FB2024_02 , released April 23, 2024
Gene: Dmel\Cln3
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General Information
Symbol
Dmel\Cln3
Species
D. melanogaster
Name
Cln3
Annotation Symbol
CG5582
Feature Type
protein_coding_gene
FlyBase ID
FBgn0036756
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Summary
Contribute a Gene Snapshot for this gene.
All Summaries
Key Links
Genomic Location
Cytogenetic map
75A2-75A2
Sequence location
Recombination map
3-45
RefSeq locus
NT_037436 REGION:17809231..17814119
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 (14 terms)
Molecular Function (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
enables transmembrane transporter activity
inferred from sequence model
(Perland et al., 2017)
Biological Process (6 terms)
Terms Based on Experimental Evidence (3 terms)
CV Term
Evidence
References
involved_in determination of adult lifespan
inferred from mutant phenotype
(Tuxworth et al., 2011)
involved_in regulation of JNK cascade
inferred from mutant phenotype
(Tuxworth et al., 2009)
involved_in response to oxidative stress
inferred from mutant phenotype
(Tuxworth et al., 2011)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
involved_in lysosome organization
inferred from biological aspect of ancestor with PANTHER:PTN000104834
(GO Reference Genome Project, 2011-)
involved_in regulation of intracellular pH
inferred from biological aspect of ancestor with PANTHER:PTN000104831
(GO Reference Genome Project, 2011-)
involved_in transmembrane transport
inferred from sequence model
(Perland et al., 2017)
Cellular Component (7 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
located_in apical plasma membrane
inferred from direct assay
(Mohammed et al., 2017)
located_in late endosome
inferred from direct assay
(Tuxworth et al., 2009)
located_in lysosome
inferred from direct assay
(Tuxworth et al., 2009)
located_in microvillus membrane
inferred from direct assay
(Mohammed et al., 2017)
located_in mitochondrial membrane
inferred from direct assay
(Mohammed et al., 2017)
located_in vesicle
inferred from direct assay
(Tuxworth et al., 2009)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
is_active_in lysosome
inferred from biological aspect of ancestor with PANTHER:PTN000104834
(GO Reference Genome Project, 2011-)
is_active_in membrane
inferred from sequence model
(Perland et al., 2017)
located_in membrane
inferred from electronic annotation with InterPro:IPR003492, InterPro:IPR018460
(InterPro Project Members, 2004-)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
ATYPICAL SOLUTE CARRIERS -
Most atypical Solute Carriers (ASLCs) are Major Facilitator Superfamily (MFS) domain-containing proteins. ASLCs share ancestral background with the known SLC families but have not been assigned in the SLC classification system. (Adapted from FBrf0251874.)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Cln3 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 Q9VVL0)

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

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Cln3-RA
FBtr0075167
NM_140754
1553
422
Cln3-RB
FBtr0333693
NM_001275070
1589
422
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
Cln3-PA
FBpp0074933
47.6
422
4.92
Q9VVL0
NP_649011
AAF49301
Cln3-PB
FBpp0305846
47.6
422
4.92
Q9VVL0
NP_001261999
AGB94692
Polypeptides with Identical Sequences

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

422 aa isoforms: Cln3-PA, Cln3-PB
Additional Polypeptide Data and Comments
Reported size (kDa)
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\Cln3 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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
Additional Descriptive Data
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)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in apical plasma membrane
inferred from direct assay
(Mohammed et al., 2017)
located_in late endosome
inferred from direct assay
(Tuxworth et al., 2009)
located_in lysosome
inferred from direct assay
(Tuxworth et al., 2009)
located_in microvillus membrane
inferred from direct assay
(Mohammed et al., 2017)
located_in mitochondrial membrane
inferred from direct assay
(Mohammed et al., 2017)
located_in vesicle
inferred from direct assay
(Tuxworth et al., 2009)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\Cln3 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 ( 4 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 10 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Cln3
Transgenic constructs containing regulatory region of Cln3
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(3L)Exel9005
(Ryder, 2004.4.26)
Inferred from location ( 0 )
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
viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
viable, with Scer\GAL4Mef2.PR
viable, with Scer\GAL4pnr-MD237
viable, with Scer\GAL4tin.CΔ4
Sterility
Allele
fertile
Other Phenotypes
Allele
abnormal neuroanatomy | third instar larval stage
abnormal neuroanatomy | third instar larval stage, with Scer\GAL4VGlut-OK371
abnormal oxidative stress response, with Scer\GAL4Ilp2.215-3
abnormal oxidative stress response | recessive
abnormal size | adult stage, with Scer\GAL4GMR.PU
abnormal starvation stress response | female limited | recessive
increased cell death, with Scer\GAL4en-e16E
long lived, with Scer\GAL4Ilp2.215-3
short lived | recessive
visible, with Scer\GAL4en-e16E
visible, with Scer\GAL4GMR.PF
visible | adult stage, with Scer\GAL4GMR.PU
Phenotype manifest in
Allele
embryo | dorsal closure stage, with Scer\GAL4pnr-MD237
embryonic/larval neuromuscular junction | third instar larval stage
embryonic/larval neuromuscular junction | third instar larval stage, with Scer\GAL4VGlut-OK371
eye, with Scer\GAL4GMR.PF
eye, with Scer\GAL4GMR.PU
interommatidial bristle, with Scer\GAL4GMR.PU
NMJ bouton | third instar larval stage
NMJ bouton | third instar larval stage, with Scer\GAL4VGlut-OK371
ommatidium, with Scer\GAL4GMR.PF
ommatidium, with Scer\GAL4GMR.PU
wing blade, with Scer\GAL4en-e16E
wing disc, with Scer\GAL4en-e16E
wing margin, with Scer\GAL4en-e16E
wing vein, with Scer\GAL4en-e16E
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) (1)
Hsap\CLN3
12 of 14
Yes
Yes
2  
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) (1)
Rnor\Cln3
13 of 14
Yes
Yes
Mus musculus (laboratory mouse) (1)
Mmus\Cln3
12 of 14
Yes
Yes
Xenopus tropicalis (Western clawed frog) (2)
Xtro\cln3
8 of 13
Yes
Yes
Xtro\mis18bp1
1 of 13
No
Yes
Danio rerio (Zebrafish) (1)
Drer\cln3
13 of 14
Yes
Yes
Caenorhabditis elegans (Nematode, roundworm) (4)
Cele\cln-3.2
13 of 14
Yes
Yes
Cele\cln-3.3
13 of 14
Yes
Yes
Cele\cln-3.1
12 of 14
No
Yes
Cele\ril-2
1 of 14
No
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP003934
12 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\YHC3
12 of 13
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\btn1
11 of 12
Yes
Yes
Escherichia coli (enterobacterium) (0)
Other Organism Orthologs (via OrthoDB)
Data provided directly from OrthoDB:Cln3. 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 ( 1 )
Allele
Disease
Evidence
References
Cln3ΔMB1
model of  neuronal ceroid lipofuscinosis 1
CEA
(Wong et al., 2015)
Potential Models Based on Orthology ( 1 )
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?
CLN3; CLN3 lysosomal/endosomal transmembrane protein, battenin
12 of 14
607042
 
