Human Gene SYT6 (uc001eev.3) Description and Page Index
  Description: Homo sapiens synaptotagmin VI (SYT6), transcript variant 3, mRNA.
RefSeq Summary (NM_001270805): The protein encoded by this gene belongs to the synaptotagmin family. Synaptotagmins share a common domain structure that includes a transmembrane domain and a cytoplasmic region composed of 2 C2 domains, and are involved in calcium-dependent exocytosis of synaptic vesicles. This protein has been shown to be a key component of the secretory machinery involved in acrosomal exocytosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2011].
Transcript (Including UTRs)
   Position: hg19 chr1:114,631,914-114,696,472 Size: 64,559 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr1:114,636,408-114,682,493 Size: 46,086 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:114,631,914-114,696,472)mRNA (may differ from genome)Protein (425 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDHuman Cortex Gene ExpressionLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SYT6_HUMAN
DESCRIPTION: RecName: Full=Synaptotagmin-6; AltName: Full=Synaptotagmin VI; Short=SytVI;
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. May mediate Ca(2+)- regulation of exocytosis in acrosomal reaction in sperm (By similarity).
COFACTOR: Binds 3 calcium ions per subunit. The ions are bound to the C2 domains (By similarity).
SUBUNIT: Homodimer (isoform 1). Isoform 1 forms heterodimers with SytIII, SytV and SytX. Interacts with STX1A, STX1B and STX2; the interaction is Ca(2+)-dependent. Isoform 2 is not able to form homodimer and heterodimers (By similarity).
SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass membrane protein (By similarity).
SUBCELLULAR LOCATION: Isoform 1: Membrane; Single-pass membrane protein (By similarity). Note=Localized predominantly to endoplasmic reticulum (ER) and/or Golgi-like perinuclear compartment (By similarity).
SUBCELLULAR LOCATION: Isoform 2: Cytoplasm, cytosol (By similarity). Cell membrane; Peripheral membrane protein (By similarity).
SIMILARITY: Belongs to the synaptotagmin family.
SIMILARITY: Contains 2 C2 domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SYT6
CDC HuGE Published Literature: SYT6
Positive Disease Associations: Calcium , E-Selectin , Forced Expiratory Volume , Inflammation , Mental Disorders , Potassium
Related Studies:
  1. Calcium
    , , . [PubMed 0]
  2. E-Selectin
    Andrew D Paterson et al. Arteriosclerosis, thrombosis, and vascular biology 2009, Genome-wide association identifies the ABO blood group as a major locus associated with serum levels of soluble E-selectin., Arteriosclerosis, thrombosis, and vascular biology. [PubMed 19729612]
    ABO is a major locus for serum soluble E-selectin levels. We excluded population stratification, fine-mapped the association to sub-A alleles, and also document association with additional variation in the ABO region.
  3. Forced Expiratory Volume
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.68 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 22.10 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -141.40250-0.566 Picture PostScript Text
3' UTR -854.912842-0.301 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000008 - C2_Ca-dep
IPR008973 - C2_Ca/lipid-bd_dom_CaLB
IPR020477 - C2_dom
IPR018029 - C2_membr_targeting
IPR001565 - Synaptotagmin

Pfam Domains:
PF00168 - C2 domain

SCOP Domains:
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)

ModBase Predicted Comparative 3D Structure on Q5T7P8
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001786 phosphatidylserine binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0019905 syntaxin binding
GO:0030276 clathrin binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0048306 calcium-dependent protein binding
GO:0005544 calcium-dependent phospholipid binding

Biological Process:
GO:0006906 vesicle fusion
GO:0007340 acrosome reaction
GO:0017158 regulation of calcium ion-dependent exocytosis
GO:0048791 calcium ion-regulated exocytosis of neurotransmitter
GO:0060478 acrosomal vesicle exocytosis

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0019898 extrinsic component of membrane
GO:0030054 cell junction
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0045202 synapse
GO:0097038 perinuclear endoplasmic reticulum


-  Descriptions from all associated GenBank mRNAs
  AK056448 - Homo sapiens cDNA FLJ31886 fis, clone NT2RP7003025, highly similar to Synaptotagmin-6.
BC044948 - Homo sapiens synaptotagmin VI, mRNA (cDNA clone MGC:50299 IMAGE:5245305), complete cds.
AK096744 - Homo sapiens cDNA FLJ39425 fis, clone PROST2000162, moderately similar to Mus musculus mRNA for synaptotagmin VIdeltaTM1.
JD533963 - Sequence 514987 from Patent EP1572962.
JD230220 - Sequence 211244 from Patent EP1572962.
JD390252 - Sequence 371276 from Patent EP1572962.
JD333520 - Sequence 314544 from Patent EP1572962.
JD167202 - Sequence 148226 from Patent EP1572962.
JD085728 - Sequence 66752 from Patent EP1572962.
JD462777 - Sequence 443801 from Patent EP1572962.
JD393020 - Sequence 374044 from Patent EP1572962.
JD302114 - Sequence 283138 from Patent EP1572962.
JD324781 - Sequence 305805 from Patent EP1572962.
HQ448594 - Synthetic construct Homo sapiens clone IMAGE:100072032; CCSB011334_01 synaptotagmin VI (SYT6) gene, encodes complete protein.
KJ895616 - Synthetic construct Homo sapiens clone ccsbBroadEn_05010 SYT6 gene, encodes complete protein.
CU692244 - Synthetic construct Homo sapiens gateway clone IMAGE:100021402 5' read SYT6 mRNA.
JD274155 - Sequence 255179 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B1AMB8, B3KPK1, NM_001270805, NP_995320, Q5T7P8, SYT6_HUMAN, uc021osa.1
UCSC ID: uc001eev.3
RefSeq Accession: NM_001270805
Protein: Q5T7P8 (aka SYT6_HUMAN)
CCDS: CCDS871.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001270805.1
exon count: 8CDS single in 3' UTR: no RNA size: 4375
ORF size: 1278CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2484.00frame shift in genome: no % Coverage: 99.89
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.