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Aliases for CLSTN3 Gene

Aliases for CLSTN3 Gene

  • Calsyntenin 3 2 3
  • Cadherin-Related Family Member 14 2 3
  • Alcadein-Beta 3 4
  • Alc-Beta 3 4
  • KIAA0726 4 6
  • Alcadein Beta 3
  • Calsyntenin-3 3
  • Alcbeta 3
  • CDHR14 3
  • CSTN3 3
  • CS3 4

External Ids for CLSTN3 Gene

Previous GeneCards Identifiers for CLSTN3 Gene

  • GC12P007242
  • GC12P007418
  • GC12P007174
  • GC12P007282
  • GC12P007095

Summaries for CLSTN3 Gene

GeneCards Summary for CLSTN3 Gene

CLSTN3 (Calsyntenin 3) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is CLSTN2.

UniProtKB/Swiss-Prot for CLSTN3 Gene

  • May modulate calcium-mediated postsynaptic signals. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLSTN3 Gene

Genomics for CLSTN3 Gene

Regulatory Elements for CLSTN3 Gene

Genomic Location for CLSTN3 Gene

7,129,698 bp from pter
7,158,945 bp from pter
29,248 bases
Plus strand

Genomic View for CLSTN3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLSTN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLSTN3 Gene

Proteins for CLSTN3 Gene

  • Protein details for CLSTN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • D3DUT6
    • O94831
    • Q2T9J5
    • Q5UE57

    Protein attributes for CLSTN3 Gene

    956 amino acids
    Molecular mass:
    106098 Da
    Quaternary structure:
    • Directly interacts with APBA2. Forms a tripartite complex with APBA2 and APP. Interacts with low affinity with KLC1 (By similarity).
    • Sequence=BAA34446.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for CLSTN3 Gene


neXtProt entry for CLSTN3 Gene

Proteomics data for CLSTN3 Gene at MOPED

Post-translational modifications for CLSTN3 Gene

  • Proteolytically processed under normal cellular conditions. A primary zeta-cleavage generates a large extracellular (soluble) N-terminal domain (sAlc) and a short C-terminal transmembrane fragment (CTF1). A secondary cleavage catalyzed by gamma-secretase within the transmembrane domain releases the beta-Alc-beta chain in the extracellular milieu and produces an intracellular fragment (AlcICD). This processing is strongly suppressed in the tripartite complex formed with APBA2 and APP, which seems to prevent the association with gamma-secretase (By similarity).
  • Glycosylation at Asn299, Asn327, Asn347, Asn507, Thr691, Thr693, and Asn740
  • Modification sites at PhosphoSitePlus

Other Protein References for CLSTN3 Gene

Antibody Products

  • R&D Systems Antibodies for CLSTN3 (Calsyntenin-3)

No data available for DME Specific Peptides for CLSTN3 Gene

Domains for CLSTN3 Gene

Gene Families for CLSTN3 Gene

  • CDHR :Cadherins / Cadherin-related

Protein Domains for CLSTN3 Gene

Suggested Antigen Peptide Sequences for CLSTN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Q9BQT9
  • Binds synaptic Ca(2+) with its cytoplasmic domain.
  • Contains 2 cadherin domains.
genes like me logo Genes that share domains with CLSTN3: view

Function for CLSTN3 Gene

Molecular function for CLSTN3 Gene

UniProtKB/Swiss-Prot Function:
May modulate calcium-mediated postsynaptic signals. Complex formation with APBA2 and APP, stabilizes APP metabolism and enhances APBA2-mediated suppression of beta-APP40 secretion, due to the retardation of intracellular APP maturation.

Gene Ontology (GO) - Molecular Function for CLSTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with CLSTN3: view
genes like me logo Genes that share phenotypes with CLSTN3: view

Animal Models for CLSTN3 Gene

MGI Knock Outs for CLSTN3:

Animal Model Products

miRNA for CLSTN3 Gene

miRTarBase miRNAs that target CLSTN3

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for CLSTN3 Gene

Localization for CLSTN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLSTN3 Gene

Cell membrane; Single-pass type I membrane protein. Endoplasmic reticulum membrane. Golgi apparatus membrane. Note=Most prominent in the postsynaptic specializations of asymmetric (type I) synapses with both axodendritic and axospinous localization. {ECO:0000250}.

Subcellular locations from

Jensen Localization Image for CLSTN3 Gene COMPARTMENTS Subcellular localization image for CLSTN3 gene
Compartment Confidence
endoplasmic reticulum 5
golgi apparatus 5
plasma membrane 5
extracellular 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLSTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005783 endoplasmic reticulum --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005794 Golgi apparatus --
GO:0016020 membrane --
genes like me logo Genes that share ontologies with CLSTN3: view

Pathways for CLSTN3 Gene

SuperPathways for CLSTN3 Gene

No Data Available

Interacting Proteins for CLSTN3 Gene

Gene Ontology (GO) - Biological Process for CLSTN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007416 synapse assembly IEA --
GO:0035249 synaptic transmission, glutamatergic IEA --
GO:0051932 synaptic transmission, GABAergic IEA --
genes like me logo Genes that share ontologies with CLSTN3: view

No data available for Pathways by source for CLSTN3 Gene

Compounds for CLSTN3 Gene

(1) HMDB Compounds for CLSTN3 Gene

Compound Synonyms Cas Number PubMed IDs
  • Ca
genes like me logo Genes that share compounds with CLSTN3: view

