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

SYT9 Gene

protein-coding   GIFtS: 52
GCID: GC11P007273

Synaptotagmin IX

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Synaptotagmin IX1 2 3
synaptotagmin-92
sytIX2
SytIX3

External Ids:    HGNC: 192651   Entrez Gene: 1434252   Ensembl: ENSG000001707437   OMIM: 6135285   UniProtKB: Q86SS63   

Export aliases for SYT9 gene to outside databases

Previous GC identifers: GC00U906273 GC11P007229 GC11P006931


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

GeneCards Summary for SYT9 Gene: 
SYT9 (synaptotagmin IX) is a protein-coding gene. Diseases associated with SYT9 include lateral sclerosis, and amyotrophic lateral sclerosis. GO annotations related to this gene include transporter activity and identical protein binding. An important paralog of this gene is DOC2B.

UniProtKB/Swiss-Prot: SYT9_HUMAN, Q86SS6
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

Gene Wiki entry for SYT9 Gene


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000011.9  NT_009237.18  NC_018922.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SYT9 gene promoter:
         TBP   STAT1   STAT4   p300   MyoD   STAT1alpha   CREB   TFIID   deltaCREB   Cart-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSYT9 promoter sequence
   Search SABiosciences Chromatin IP Primers for SYT9

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SYT9


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

Entrez Gene cytogenetic band: 11p15.4   Ensembl cytogenetic band:  11p15.4   HGNC cytogenetic band: 11p15.4

SYT9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SYT9 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P007273:  view genomic region     (about GC identifiers)

Start:
7,260,009 bp from pter      End:
7,490,276 bp from pter
Size:
230,268 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SYT9_HUMAN, Q86SS6 (See protein sequence)
Recommended Name: Synaptotagmin-9  
Size: 491 amino acids; 56188 Da
Cofactor: Binds 3 calcium ions per subunit. The ions are bound to the C2 domains (By similarity)
Subcellular location: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass membrane
protein (By similarity)

Explore the universe of human proteins at neXtProt for SYT9: NX_Q86SS6

Explore proteomics data for SYT9 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q86SS6

  • SYT9 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SYT9 Protein Expression
    REFSEQ proteins: NP_783860.1  
    ENSEMBL proteins: 
     ENSP00000432141   ENSP00000324419   ENSP00000434558   ENSP00000379944  

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    Cloud-Clone Corp. Proteins for SYT9 

    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008021synaptic vesicle ----
    GO:0016020membrane ----
    GO:0016021integral to membrane IEA--
    GO:0030054cell junction IEA--
    GO:0030667secretory granule membrane IEA--

    SYT9 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    SYT: Synaptotagmins

    5 InterPro protein domains:
     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 Q86SS6

    ProtoNet protein and cluster: Q86SS6

    1 Blocks protein domain: IPB000008 C2 domain

    UniProtKB/Swiss-Prot: SYT9_HUMAN, Q86SS6
    Similarity: Belongs to the synaptotagmin family
    Similarity: Contains 2 C2 domains


    SYT9 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SYT9_HUMAN, Q86SS6
    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

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005215transporter activity IEA--
    GO:0005515protein binding ----
    GO:0042802identical protein binding IEA--
    GO:0046872metal ion binding IEA--
         
    SYT9 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, 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 Oct 2013 via Entrez Gene).
    About This Section




    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SYT9

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    5/16 Interacting proteins for SYT9 (Q86SS63 ENSP000003244194) via UniProtKB, MINT, STRING, and/or I2D (see all 16)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000232575P074373, ENSP000004100714I2D: score=1 STRING: ENSP00000410071
    ENSG00000183311P074373I2D: score=1 
    ENSG00000224156P074373I2D: score=1 
    ENSG00000227739P074373I2D: score=1 
    ENSG00000229684P074373I2D: score=1 
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0017158regulation of calcium ion-dependent exocytosis IEA--
    GO:0050796regulation of insulin secretion IEA--

    SYT9 for ontologies           About GeneDecksing



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

    SYT9 for compounds           About GeneDecksing

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

    Browse Tocris compounds for SYT9

    1 HMDB Compound for SYT9    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    1 Novoseek inferred chemical compound relationship for SYT9 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    calcium 5.82 1 14983047 (1)

    Search CenterWatch for drugs/clinical trials and news about SYT9

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SYT9 gene: 
    NM_175733.3  

    Unigene Cluster for SYT9:

    Synaptotagmin IX
    Hs.177193  [show with all ESTs]
    Unigene Representative Sequence: BC046367
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000524820(uc001mfd.3) ENST00000318881(uc001mfe.3 uc009yfi.3)
    ENST00000532592 ENST00000396716
    miRNA
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    Inhib. RNA
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    Additional mRNA sequence: 

    AK055003.1 AK055929.1 AK127795.1 AK315013.1 AL137512.1 BC046367.1 

    3 DOTS entries:

    DT.434225  DT.101955565  DT.99939354 

    23 AceView cDNA sequences:

    BC029605 AK055929 AK055003 Z39450 BM561215 AL137512 CD250937 BC046367 
    AI955186 NM_175733 BE047105 BI560415 BF197562 BX108745 BM928247 H17258 
    AK127795 Z43379 BM553771 BQ720470 H17257 H08332 H08235 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for SYT9    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
    SP1:                                                                  
    SP2:                          -                       -     -         
    SP3:                    -     -                       -     -         


