotype
(Deng et al., 2016)
involved_in mitochondrial fusion
inferred from mutant phenotype
(Deng et al., 2016)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in inner mitochondrial membrane organization
inferred from biological aspect of ancestor with PANTHER:PTN004549352
(GO Reference Genome Project, 2011-)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
part_of MICOS complex
inferred from genetic interaction with FLYBASE:Mic10b; FB:FBgn0069923
(Stephan et al., 2024)
located_in mitochondrial inner membrane
inferred from direct assay
(Deng et al., 2016)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of MICOS complex
inferred from biological aspect of ancestor with PANTHER:PTN004549352
(GO Reference Genome Project, 2011-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Snapshot
Coiled-coil-helix-coiled-coil-helix domain containing 3 (Chchd3) encodes a mitochondrial inner membrane protein that is required for mitochondrial fusion. Loss of Chchd3 leads to inactivation of Hippo activity, decreased tissue growth, cell proliferation defects, oxidative stress and JNK pathway activation. [Date last reviewed: 2019-03-07]
Gene Group (FlyBase)
MICOS COMPLEX - MIC10B VARIANT -
The mitochondrial contact site and cristae organizing system (MICOS) is a large hetero-oligomeric complex inner mitochondrial membrane complex that is involved in the structural maintenance of the inner membrane and cristae formation. (Adapted from FBrf0258588.)
MICOS COMPLEX - MIC10A TESTIS-SPECIFIC VARIANT -
The mitochondrial contact site and cristae organizing system (MICOS) is a large hetero-oligomeric complex inner mitochondrial membrane complex that is involved in the structural maintenance of the inner membrane and cristae formation. (Adapted from FBrf0258588.)
MICOS COMPLEX - MIC10C TESTIS-SPECIFIC VARIANT -
The mitochondrial contact site and cristae organizing system (MICOS) is a large hetero-oligomeric complex inner mitochondrial membrane complex that is involved in the structural maintenance of the inner membrane and cristae formation. (Adapted from FBrf0258588.)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Chchd3 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 Q9VA18)

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 5.46

Gene model reviewed during 5.47

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Chchd3-RA
FBtr0085745
NM_143581
940
223
Additional Transcript Data and Comments
Reported size (kB)

1.0 (northern blot)

(Yang et al., 2000)

1.1 (northern blot)

(Kloss et al., 1998)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
Chchd3-PA
FBpp0085107
24.2
223
9.43
Q9VA18
NP_651838
AAF57107
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)

223 (aa)

(Yang et al., 2000)
Comments
External Data
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\Chchd3 using the Feature Mapper tool.

External Data
Crossreferences
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).

-0.78

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
anterior endoderm
(Fisher et al., 2012)
head mesoderm
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior endoderm
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
embryonic stage 11 -- 12
anterior midgut primordium
(Fisher et al., 2012)
hindgut proper primordium
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
posterior midgut primordium
(Fisher et al., 2012)
somatic muscle primordium
(Fisher et al., 2012)
trunk mesoderm
(Fisher et al., 2012)
embryonic stage 13 -- 16
dorsal pharyngeal muscle cell
(Fisher et al., 2012)
embryonic hindgut
(Fisher et al., 2012)
embryonic midgut chamber
(Fisher et al., 2012)
embryonic/larval midgut
(Fisher et al., 2012)
larval muscle system
(Fisher et al., 2012)
larval somatic muscle cell
(Fisher et al., 2012)
larval visceral muscle cell
(Fisher et al., 2012)
gastric caecum
(Fisher et al., 2012)
organism | ubiquitous
(Fisher et al., 2012)
wandering third instar larval stage
wing pouch | restricted
(Molnar et al., 2012)
wing hinge primordium | restricted
(Molnar et al., 2012)
northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
(Yang et al., 2000)
Additional Descriptive Data

l(3)03670 transcripts are expressed in adults with slightly elevated levels in the head.

