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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SYT3 Gene

protein-coding   GIFtS: 49
GCID: GC19M051125

synaptotagmin III

 Explore 3 diseases affiliated with
SYT3 via our new
 Human Malady Compendium 
Biological research products
for SYT3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Synaptotagmin III1 2 3
SytIII2 3
Synaptotagmin-31

External Ids:    HGNC: 115111   Entrez Gene: 842582   Ensembl: ENSG000002130237   OMIM: 6003275   UniProtKB: Q9BQG13   

Export aliases for SYT3 gene to outside databases

Previous GC identifers: GC19U990091 GC19M051486 GC19M055801 GC19M055817 GC19M047460


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: SYT3_HUMAN, Q9BQG1
Function: May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding
to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis (By similarity)

Gene Wiki entry for SYT3


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.1  NT_011109.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SYT3 gene promoter:
         ER-alpha   NF-1/L   NF-1   Tal-1beta   C/EBPalpha   E47   RORalpha1   MZF-1   ZIC2/Zic2   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSYT3 promoter sequence
   Search SABiosciences Chromatin IP Primers for SYT3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SYT3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.33   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.41

SYT3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SYT3 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M051125:  view genomic region     (about GC identifiers)

Start:
51,125,234 bp from pter      End:
51,171,651 bp from pter
Size:
46,418 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: SYT3_HUMAN, Q9BQG1 (See protein sequence)
Recommended Name: Synaptotagmin-3  
Size: 590 amino acids; 63304 Da
Cofactor: Binds 3 calcium ions per subunit. The ions are bound to the C2 domains (By similarity)
Subunit: Homodimer. Can also form heterodimers with SYT6 (By similarity)
Subcellular location: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass membrane protein
(By similarity)
Secondary accessions: Q8N5Z1 Q8N640

Explore the universe of human proteins at neXtProt for SYT3: NX_Q9BQG1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9BQG1

  • SYT3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001153800.1  NP_001153801.1  NP_115674.1  

    ENSEMBL proteins: 
     ENSP00000438883   ENSP00000340914  

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    Novus Biologicals SYT3 Lysates
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    Uscn Proteins for SYT3

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005768endosome IDA--
    GO:0016021integral to membrane IEA--
    GO:0030054cell junction IEA--
    GO:0030672synaptic vesicle membrane IEA--


    SYT3 for ontologies           About GeneDecksing



    SYT3 Antibody Products: 
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    Uscn Antibodies for SYT3
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    Uscn ELISAs and CLIAs for SYT3


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    SYT3 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR008973 C2_Ca/lipid-bd_dom_CaLB
     IPR001565 Synaptotagmin
     IPR018029 C2_membr_targeting
     IPR020477 C2_dom
     IPR000008 C2_Ca-dep

    Graphical View of Domain Structure for InterPro Entry Q9BQG1

    ProtoNet protein and cluster: Q9BQG1

    1 Blocks protein family: IPB000008 C2 domain

    UniProtKB/Swiss-Prot: SYT3_HUMAN, Q9BQG1
    Domain: The first C2 domain mediates Ca(2+)-dependent phospholipid binding
    Similarity: Belongs to the synaptotagmin family
    Similarity: Contains 2 C2 domains


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: SYT3_HUMAN, Q9BQG1
    Function: May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding
    to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis (By similarity)

         Genatlas biochemistry entry for SYT3:
    synaptotagmin 3,multifunctional intrinsic membrane protein of synaptic vesicles and chromaffin granules,involved in
    exocytosis and endocytosis

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat SYT3
    8/24 QIAGEN miScript miRNA Assays for microRNAs that regulate SYT3 (see all 24):
    hsa-miR-4311 hsa-miR-3917 hsa-miR-181c hsa-miR-15a hsa-miR-503 hsa-miR-424 hsa-miR-195 hsa-miR-15b
    SwitchGear 3'UTR luciferase reporter plasmidSYT3 3' UTR sequence
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    Gene Ontology (GO): 5/6 molecular function terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005215transporter activity IEA--
    GO:0005515protein binding ----
    GO:0005544calcium-dependent phospholipid binding IEA--
    GO:0019905syntaxin binding IEA--
    GO:0030276clathrin binding IEA--


    SYT3 for ontologies           About GeneDecksing


    Animal Models:
         Mouse knock-out Syt3tm1Sud for SYT3
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Syt3):
     normal 

    SYT3 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SYT3

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    5/8 Interacting proteins for SYT3 (Q9BQG13 ENSP000003409144) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SYT5O004453, ENSP000003462654I2D: score=1 STRING: ENSP00000346265
    SNAP25P608803, ENSP000002549764I2D: score=2 STRING: ENSP00000254976
    SYNCRIPO605063, ENSP000003586354I2D: score=2 STRING: ENSP00000358635
    AP2A1O957823, ENSP000003519264I2D: score=1 STRING: ENSP00000351926
    CACNA1BQ009753I2D: score=1 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    SYT3 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SYT3

    1 HMDB Compound for SYT3    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    3 Novoseek chemical compound relationships for SYT3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    inositol 40.3 1 10358928 (1)
    phospholipid 20.2 3 9163333 (3)
    calcium 16.9 2 9830048 (1)

    Search CenterWatch for drugs/clinical trials and news about SYT3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SYT3 gene (3 alternative transcripts): 
    NM_001160328.1  NM_001160329.1  NM_032298.2  

    Unigene Cluster for SYT3:

    Synaptotagmin III
    Hs.515554  [show with all ESTs]
    Unigene Representative Sequence: AL136594
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000544769(uc002psv.3 uc010ycd.2) ENST00000338916(uc002pst.3)