    ECgene alternative splicing isoforms for SYT9

    (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

    SYT9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCAGGCAGGT
    SYT9 Expression
    About this image


    See SYT9 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SYT9

    SOURCE GeneReport for Unigene cluster: Hs.177193
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    In Situ
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    (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 SYT9 gene from 5/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Syt91 , 5 synaptotagmin IX1, 5 90.77(n)1
    97.56(a)1
      7 (56.33 cM)5
    605101  NM_021889.41  NP_068689.21 
     1073707285 
    chicken
    (Gallus gallus)
    Aves SYT91 synaptotagmin IX 81.06(n)
    88.86(a)
      423026  XM_003641313.1  XP_003641361.1 
    lizard
    (Anolis carolinensis)
    Reptilia SYT96
    synaptotagmin IX
    78(a)
    1 ↔ 1
    GL343237.1(2045893-2146467)
    zebrafish
    (Danio rerio)
    Actinopterygii sbcb8442 sbcb844 72.16(n)   378858  BI475373.1 
    worm
    (Caenorhabditis elegans)
    Secernentea snt-26
    snt-16
    (see all 3)
    Synaptotagmin-1
    (see all 3)
    33(a)
    33(a)
    (see all 3)
    many ↔ many
    many ↔ many
    (see all 3)
    III(786698-793687)
    II(6810963-6816454)


    ENSEMBL Gene Tree for SYT9 (if available)
    TreeFam Gene Tree for SYT9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SYT9 gene
    DOC2B2  SYT42  SYT52  SYT82  SYT102  SYT32  SYT62  SYT172  
    SYT112  SYT122  SYT22  DOC2A2  SYT72  RPH3A2  SYT12  
    15 SIMAP similar genes for SYT9 using alignment to 6 protein entries:     SYT9_HUMAN (see all proteins):
    SYT3    SYT10    SYT2    SYT1    SYT6    PRKCG
    SYT7    SYT4    SYTL2    SYT5    CHR11SYT    SYT15
    SYT11    SYT17    SYT12

    SYT9 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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

    10/4022 SNPs in SYT9 are shown (see all 4022)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0363904
    A colorectal cancer sample4--see VAR_0363902 D N mis40--------
    VAR_0657614
    ----see VAR_0657612 I V mis40--------
    rs678100751,2
    C--6950429(+) CACAG-/AC    
       
    /ACAC
    ACACA
    1 -- int11NA 2
    rs105006871,2
    C,F,A,H--7271224(+) GTTCTC/GATTGC 1 -- us2k199Minor allele frequency- G:0.04NS NA EA PA EU CA WA CSA 5123
    rs118203261,2
    C,F,H--7271315(+) TTCCAA/GTGATG 1 -- us2k122Minor allele frequency- G:0.10NA NS EA WA CSA 2198
    rs766070231,2
    F--7271323(+) ATGATT/CGCCAG 1 -- us2k11Minor allele frequency- C:0.01EA 120
    rs107697721,2
    C,H--7271334(+) TCTTCC/ACTCTC 1 -- us2k111Minor allele frequency- A:0.00NA WA CSA 138
    rs118208351,2
    C,F,H--7271381(+) GGGTGT/CGAGCA 1 -- us2k19Minor allele frequency- C:0.04NS EA NA CSA WA 644
    rs1443961761,2
    --7271403(+) GGTAAC/TGTTTT 1 -- us2k10--------
    rs1921259791,2
    --7271410(+) TTTTGA/TAACGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SYT9 (7260009 - 7490276 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/17 variations for SYT9 (see all 17):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2288433CNV Deletion18987734
    esv2663215CNV Deletion23128226
    esv2448178CNV Deletion19546169
    esv2744079CNV Deletion23290073
    esv268316CNV Insertion20981092
    esv274595CNV Insertion20981092
    esv269864CNV Insertion20981092
    esv2450231CNV Insertion19546169
    nsv896976CNV Loss21882294
    dgv57n21CNV Loss19592680

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 613528    OMIM disorders: --

    3 diseases for SYT9:    About MalaCards
    lateral sclerosis    amyotrophic lateral sclerosis    neuronitis


    SYT9 for disorders           About GeneDecksing

    Genetic Association Database (GAD): SYT9
    Human Genome Epidemiology (HuGE) Navigator: SYT9 (1 document)

    Export disorders for SYT9 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 SYT9 gene, integrated from 9 sources (see all 25):
    (articles sorted by number of sources associating them with SYT9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genome-wide association study identifies novel loci as sociated with circulating phospho- and sphingolipid concentrations. (PubMed id 22359512)1, 4 Demirkan A....Schmitz G. (2012)
    2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (2010)
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    4. Genomic analysis of synaptotagmin genes. (PubMed id 11543631)1, 3 Craxton M.A. (2001)
    5. Synaptotagmin IX regulates Ca2+-dependent secretion in PC12 cells. (PubMed id 11751925)1, 9 Fukuda M....Mikoshiba K. (2002)
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    7. Resequencing of 29 candidate genes in patients with familial and sporadic amyotrophic lateral sclerosis. (PubMed id 21220648)2 Daoud H....Rouleau G.A. (2011)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 143425 HGNC: 19265 AceView: SYT9 Ensembl:ENSG00000170743 euGenes: HUgn143425
    ECgene: SYT9 H-InvDB: SYT9

    (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 SYT9 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 SYT9 gene:
    Search GeneIP for patents involving SYT9

    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, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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, In Situ Hybridization Assays from
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