Aliases for SYT3 Gene

Aliases for SYT3 Gene

  • Synaptotagmin 3 2 3 5
  • Synaptotagmin III 2 3 4
  • Synaptotagmin-3 3 4
  • SytIII 3 4
  • SYT3 5

External Ids for SYT3 Gene

Previous GeneCards Identifiers for SYT3 Gene

  • GC19U990091
  • GC19M051486
  • GC19M055801
  • GC19M055817
  • GC19M051125
  • GC19M047460

Summaries for SYT3 Gene

GeneCards Summary for SYT3 Gene

SYT3 (Synaptotagmin 3) is a Protein Coding gene. Diseases associated with SYT3 include Foodborne Botulism and Deafness, Autosomal Recessive 9. Gene Ontology (GO) annotations related to this gene include calcium ion binding and syntaxin binding. An important paralog of this gene is SYT9.

UniProtKB/Swiss-Prot Summary for SYT3 Gene

  • Ca(2+) sensor involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain. Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003).

Gene Wiki entry for SYT3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYT3 Gene

Genomics for SYT3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SYT3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J050657 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 269.2 -19.0 -19023 3 ZSCAN16 TBP ZBTB10 SP1 MNT SMAD5 ETS1 IRF2 MBD2 BHLHE40 SYT3 lnc-SHANK1-3 POLD1 NUP62 PTOV1-AS2 ZNF175 IRF3 PNKP CTU1 CPT1C
GH19J050639 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 273.7 +0.1 108 1.3 ZBTB10 SIX5 ETS1 IRF2 ZNF217 ZEB1 THAP11 SIN3A ZNF395 ZNF740 SYT3 SHANK1 ENSG00000267890 CPT1C IGLON5 LRRC4B HSALNG0127120
GH19J050637 Promoter 0.6 EPDnew 255.8 +1.9 1916 0.1 GLIS1 ZNF366 ZNF24 SYT3 HSALNG0127120 LRRC4B
GH19J050329 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 20.3 +308.9 308880 7.2 TBP ZBTB10 SP1 MXD4 FEZF1 CEBPA SIX5 NR2C1 MNT IKZF1 KCNC3 NR1H2 HSALNG0127087 LOC105372437 lnc-POLD1-3 NUP62 PRR12 POLD1 CPT1C ENSG00000268047
GH19J049637 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 18.9 +999.2 999227 6.4 CHD2 TBP ZBTB10 SP1 CEBPA SIX5 NR2C1 MNT IKZF1 SMAD5 RRAS SCAF1 CPT1C CA11 SYT3 PRR12 ENSG00000267890 PPFIA3 SNRNP70 LRRC4B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYT3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYT3

Top Transcription factor binding sites by QIAGEN in the SYT3 gene promoter:
  • C/EBPalpha
  • E47
  • ER-alpha
  • MZF-1
  • NF-1
  • NF-1/L
  • Pax-4a
  • RORalpha1
  • Tal-1beta
  • ZIC2

Genomic Locations for SYT3 Gene

Latest Assembly
chr19:50,621,307-50,639,881
(GRCh38/hg38)
Size:
18,575 bases
Orientation:
Minus strand

Previous Assembly
chr19:51,125,234-51,143,138
(GRCh37/hg19 by Entrez Gene)
Size:
17,905 bases
Orientation:
Minus strand

chr19:51,124,564-51,171,651
(GRCh37/hg19 by Ensembl)
Size:
47,088 bases
Orientation:
Minus strand

Genomic View for SYT3 Gene

Genes around SYT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYT3 Gene

Proteins for SYT3 Gene

  • Protein details for SYT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BQG1-SYT3_HUMAN
    Recommended name:
    Synaptotagmin-3
    Protein Accession:
    Q9BQG1
    Secondary Accessions:
    • Q8N5Z1
    • Q8N640

    Protein attributes for SYT3 Gene

    Size:
    590 amino acids
    Molecular mass:
    63304 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    • Homodimer; disulfide-linked via the cysteine motif. Can also form heterodimers with SYT6, SYT9 and SYT10.

