Aliases for ESYT3 Gene

Aliases for ESYT3 Gene

  • Extended Synaptotagmin 3 2 3 5
  • Family With Sequence Similarity 62 (C2 Domain Containing), Member C 2 3
  • Extended Synaptotagmin-3 3 4
  • CHR3SYT 2 3
  • E-Syt3 3 4
  • FAM62C 3 4
  • Extended Synaptotagmin-Like Protein 3 2
  • Extended Synaptotagmin Protein 3 3
  • Chr3 Synaptotagmin 3
  • Chr3Syt 4
  • ESYT3 5

External Ids for ESYT3 Gene

Previous HGNC Symbols for ESYT3 Gene

  • FAM62C

Previous GeneCards Identifiers for ESYT3 Gene

  • GC03P139638
  • GC03P138153
  • GC03P135528

Summaries for ESYT3 Gene

GeneCards Summary for ESYT3 Gene

ESYT3 (Extended Synaptotagmin 3) is a Protein Coding gene. Among its related pathways are Sphingolipid metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include lipid binding and phospholipid binding. An important paralog of this gene is ESYT2.

UniProtKB/Swiss-Prot Summary for ESYT3 Gene

  • Binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport (By similarity). Tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ESYT3 Gene

Genomics for ESYT3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ESYT3 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
GH03J138434 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 250.7 +0.2 224 2 KLF9 MXD4 KLF11 MAX ZNF217 KMT2B THAP11 HES1 ELF1 FOXA2 ESYT3 HSALNG0029266 MRAS CEP70
GH03J138410 Enhancer 0.8 ENCODE dbSUPER 7.5 -22.1 -22127 3.7 BHLHE40 MNT FOSL2 RELA SMARCA4 ETV1 L3MBTL2 IKZF1 ZNF507 ATF3 HSALNG0029265 NME9 MRAS DBR1 ESYT3 LOC105374129
GH03J138440 Enhancer 0.9 Ensembl ENCODE 5.1 +8.0 8018 5.6 MYC IKZF1 NCOR1 JUND CUX1 TAL1 FOSL2 STAT5A PKNOX1 FOXM1 MRAS ESYT3 HSALNG0029266 HSALNG0029269 CEP70
GH03J138469 Enhancer 0.5 Ensembl ENCODE 5.3 +34.5 34524 1 PKNOX1 ZNF335 HSALNG0029269 HSALNG0029270 FAIM ESYT3 CEP70
GH03J138381 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 1.5 -45.5 -45476 17 NCOR1 JUND CEBPA ZIC2 YY1 MXD4 CEBPB MAX EP300 THAP11 MRAS NME9 ESYT3 AB372650-002 piR-32850
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ESYT3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ESYT3

Genomic Locations for ESYT3 Gene

Latest Assembly
chr3:138,434,577-138,481,686
(GRCh38/hg38)
Size:
47,110 bases
Orientation:
Plus strand

Previous Assembly
chr3:138,153,458-138,200,528
(GRCh37/hg19 by Entrez Gene)
Size:
47,071 bases
Orientation:
Plus strand

chr3:138,153,428-138,200,528
(GRCh37/hg19 by Ensembl)
Size:
47,101 bases
Orientation:
Plus strand

Genomic View for ESYT3 Gene

Genes around ESYT3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ESYT3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ESYT3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ESYT3 Gene

Proteins for ESYT3 Gene

  • Protein details for ESYT3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A0FGR9-ESYT3_HUMAN
    Recommended name:
    Extended synaptotagmin-3
    Protein Accession:
    A0FGR9
    Secondary Accessions:
    • A8K0G5
    • Q6ZV21
    • Q8NDZ5
    • Q9BQR9

    Protein attributes for ESYT3 Gene

    Size:
    886 amino acids
    Molecular mass:
    100035 Da
    Quaternary structure:
    • Interacts with ESYT1 and ESYT2.

