FB2026_01 , released March 12, 2026
FB2026_01 , released March 12, 2026
Gene: Dmel\Cals
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General Information
Symbol
Dmel\Cals
Species
D. melanogaster
Name
Calsyntenin
Annotation Symbol
CG11059
Feature Type
protein_coding_gene
FlyBase ID
FBgn0039928
Gene Model Status
Current
Stock Availability
13 publicly available
Gene Summary
Postsynaptic adhesion molecule that binds to presynaptic neurexins to mediate both excitatory and inhibitory synapse formation (By similarity). Promotes synapse development by acting as a cell adhesion molecule at the postsynaptic membrane, which associates with neurexin-alpha at the presynaptic membrane (By similarity). (UniProt, Q9V498)
Contribute a Gene Snapshot for this gene.
All Summaries
Also Known As

Calsyntenin-1

Key Links
Genomic Location
Cytogenetic map
102F8-102F8
Sequence location
Recombination map
4-0
RefSeq locus
NC_004353 REGION:1112874..1123357
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
Function
Gene Ontology (GO) Annotations (13 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables calcium ion binding
inferred from electronic annotation with InterPro:IPR002126, InterPro:IPR015919
(InterPro Project Members, 2004-)
inferred from sequence model
(Hill et al., 2001)
enables cell-cell adhesion mediator activity
inferred from biological aspect of ancestor with PANTHER:PTN001020450
(GO Reference Genome Project, 2011-)
Biological Process (5 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
involved_in calcium-dependent cell-cell adhesion
traceable author statement
(Hynes and Zhao, 2000)
involved_in cell-cell adhesion mediated by cadherin
inferred from sequence model
(Hill et al., 2001)
involved_in homophilic cell-cell adhesion
inferred from biological aspect of ancestor with PANTHER:PTN001020450
(GO Reference Genome Project, 2011-)
inferred from electronic annotation with InterPro:IPR002126
(InterPro Project Members, 2004-)
involved_in positive regulation of synapse assembly
inferred from biological aspect of ancestor with PANTHER:PTN001020450
(GO Reference Genome Project, 2011-)
involved_in positive regulation of synaptic transmission
inferred from biological aspect of ancestor with PANTHER:PTN001020450
(GO Reference Genome Project, 2011-)
Cellular Component (6 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (6 terms)
CV Term
Evidence
References
is_active_in cell surface
inferred from biological aspect of ancestor with PANTHER:PTN001020450
(GO Reference Genome Project, 2011-)
located_in extracellular region
inferred from sequence or structural similarity with UniProtKB:Q9EPL2
(Vogt et al., 2001)
located_in membrane
inferred from electronic annotation with InterPro:IPR002126, InterPro:IPR015919
(InterPro Project Members, 2004-)
located_in plasma membrane
traceable author statement
(Hynes and Zhao, 2000)
is_active_in postsynaptic density membrane
inferred from biological aspect of ancestor with PANTHER:PTN001020450
(GO Reference Genome Project, 2011-)
located_in postsynaptic membrane
inferred from sequence or structural similarity with UniProtKB:Q9EPL2
(Vogt et al., 2001)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the calsyntenin family. (Q9V498)
Protein Signatures (InterPro)
Summaries
Gene Group (FlyBase)
CADHERINS -
The cadherin superfamily represent a diverse group of transmembrane receptors which mediate cell-cell adhesion. Cadherins are defined by the presence of cadherin domains, typically organised in tandem repeats, which mediate calcium-dependent homophilic interactions between cadherin molecules. (Adapted from FBrf0146675).
Protein Function (UniProtKB)
Postsynaptic adhesion molecule that binds to presynaptic neurexins to mediate both excitatory and inhibitory synapse formation (By similarity). Promotes synapse development by acting as a cell adhesion molecule at the postsynaptic membrane, which associates with neurexin-alpha at the presynaptic membrane (By similarity).
(UniProt, Q9V498)
Gene Model and Products
Number of Transcripts
4
Number of Unique Polypeptides
2

Please see the JBrowse view of Dmel\Cals 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 Q9V498)

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.

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Gene model reviewed during 5.46

Gene model reviewed during 5.55

Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Cals-RA
FBtr0089207
NM_079893
3693
978
Cals-RB
FBtr0089208
NM_166823
3872
978
Cals-RC
FBtr0333700
NM_001272157
3696
979
Cals-RD
FBtr0345193
NM_001297793
6077
978
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
Cals-PA
FBpp0088271
110.5
978
5.48
Q9V498
NP_524632
AAF59384
Cals-PB
FBpp0088272
110.5
978
5.48
Q9V498
NP_726646
AAN06580
Cals-PC
FBpp0305853
110.6
979
5.48
L0MQ08
NP_001259086
AGB96576
Cals-PD
FBpp0311392
110.5
978
5.48
Q9V498
NP_001284722
AHN58223
Polypeptides with Identical Sequences

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

978 aa isoforms: Cals-PA, Cals-PB, Cals-PD
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Domain

The cytoplasmic domain binds synaptic Ca(2+).