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    8/24 QIAGEN miScript miRNA Assays for microRNAs that regulate SYT3 (see all 24):
    hsa-miR-4311 hsa-miR-3917 hsa-miR-181c hsa-miR-15a hsa-miR-503 hsa-miR-424 hsa-miR-195 hsa-miR-15b
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    Inhib. RNA
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    Clone
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    Additional cDNA sequence: 

    AL136594.1 BC028379.1 BC031067.1 

    5 DOTS entries:

    DT.40114794  DT.100021968  DT.95157972  DT.121414988  DT.92033316 

    24/25 AceView cDNA sequences (see all 25):

    AA594745 AW451023 BF593902 BU176847 BM710834 BM667671 AL136594 F08666 
    NM_032298 BC028379 BX283781 Z41650 BF307829 BC031067 BE220745 BU726788 
    BI916739 BI550777 BG702285 BI912995 BM688060 CK004629 BI522420 BG704063 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SYT3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TCTGGGGGAC

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    SYT3 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    Skeletal MuscleExtraocular MusclesSkeletal Muscle
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SYT3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SYT3

    SOURCE GeneReport for Unigene cluster: Hs.515554
        SABiosciences Custom PCR Arrays for SYT3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SYT3

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SYT3 gene from 4/12 species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia SYT36
    --
    70(a)
    1 ↔ 1
    6(79535799-79566876)
    zebrafish
    (Danio rerio)
    Actinopterygii syt36
    synaptotagmin III
    64(a)
    1 ↔ 1
    3(30666484-30776338)
    fruit fly
    (Drosophila melanogaster)
    Insecta Sytbeta6
    Synaptotagmin beta
    19(a)
    possible ortholog
    3L(15007795-15058077)
    worm
    (Caenorhabditis elegans)
    Secernentea snt-66
    SyNapTotagmin family member (snt-6)
    31(a)
    possible ortholog
    II(745469-750171)


    ENSEMBL Gene Tree for SYT3 (if available)
    TreeFam Gene Tree for SYT3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SYT3 gene
    SYT152  SYT42  SYT52  SYT82  SYT92  SYT102  SYT62  SYT172  
    SYT112  SYT22  SYT122  SYT72  SYT12  
    8 SIMAP similar genes for SYT3 using alignment to 3 protein entries:     SYT3_HUMAN (see all proteins):
    SYT1    SYT10    SYT2    SYT5    SYT6    SYT9
    SYT7    SYT4

    SYT3 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/373 NCBI SNPs in SYT3 are shown (see all 373    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1176571131,2
    --51124750(+) AGACCG/AGCCTG 3 -- int11Minor allele frequency- A:0.01NA 120
    rs116722831,2
    C,H,--51124774(+) accccA/Gtctct 3 -- int10--------
    rs1135609621,2
    C,--51124806(+) CCAGGC/TGTGGT 3 -- int11Minor allele frequency- T:0.50WA 2
    rs1493644151,2
    --51124809(+) GGCGTG/TGTGGC 3 -- int10--------
    rs1446892851,2
    --51124818(+) GCGAGC/TGGCTG 3 -- int10--------
    rs39561581,2
    C--51125485(-) GGGGCC/AATGCA 3 -- ut311Minor allele frequency- A:0.00NA 2
    rs1865221771,2
    --51125546(+) GAATGA/CCCCCC 3 -- ut310--------
    rs1180788461,2
    F,--51125896(+) TCAGAC/TGCAGG 3 -- int11Minor allele frequency- T:0.08NA 120
    rs2016862781,2
    --51125939(+) GGCTGC/TTTACC 3 -- int10--------
    rs1396728521,2
    C,F,--51125953(+) CACTCG/AGAGTT 6 /S syn12Minor allele frequency- A:0.02NA EU 5291

    HapMap Linkage Disequilibrium report for SYT3 (51125234 - 51171651 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for SYT3
         2 CNVs: 7212 7213

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SYT3 for disorders           About GeneDecksing

    OMIM gene information: 600327    OMIM disorders: --

    3 diseases for SYT3:    About MalaCards
    seizures    pancreatitis    neuronitis


    Export disorders for SYT3 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SYT3 gene, integrated from 9 sources (see all 33):
    (articles sorted by number of sources associating them with SYT3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    2. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (2001)
    3. Synaptotagmin genes on mouse chromosomes 1, 7, and 10 and human chromosome 19. (PubMed id 7749232)1, 3 Jones J.M....Meisler M.H. (1995)
    4. The consensus coding sequences of human breast and colorectal cancers. (PubMed id 16959974)2 Sjoeblom T.... Velculescu V.E. (2006)
    5. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (2006)
    6. From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)1 Wiemann S....Poustka A. (2004)
    7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    8. Genomic analysis of synaptotagmin genes. (PubMed id 11543631)1 Craxton M.A. (2001)
    9. SYNCRIP, a cytoplasmic counterpart of heterogeneous nuclear ribonucleoprotein R, interacts with ubiquitous synaptotagmin isoforms. (PubMed id 10734137)1 Mizutani A....Mikoshiba K. (2000)
    10. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. (PubMed id 11256614)1 Simpson J.C.... Wiemann S. (2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 84258 HGNC: 11511 AceView: SYT3 Ensembl:ENSG00000213023 euGenes: HUgn84258
    ECgene: SYT3 H-InvDB: SYT3

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SYT3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SYT3 gene:
    Search GeneIP for patents involving SYT3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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