(Yang et al., 2000)
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
day 7 of adulthood -- day 49 of adulthood
adult heart
(Cammarato et al., 2011)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
part_of MICOS complex
inferred from genetic interaction with FLYBASE:Mic10b; FB:FBgn0069923
(Stephan et al., 2024)
located_in mitochondrial inner membrane
inferred from direct assay
(Deng et al., 2016)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Chchd3 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
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
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 ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Chchd3
Transgenic constructs containing regulatory region of Chchd3
Aberrations (Deficiencies and Duplications) ( 18 )
Variants
Variant Molecular Consequences
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
lethal (with Df(3R)A177der21)
lethal | recessive
lethal - all die before end of P-stage | recessive
lethal - all die before end of pupal stage | recessive
lethal - all die during larval stage (with Df(3R)BSC749)
lethal - all die during larval stage | recessive
lethal - all die during P-stage, with Scer\GAL4Mef2.PR
viable
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4tin.CΔ4
Other Phenotypes
Allele
abnormal developmental rate
abnormal developmental rate (with Df(3R)BSC749)
abnormal size | somatic clone | third instar larval stage
abnormal size | third instar larval stage, with Scer\GAL4Cg.PA
decreased occurrence of cell division | somatic clone
decreased rate of adult locomotory behavior, with Scer\GAL4Mef2.PR
short lived, with Scer\GAL4Mef2.PR
some die during pharate adult stage | recessive
some die during pupal stage | recessive
visible | adult stage, with Scer\GAL4ey.PU
wild-type
Phenotype manifest in
Allele
adult heart, with Chchd3D1, Scer\GAL4HCH.Hand
adult heart, with Chchd3GD9297, Scer\GAL4HCH.Hand
adult heart, with Scer\GAL4HCH.Hand
embryonic/larval fat body | third instar larval stage, with Scer\GAL4Cg.PA
embryonic/larval hypodermal muscle cell | third instar larval stage, with Scer\GAL4Mef2.PU
eye | adult stage, with Scer\GAL4ey.PU
filamentous actin | adult stage, with Chchd3D1, Scer\GAL4HCH.Hand
filamentous actin | adult stage, with Chchd3GD9297, Scer\GAL4HCH.Hand
filamentous actin | adult stage, with Scer\GAL4HCH.Hand
filamentous actin | adult stage, with Scer\GAL4Mef2.PR
indirect flight muscle | adult stage, with Scer\GAL4Mef2.PR
indirect flight muscle cell | adult stage, with Scer\GAL4Mhc.PU
mitochondrial crista | adult stage, with Scer\GAL4Mhc.PU
mitochondrial crista | larval stage
mitochondrion | adult stage, with Scer\GAL4Mhc.PU
mitochondrion | larval stage
mitochondrion | third instar larval stage, with Scer\GAL4Cg.PA
mitochondrion | third instar larval stage, with Scer\GAL4Mef2.PU
sarcomere | adult stage, with Scer\GAL4Mef2.PR
wing disc | somatic clone | third instar larval stage
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\CHCHD3
9 of 14
Yes
Yes
1  
Hsap\CHCHD6
5 of 14
No
Yes
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) (2)
Rnor\Chchd3
8 of 14
Yes
Yes
Rnor\Chchd6
3 of 14
No
Yes
Mus musculus (laboratory mouse) (2)
Mmus\Chchd3
7 of 14
Yes
Yes
Mmus\Chchd6
4 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (3)
Xtro\chchd3
4 of 13
Yes
Yes
Xtro\chchd6
3 of 13
No
Yes
Xtro\lmod2
3 of 13
No
Yes
Danio rerio (Zebrafish) (4)
Drer\chchd3b
9 of 14
Yes
Yes
Drer\chchd3a
7 of 14
No
Yes
Drer\chchd6a
5 of 14
No
Yes
Drer\chchd6b
5 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\chch-3
6 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP000375
11 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\AT4G12340
2 of 13
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (0)
Schizosaccharomyces pombe (Fission yeast) (0)
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Chchd3. Refer to their site for version information.
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v9.1)
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 2 )
Potential Models Based on Orthology ( 0 )
Human Ortholog
Disease
Evidence
References
Modifiers Based on Experimental Evidence ( 1 )
Allele
Disease
Interaction
References
Chchd3HMC02376
model of  hypoplastic left heart syndrome
is exacerbated by Cdk12GD9926
(Birker et al., 2023)
is exacerbated by Drp1JF02762
(Birker et al., 2023)
is ameliorated by Drp1UAS.cDa
(Birker et al., 2023)
is exacerbated by Opa1HMS00349
(Birker et al., 2023)
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?
CHCHD3; coiled-coil-helix-coiled-coil-helix domain containing 3
9 of 14
COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING PROTEIN 3; CHCHD3
       