neXtProt entry for SYT3 Gene

Post-translational modifications for SYT3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYT3 Gene

No data available for DME Specific Peptides for SYT3 Gene

Domains & Families for SYT3 Gene

Gene Families for SYT3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SYT3 Gene

InterPro:
Blocks:
  • C2 domain
ProtoNet:

Suggested Antigen Peptide Sequences for SYT3 Gene

GenScript: Design optimal peptide antigens:
  • Synaptotagmin III (SYT3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BQG1

UniProtKB/Swiss-Prot:

SYT3_HUMAN :
  • The cysteine motif mediates homo- or heterodimer formation via formation of disulfide bonds.
  • Belongs to the synaptotagmin family.
Domain:
  • The cysteine motif mediates homo- or heterodimer formation via formation of disulfide bonds.
  • The first C2 domain mediates Ca(2+)-dependent phospholipid binding.
Family:
  • Belongs to the synaptotagmin family.
genes like me logo Genes that share domains with SYT3: view

Function for SYT3 Gene

Molecular function for SYT3 Gene

UniProtKB/Swiss-Prot Function:
Ca(2+) sensor involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain. Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis (By similarity). Plays a role in dendrite formation by melanocytes (PubMed:23999003).
GENATLAS Biochemistry:
synaptotagmin 3,multifunctional intrinsic membrane protein of synaptic vesicles and chromaffin granules,involved in exocytosis and endocytosis

Phenotypes From GWAS Catalog for SYT3 Gene

Gene Ontology (GO) - Molecular Function for SYT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IBA 21873635
GO:0001786 phosphatidylserine binding IBA 21873635
GO:0005509 calcium ion binding IBA 21873635
GO:0005515 protein binding IPI 32296183
GO:0005544 calcium-dependent phospholipid binding NAS 12526776
genes like me logo Genes that share ontologies with SYT3: view
genes like me logo Genes that share phenotypes with SYT3: view

Animal Models for SYT3 Gene

MGI Knock Outs for SYT3:

Animal Models for research

  • Taconic Biosciences Mouse Models for SYT3

miRNA for SYT3 Gene

miRTarBase miRNAs that target SYT3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYT3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SYT3 Gene

Localization for SYT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYT3 Gene

Cell membrane. Single-pass membrane protein. Cytoplasmic vesicle, secretory vesicle membrane. Single-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYT3 gene
Compartment Confidence
plasma membrane 4
endosome 4
cytosol 4
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
lysosome 2
golgi apparatus 2
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SYT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IDA --
GO:0005886 plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030658 transport vesicle membrane IEA --
genes like me logo Genes that share ontologies with SYT3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SYT3 Gene

Pathways & Interactions for SYT3 Gene

PathCards logo

SuperPathways for SYT3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SYT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0014059 regulation of dopamine secretion IBA 21873635
GO:0016192 vesicle-mediated transport IBA 21873635
GO:0017156 calcium ion regulated exocytosis IEA,IBA 21873635
GO:0017158 regulation of calcium ion-dependent exocytosis IBA 21873635
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with SYT3: view

No data available for Pathways by source and SIGNOR curated interactions for SYT3 Gene

Drugs & Compounds for SYT3 Gene

(2) Drugs for SYT3 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6876

(1) Additional Compounds for SYT3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with SYT3: view

Transcripts for SYT3 Gene

mRNA/cDNA for SYT3 Gene

3 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYT3

Alternative Splicing Database (ASD) splice patterns (SP) for SYT3 Gene

No ASD Table

Relevant External Links for SYT3 Gene

GeneLoc Exon Structure for
SYT3

Expression for SYT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYT3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYT3 Gene

This gene is overexpressed in Brain - Cortex (x6.0), Brain - Frontal Cortex (BA9) (x5.6), Brain - Anterior cingulate cortex (BA24) (x4.9), Brain - Cerebellum (x4.8), Brain - Hippocampus (x4.6), and Brain - Cerebellar Hemisphere (x4.5).