    Alternative splice isoforms for ESYT3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ESYT3 Gene

Post-translational modifications for ESYT3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ESYT3 Gene

No data available for DME Specific Peptides for ESYT3 Gene

Domains & Families for ESYT3 Gene

Gene Families for ESYT3 Gene

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

Suggested Antigen Peptide Sequences for ESYT3 Gene

GenScript: Design optimal peptide antigens:
  • Chr3Syt (ESYT3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A0FGR9

UniProtKB/Swiss-Prot:

ESYT3_HUMAN :
  • Anchored to the endoplasmic reticulum membrane by a transmembrane hairpin structure; both N-terminus and C-terminus are cytoplasmic.
  • Belongs to the extended synaptotagmin family.
Domain:
  • Anchored to the endoplasmic reticulum membrane by a transmembrane hairpin structure; both N-terminus and C-terminus are cytoplasmic.
  • The C2 domains mediate lipid and calcium binding. The N-terminal C2 domain binds calcium ions and is important for calcium-dependent lipid binding and interaction with membranes. Two calcium ions are bound at a high-affinity site and a third calcium ion is bound with lower affinity. May bind up to four calcium ions. In contrast, the second C2 domain apparently does not bind calcium (By similarity). The third C2 domain mediates interaction with membranes enriched in phosphatidylinositol 4,5-bisphosphate and is required for location at the cell membrane (PubMed:23791178).
  • The SMP-LTD domain is a barrel-like domain that binds glycerophospholipids in its interior (By similarity).
Family:
  • Belongs to the extended synaptotagmin family.
genes like me logo Genes that share domains with ESYT3: view

Function for ESYT3 Gene

Molecular function for ESYT3 Gene

UniProtKB/Swiss-Prot Function:
Binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport (By similarity). Tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane.

Phenotypes From GWAS Catalog for ESYT3 Gene

Gene Ontology (GO) - Molecular Function for ESYT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IBA 21873635
GO:0005515 protein binding IPI 23791178
GO:0005544 calcium-dependent phospholipid binding IBA 21873635
GO:0008289 lipid binding IEA --
GO:0008429 phosphatidylethanolamine binding IBA 21873635
genes like me logo Genes that share ontologies with ESYT3: view
genes like me logo Genes that share phenotypes with ESYT3: view

Animal Models for ESYT3 Gene

MGI Knock Outs for ESYT3:
  • Esyt3 Esyt3<tm1d(EUCOMM)Wtsi>
  • Esyt3 Esyt3<tm1b(EUCOMM)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ESYT3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for ESYT3 Gene

Localization for ESYT3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ESYT3 Gene

Cell membrane. Peripheral membrane protein. Endoplasmic reticulum membrane. Multi-pass membrane protein. Note=Localizes to endoplasmic reticulum-plasma membrane contact sites (EPCS) (PubMed:29469807, PubMed:30220461). Recruited to the cell membrane via the third C2 domain. {ECO:0000269 PubMed:17360437, ECO:0000269 PubMed:29469807, ECO:0000269 PubMed:30220461}.

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 ESYT3 gene
Compartment Confidence
plasma membrane 5
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
golgi apparatus 2
extracellular 1
cytoskeleton 1
peroxisome 1
endosome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for ESYT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IDA 17360437
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with ESYT3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ESYT3 Gene

Pathways & Interactions for ESYT3 Gene

genes like me logo Genes that share pathways with ESYT3: view

Pathways by source for ESYT3 Gene

Gene Ontology (GO) - Biological Process for ESYT3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006687 glycosphingolipid metabolic process TAS --
GO:0006869 lipid transport IEA --
GO:0061817 endoplasmic reticulum-plasma membrane tethering IEA --
genes like me logo Genes that share ontologies with ESYT3: view

No data available for SIGNOR curated interactions for ESYT3 Gene

Drugs & Compounds for ESYT3 Gene

(1) Drugs for ESYT3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6959
genes like me logo Genes that share compounds with ESYT3: view

Transcripts for ESYT3 Gene

mRNA/cDNA for ESYT3 Gene

3 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
7 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 ESYT3

Alternative Splicing Database (ASD) splice patterns (SP) for ESYT3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17 ^ 18a · 18b ^ 19a · 19b ^ 20 ^ 21 ^ 22 ^
SP1: - -
SP2: - - - -
SP3:
SP4:

ExUns: 23
SP1:
SP2:
SP3:
SP4:

Relevant External Links for ESYT3 Gene

GeneLoc Exon Structure for
ESYT3

Expression for ESYT3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ESYT3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ESYT3 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x5.0), Brain - Cerebellum (x4.8), and Skin - Sun Exposed (Lower leg) (x4.3).