Transcripts for CLSTN3 Gene

Unigene Clusters for CLSTN3 Gene

Calsyntenin 3:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLSTN3

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLSTN3 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c · 9d ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^
SP1: - - - - - - - - -
SP2: - - -
SP4: - - - - - - - - - - -
SP5: - - - - - -
SP6: - - - - -
SP7: - - - -
SP8: - - -
SP11: - - - - - - -

ExUns: 17 ^ 18a · 18b ^ 19 ^ 20 ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24a · 24b ^ 25a · 25b · 25c · 25d
SP1: - - - -
SP2: - - - -
SP10: -

Relevant External Links for CLSTN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLSTN3 Gene

mRNA expression in normal human tissues for CLSTN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues for CLSTN3 Gene

This gene is overexpressed in Amniocyte (29.0), Urine (15.2), Vitreous humor (10.3), and Fetal Brain (8.8).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLSTN3 Gene

SOURCE GeneReport for Unigene cluster for CLSTN3 Gene Hs.535378

mRNA Expression by UniProt/SwissProt for CLSTN3 Gene

Tissue specificity: According to PubMed:12498782, expressed predominantly in the brain and in kidney. Low levels in heart, skeletal muscle, liver, placenta, pancreas and lung. According to PubMed:12972431, predominant expression in brain, and only marginal in kidney. In brain, present throughout all cortical layers, highest levels in GABAergic neurons (based on morphology and distribution pattern).
genes like me logo Genes that share expressions with CLSTN3: view

Expression partners for CLSTN3 Gene

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for CLSTN3 Gene

Orthologs for CLSTN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLSTN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CLSTN3 35
  • 92.08 (n)
  • 97.23 (a)
  • 97 (a)
(Canis familiaris)
Mammalia CLSTN3 35
  • 92.45 (n)
  • 97.45 (a)
  • 97 (a)
(Mus musculus)
Mammalia Clstn3 35
  • 89.99 (n)
  • 96.17 (a)
Clstn3 16
Clstn3 36
  • 96 (a)
(Pan troglodytes)
Mammalia CLSTN3 35
  • 98.14 (n)
  • 98.32 (a)
  • 99 (a)
(Rattus norvegicus)
Mammalia Clstn3 35
  • 90.24 (n)
  • 95.85 (a)
(Monodelphis domestica)
Mammalia CLSTN3 36
  • 93 (a)
(Ornithorhynchus anatinus)
Mammalia CLSTN3 36
  • 69 (a)
(Gallus gallus)
Aves CLSTN3 35
  • 77.28 (n)
  • 84.03 (a)
  • 77 (a)
(Anolis carolinensis)
Reptilia CLSTN3 36
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100036725 35
  • 65.36 (n)
  • 65.47 (a)
Str.13295 35
(Danio rerio)
Actinopterygii clstn3 35
  • 65.46 (n)
  • 64.11 (a)
clstn3 36
  • 60 (a)
fruit fly
(Drosophila melanogaster)
Insecta calsyntenin-1 37
  • 27 (a)
cals 36
  • 26 (a)
(Caenorhabditis elegans)
Secernentea casy-1 36
  • 24 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 35 (a)
-- 36
  • 23 (a)
Species with no ortholog for CLSTN3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CLSTN3 Gene

Gene Tree for CLSTN3 (if available)
Gene Tree for CLSTN3 (if available)

Paralogs for CLSTN3 Gene

Paralogs for CLSTN3 Gene

Selected SIMAP similar genes for CLSTN3 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with CLSTN3: view

Variants for CLSTN3 Gene

Sequence variations from dbSNP and Humsavar for CLSTN3 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type MAF
rs1470725 -- 7,159,293(+) GGGCG(G/T)CCCCA downstream-variant-500B
rs1801869 -- 7,158,912(+) CTAGG(C/G)TTTTC utr-variant-3-prime
rs1868798 -- 7,131,485(+) GAGGG(A/G)ATGGA intron-variant, utr-variant-5-prime
rs2167285 -- 7,131,705(+) TTCCA(C/T)CGCTC intron-variant, utr-variant-5-prime
rs2278821 -- 7,132,339(+) GGCCA(A/G)CCCGA intron-variant, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for CLSTN3 Gene

Variant ID Type Subtype PubMed ID
nsv818882 CNV Gain 17921354
nsv832325 CNV Gain+Loss 17160897

Relevant External Links for CLSTN3 Gene

HapMap Linkage Disequilibrium report

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLSTN3 Gene

Disorders for CLSTN3 Gene

No disorders were found for CLSTN3 Gene.

No data available for MalaCards , OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES , Novoseek inferred disease relationships , Genatlas and External Links for CLSTN3 Gene

Publications for CLSTN3 Gene

  1. The calsyntenins - a family of postsynaptic membrane proteins with distinct neuronal expression patterns. (PMID: 12498782) Hintsch G. … Sonderegger P. (Mol. Cell. Neurosci. 2002) 2 3 4
  2. Novel cadherin-related membrane proteins, Alcadeins, enhance the X11- like protein-mediated stabilization of amyloid beta-protein precursor metabolism. (PMID: 12972431) Araki Y. … Suzuki T. (J. Biol. Chem. 2003) 3 4
  3. Coordinated metabolism of Alcadein and amyloid beta-protein precursor regulates FE65-dependent gene transactivation. (PMID: 15037614) Araki Y. … Suzuki T. (J. Biol. Chem. 2004) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  5. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9872452) Nagase T. … Ohara O. (DNA Res. 1998) 3 4

Products for CLSTN3 Gene

Sources for CLSTN3 Gene

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