      CHCHD6; coiled-coil-helix-coiled-coil-helix domain containing 6
      5 of 14
      COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING PROTEIN 6; CHCHD6
           
          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
          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
          Chchd3
          enhanceable
          Opa1
          (Birker et al., 2023)
          Starting gene(s)
          Interaction type
          Interacting gene(s)
          Reference
          Cdk12
          enhanceable
          Chchd3
          (Birker et al., 2023)
          External Data
          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
          Class of Gene
          Genomic Location and Detailed Mapping Data
          Chromosome (arm)
          3R
          Recombination map
          3-102
          Cytogenetic map
          100B1-100B1
          Sequence location
          FlyBase Computed Cytological Location
          Cytogenetic map
          Evidence for location
          100B1-100B1
          Limits computationally determined from genome sequence between P{PZ}Aph-407028&P{PZ}dcorK215 and P{PZ}l(3)rM731rM731
          Experimentally Determined Cytological Location
          Cytogenetic map
          Notes
          References
          100B2-100B2
          (determined by in situ hybridisation)
          (Yang et al., 2000)
          100B-100B
          (Yang, 1995.12.20)
          100B1-100B2
          (determined by in situ hybridisation)
          (Spradling et al., 1999)
          100A-100A
          (determined by in situ hybridisation) 100B (determined by in situ hybridisation)
          (Szeged Stock Center, 1998-)
          100B-100B
          (determined by in situ hybridisation) 100A (determined by in situ hybridisation)
          (Deak et al., 1997)
          100B1-100B2
          (BDGP Project Members, 1994-1999)
          Experimentally Determined Recombination Data
          Location

          3-102

          (FlyBase, 2016)

          3-98.9

          (Comeron et al., 2012)

          3-

          (Yang, 1995.12.20)
          Left of (cM)
          Right of (cM)
          Notes

          Among 20,000 progeny, no recombinants between dco and l(3)03670 were recovered

          (Zilian et al., 1999)
          Stocks and Reagents
          Stocks (9)
          Genomic Clones (11)
           

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

          cDNA Clones (46)
           

          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

            (Murari et al., 2020)
            Commercially Available Antibodies
             
            Cell Line Information
            Publicly Available Cell Lines
             
              Other Stable Cell Lines
               
                Other Comments
                Relationship to Other Genes
                Source for database merge of

                Source for merge of: l(3)03670 anon-l

                (Zilian et al., 1999)

                Source for merge of: l(3)03670 l(3)S127408

                (Yang et al., 2000)
                Additional comments
                Nomenclature History
                Source for database identify of

                Source for identity of: anon-l CG1715

                (Yao, 1999.11)

                Source for identity of: Chchd3 l(3)03670

                (Deng et al., 2016)
                Nomenclature comments
                Etymology

                Appears to be named 'Chchd3' based on orthology.

                (Deng et al., 2016)
                Synonyms and Secondary IDs (21)
                Datasets (0)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                Study result (0)
                Result
                Result Type
                Title
                External Crossreferences and Linkouts ( 35 )
                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/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
                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)
                MIST (protein-protein) - An integrated Molecular Interaction Database
                References (58)