(UniProt, Q9V498)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

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

-1.06

Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | ubiquitous
(Fisher et al., 2012)
oogenesis stage S7 -- S9
border follicle cell
(Zartman et al., 2009)
oogenesis stage S7 -- S10A
main body follicle cell
(Zartman et al., 2009)
oogenesis stage S10B -- S14
main body follicle cell | restricted

Comment: dorsal and midline regions

(Zartman et al., 2009)
oogenesis stage S11 -- S13
polar follicle cell
(Zartman et al., 2009)
Additional Descriptive Data

Cals is expressed in the oocyte associated follicle cells and the border cells during oogenesis stage S7-9. Expression is uniform during stage 10A but becomes restricted to the dorsal region in stage S10B with stronger expression in the midline in stage S11/12. Expression is detected in the polar follicle cells in later stages.

(Zartman et al., 2009)
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 5 of adulthood | male -- day 7 of adulthood | male
spermatozoon
(Wasbrough et al., 2010)
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\Cals 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 ( 10 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 8 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Cals
Transgenic constructs containing regulatory region of Cals
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene disrupted in
Df(4)G
(Podemski et al., 2004)
Inferred from location ( 4 )
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
short lived | heat sensitive, with Scer\GAL4tin.CΔ4
Phenotype manifest in
Allele
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) (5)
Hsap\CLSTN2
14 of 14
Yes
Yes
1  
Hsap\CLSTN1
13 of 14
No
Yes
Hsap\CLSTN3
13 of 14
No
Yes
Hsap\FAT2
1 of 14
No
No
Hsap\PCDHB8
1 of 14
No
Yes
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) (3)
Rnor\Clstn1
13 of 14
Yes
Yes
Rnor\Clstn2
13 of 14
Yes
Yes
Rnor\Clstn3
13 of 14
Yes
Yes
Mus musculus (laboratory mouse) (3)
Mmus\Clstn2
14 of 14
Yes
Yes
Mmus\Clstn3
13 of 14
No
Yes
Mmus\Clstn1
12 of 14
No
Yes
Xenopus tropicalis (Western clawed frog) (4)
Xtro\clstn1
9 of 13
Yes
Yes
Xtro\clstn2
8 of 13
No
Yes
Xtro\clstn3
7 of 13
No
Yes
Xtro\npffr1.1
1 of 13
No
No
Danio rerio (Zebrafish) (4)
Drer\clstn2a
14 of 14
Yes
Yes
Drer\clstn1
13 of 14
No
Yes
Drer\clstn2b
12 of 14
No
Yes
Drer\clstn3
12 of 14
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\casy-1
12 of 14
Yes
Yes
Anopheles gambiae (African malaria mosquito) (1)
Agam\AgaP_AGAP007103
11 of 12
Yes
Yes
Arabidopsis thaliana (thale-cress) (0)
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:Cals. 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 ( 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?
    CLSTN2; calsyntenin 2
    14 of 14
    611323
         
        CLSTN1; calsyntenin 1
        13 of 14
        611321
            CLSTN3; calsyntenin 3
            13 of 14
            611324
                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
                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
                Linkouts
                DroID - A comprehensive database of gene and protein interactions.
                Pathways
                Signaling Pathways (FlyBase)
                Metabolic Pathways
                FlyBase
                External Links
                External Data
                Linkouts
                Class of Gene
                Genomic Location and Detailed Mapping Data
                Chromosome (arm)
                4
                Recombination map
                4-0
                Cytogenetic map
                102F8-102F8
                Sequence location
                FlyBase Computed Cytological Location
                Cytogenetic map
                Evidence for location
                102F8-102F8
                Experimentally Determined Cytological Location
                Cytogenetic map
                Notes
                References
                Experimentally Determined Recombination Data
                Location

                4-0

                (FlyBase, 2016)
                Left of (cM)
                Right of (cM)
                Notes
                Stocks and Reagents
                Stocks (13)
                Genomic Clones (9)
                 

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

                cDNA Clones (272)
                 

                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

                      dsRNA made from templates generated with primers directed against this gene was tested in an RNAi screen to identify genes that regulate Ca2+ release.

                      (Zhang et al., 2006)
                      Relationship to Other Genes
                      Source for database merge of
                      Additional comments

                      Source for identity of calsyntenin-1 CG11059 was sequence comparison ( date:001216 ).

                      (FlyBase, 1996-)
                      Nomenclature History
                      Source for database identify of

                      Source for identity of: calsyntenin-1 CG11059

                      (FlyBase, 1996-)

                      Source for identity of: Cals cals

                      (FlyBase, 2009-)
                      Nomenclature comments
                      Etymology
                      Synonyms and Secondary IDs (14)
                      Datasets (0)
                      Study focus (0)
                      Experimental Role
                      Project
                      Project Type
                      Title
                      Study result (0)
                      Result
                      Result Type
                      Title
                      External Crossreferences and Linkouts ( 50 )
                      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
                      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
                      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)
                      References (66)