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
esyN Network Diagram
Interactions Browser
MIST Molecular Interaction Search Tool
Summary of Genetic Interactions
esyN Network Diagram
Show/hide secondary interactors 
(data from AllianceMine provided by esyN)
esyN Network Key:
Suppression
Enhancement
View in 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
Cln3
enhanceable
bol
(Tuxworth et al., 2011)
Cln3
enhanceable
bsk
(Tuxworth et al., 2009)
Cln3
suppressible
Cat
(Tuxworth et al., 2011)
Cln3
enhanceable
Cisd
(Jones et al., 2014)
Cln3
suppressible
flfl
(Tuxworth et al., 2011)
Cln3
suppressible
foxo
(Tuxworth et al., 2011)
Cln3
enhanceable
Hibch
(Llavero Hurtado et al., 2017)
Cln3
suppressible
Keap1
(Tuxworth et al., 2011)
Cln3
enhanceable
Mtpα
(Llavero Hurtado et al., 2017)
Cln3
suppressible
RagA-B
(Wong et al., 2015)
Cln3
suppressible
Rok
(Llavero Hurtado et al., 2017)
Cln3
suppressible
Sod1
(Tuxworth et al., 2011)
Cln3
enhanceable
tsu
(Tuxworth et al., 2009)
Starting gene(s)
Interaction type
Interacting gene(s)
Reference
foxo
enhanceable
Cln3
(Tuxworth et al., 2011)
hiw
suppressible
Cln3
(Wong et al., 2015)
Ppt1
suppressible
Cln3
(Jones et al., 2014)
Ppt1
enhanceable
Cln3
(Jones et al., 2014)
External Data
Linkouts
BioGRID - A database of protein and genetic interactions.
DroID - A comprehensive database of gene and protein interactions.
MIST (genetic) - An integrated Molecular Interaction Database
Pathways
Signaling Pathways (FlyBase)
Metabolic Pathways
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.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
3L
Recombination map
3-45
Cytogenetic map
75A2-75A2
Sequence location
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
75A2-75A2
Limits computationally determined from genome sequence between P{lacW}l(3)j11B2j11B2 and P{PZ}W05014
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
Experimentally Determined Recombination Data
Location

3-45

(FlyBase, 2016)

3-41.2

(Comeron et al., 2012)
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (6)
Genomic Clones (13)
 

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

cDNA Clones (39)
 

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

(Tuxworth et al., 2009)
Commercially Available Antibodies
 
Cell Line Information
Publicly Available Cell Lines
 
    Other Stable Cell Lines
     
      Other Comments

      dsRNA made from templates generated with primers directed against this gene tested in RNAi screen for effects on Kc167 and S2R+ cell morphology.

      (Kiger et al., 2003)
      Relationship to Other Genes
      Source for database merge of
      Additional comments
      Nomenclature History
      Source for database identify of

      Source for identity of: cln3 CG5582

      (Korey, 2005.3.2)

      Source for identity of: Cln3 cln3

      (Mohammed et al., 2017)
      Nomenclature comments
      Etymology

      Named 'Cln3' after the human ortholog.

      (Mohammed et al., 2017)
      Synonyms and Secondary IDs (5)
      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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
      EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
      FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
      FlyMine - An integrated database for Drosophila genomics
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      Flygut - An atlas of the Drosophila adult midgut
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      KEGG Pathways - A collection of manually drawn pathway maps representing knowledge of molecular interaction, reaction and relation networks.
      MIST (genetic) - An integrated Molecular Interaction Database
      Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
      References (51)