Protein differential expression in normal tissues from HIPED for SYT3 Gene

This gene is overexpressed in Frontal cortex (27.9), Fetal Brain (21.1), and Retina (20.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SYT3 Gene



Protein tissue co-expression partners for SYT3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYT3

SOURCE GeneReport for Unigene cluster for SYT3 Gene:

Hs.515554

mRNA Expression by UniProt/SwissProt for SYT3 Gene:

Q9BQG1-SYT3_HUMAN
Tissue specificity: Expressed in melanocytes (PubMed:23999003).

Evidence on tissue expression from TISSUES for SYT3 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with SYT3: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SYT3 Gene

Orthologs for SYT3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SYT3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SYT3 30 31
  • 99.38 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SYT3 30 31
  • 92.6 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SYT3 30 31
  • 92.49 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Syt3 30
  • 88 (n)
Mouse
(Mus musculus)
Mammalia Syt3 30 17 31
  • 87.75 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SYT3 31
  • 68 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SYT3 31
  • 70 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia syt3 30
  • 65.36 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC100000615 30
  • 65.55 (n)
syt3 31
  • 65 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Syt1 31
  • 34 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea snt-3 31
  • 44 (a)
ManyToMany
snt-2 31
  • 37 (a)
ManyToMany
snt-1 31
  • 35 (a)
ManyToMany
Species where no ortholog for SYT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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)
  • Oppossum (Monodelphis domestica)
  • 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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 SYT3 Gene

ENSEMBL:
Gene Tree for SYT3 (if available)
TreeFam:
Gene Tree for SYT3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYT3: view image

Paralogs for SYT3 Gene

(8) SIMAP similar genes for SYT3 Gene using alignment to 3 proteins:

  • SYT3_HUMAN
  • M0QY70_HUMAN
  • M0QYH4_HUMAN
genes like me logo Genes that share paralogs with SYT3: view

Variants for SYT3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYT3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs182688683 Benign: not provided 50,629,521(-) G/C
NM_001160329.2(SYT3):c.1063-9C>G
INTRON
rs188199665 Benign: not provided 50,630,170(-) A/G
NM_001160329.2(SYT3):c.676T>C (p.Tyr226His)
MISSENSE
VAR_036389 A breast cancer sample p.Ser474Phe

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SYT3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SYT3 Gene

Variant ID Type Subtype PubMed ID
dgv1800n106 CNV deletion 24896259
esv1000559 CNV deletion 20482838
esv1217472 CNV insertion 17803354
esv1394478 CNV deletion 17803354
esv1959087 CNV deletion 18987734
esv2718743 CNV deletion 23290073
esv32592 CNV gain 17666407
esv33599 CNV loss 17666407
esv3574587 CNV gain 25503493
nsv1065222 CNV loss 25217958
nsv1140251 OTHER inversion 24896259
nsv1148092 CNV deletion 26484159
nsv828582 CNV loss 20364138
nsv828583 CNV loss 20364138
nsv828584 CNV loss 20364138
nsv961234 CNV duplication 23825009

Variation tolerance for SYT3 Gene

Residual Variation Intolerance Score: 6.82% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.27; 25.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYT3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYT3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYT3 Gene

Disorders for SYT3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SYT3 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search SYT3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYT3

genes like me logo Genes that share disorders with SYT3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYT3 Gene

Publications for SYT3 Gene

  1. SYT14L, especially its C2 domain, is involved in regulating melanocyte differentiation. (PMID: 23999003) Yoo JC … Yoon TJ (Journal of dermatological science 2013) 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4
  4. Synaptotagmin genes on mouse chromosomes 1, 7, and 10 and human chromosome 19. (PMID: 7749232) Jones JM … Meisler MH (Mammalian genome : official journal of the International Mammalian Genome Society 1995) 2 3
  5. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. (PMID: 32814053) Haenig C … Wanker EE (Cell reports 2020) 3

Products for SYT3 Gene

Sources for SYT3 Gene