Protein differential expression in normal tissues from HIPED for ESYT3 Gene

This gene is overexpressed in Frontal cortex (66.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ESYT3 Gene



Protein tissue co-expression partners for ESYT3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ESYT3

SOURCE GeneReport for Unigene cluster for ESYT3 Gene:

Hs.477711

mRNA Expression by UniProt/SwissProt for ESYT3 Gene:

A0FGR9-ESYT3_HUMAN
Tissue specificity: Widely expressed with high level in cerebellum and skin.

Evidence on tissue expression from TISSUES for ESYT3 Gene

  • Nervous system(4.4)
  • Intestine(4.1)
genes like me logo Genes that share expression patterns with ESYT3: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for ESYT3 Gene

Orthologs for ESYT3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for ESYT3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ESYT3 29 30
  • 99.32 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ESYT3 29 30
  • 90.5 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ESYT3 29 30
  • 88.7 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Esyt3 29 16 30
  • 85.25 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Esyt3 29
  • 84.93 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia ESYT3 30
  • 83 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ESYT3 30
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves FAM62C 29
  • 61.93 (n)
ESYT3 30
  • 55 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ESYT3 30
  • 48 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia esyt3 29
  • 60.86 (n)
Str.16348 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.10001 29
Zebrafish
(Danio rerio)
Actinopterygii esyt3 29 30
  • 53.15 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Esyt2 30
  • 26 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea esyt-2 30
  • 30 (a)
OneToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons NTMC2T2.1 29
  • 43.17 (n)
Rice
(Oryza sativa)
Liliopsida Os08g0300200 29
  • 43.05 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 30 (a)
OneToMany
Species where no ortholog for ESYT3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for ESYT3 Gene

ENSEMBL:
Gene Tree for ESYT3 (if available)
TreeFam:
Gene Tree for ESYT3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ESYT3: view image
Alliance of Genome Resources:
Additional Orthologs for ESYT3

Paralogs for ESYT3 Gene

Paralogs for ESYT3 Gene

(3) SIMAP similar genes for ESYT3 Gene using alignment to 2 proteins:

  • ESYT3_HUMAN
  • H7BXJ6_HUMAN
genes like me logo Genes that share paralogs with ESYT3: view

Variants for ESYT3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ESYT3 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs10935282 -- p.Gly590Arg
rs17857138 -- p.Pro246Gln
rs35537868 -- p.Thr662Ser
rs6772467 -- p.Gly416Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ESYT3 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 ESYT3 Gene

Variant ID Type Subtype PubMed ID
esv3302999 CNV tandem duplication 20981092
esv3350188 CNV duplication 20981092
esv3597914 CNV loss 21293372
esv3597915 CNV loss 21293372
nsv428422 CNV gain+loss 18775914
nsv522517 CNV loss 19592680
nsv591853 CNV loss 21841781
nsv999041 CNV gain 25217958

Variation tolerance for ESYT3 Gene

Residual Variation Intolerance Score: 98.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.49; 96.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ESYT3 Gene

Human Gene Mutation Database (HGMD)
ESYT3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ESYT3
Leiden Open Variation Database (LOVD)
ESYT3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ESYT3 Gene

Disorders for ESYT3 Gene

Additional Disease Information for ESYT3

No disorders were found for ESYT3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ESYT3 Gene

Publications for ESYT3 Gene

  1. Genomic analysis of synaptotagmin genes. (PMID: 11543631) Craxton M (Genomics 2001) 2 3 4
  2. Aster Proteins Facilitate Nonvesicular Plasma Membrane to ER Cholesterol Transport in Mammalian Cells. (PMID: 30220461) Sandhu J … Tontonoz P (Cell 2018) 3 4
  3. PI(4,5)P(2)-dependent and Ca(2+)-regulated ER-PM interactions mediated by the extended synaptotagmins. (PMID: 23791178) Giordano F … De Camilli P (Cell 2013) 3 4
  4. E-Syts, a family of membranous Ca2+-sensor proteins with multiple C2 domains. (PMID: 17360437) Min SW … Südhof TC (Proceedings of the National Academy of Sciences of the United States of America 2007) 3 4
  5. Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans. (PMID: 17672888) Craxton M (BMC genomics 2007) 2 3

Products for ESYT3 Gene

Sources for ESYT3 Gene