Human Gene SYT1 (ENST00000261205.9_7) from GENCODE V47lift37
  Description: synaptotagmin 1, transcript variant 1 (from RefSeq NM_005639.3)
Gencode Transcript: ENST00000261205.9_7
Gencode Gene: ENSG00000067715.15_13
Transcript (Including UTRs)
   Position: hg19 chr12:79,258,554-79,845,788 Size: 587,235 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr12:79,611,300-79,842,904 Size: 231,605 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:79,258,554-79,845,788)mRNA (may differ from genome)Protein (422 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
ReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYT1_HUMAN
DESCRIPTION: RecName: Full=Synaptotagmin-1; AltName: Full=Synaptotagmin I; Short=SytI; AltName: Full=p65;
FUNCTION: May have a regulatory role in the membrane interactions during trafficking of synaptic vesicles at the active zone of the synapse. It binds acidic phospholipids with a specificity that requires the presence of both an acidic head group and a diacyl backbone. A Ca(2+)-dependent interaction between synaptotagmin and putative receptors for activated protein kinase C has also been reported. It can bind to at least three additional proteins in a Ca(2+)-independent manner; these are neurexins, syntaxin and AP2.
COFACTOR: Binds 3 calcium ions per subunit. The ions are bound to the C2 domains (By similarity).
SUBUNIT: Homotetramer (Probable). Interacts with SCAMP5, STON2, SV2A, SV2B, SV2C and RIMS1. Forms a complex with SV2B, syntaxin 1 and SNAP25 (By similarity).
INTERACTION: O00305-2:CACNB4; NbExp=2; IntAct=EBI-524909, EBI-714855; Q9Y6K9:IKBKG; NbExp=3; IntAct=EBI-524909, EBI-81279;
SUBCELLULAR LOCATION: Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Single-pass membrane protein. Cytoplasmic vesicle, secretory vesicle, chromaffin granule membrane; Single-pass membrane protein. Cytoplasm. Note=Synaptic vesicles and chromaffin granules.
DOMAIN: The first C2 domain mediates Ca(2+)-dependent phospholipid binding.
DOMAIN: The second C2 domain mediates interaction with SV2A and STN2 (By similarity).
SIMILARITY: Belongs to the synaptotagmin family.
SIMILARITY: Contains 2 C2 domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SYT1
Diseases sorted by gene-association score: foodborne botulism (10), infant botulism (9), diarrhea 1, secretory chloride, congenital (9), mast-cell leukemia (8), autosomal dominant non-syndromic intellectual disability (4), attention deficit-hyperactivity disorder (2)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 165.50 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 772.90 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -204.30552-0.370 Picture PostScript Text
3' UTR -678.302884-0.235 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
IPR015428 - Synaptotagmin1

Pfam Domains:
PF00168 - C2 domain

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2K45 - NMR MuPIT 2K4A - NMR MuPIT 2K8M - NMR MuPIT 2KI6 - NMR MuPIT 2LHA - NMR MuPIT 2R83 - X-ray MuPIT 3F00 - X-ray MuPIT 3F01 - X-ray MuPIT 3F04 - X-ray MuPIT 3F05 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P21579
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000149 SNARE binding
GO:0001786 phosphatidylserine binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005543 phospholipid binding
GO:0005544 calcium-dependent phospholipid binding
GO:0005545 1-phosphatidylinositol binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0008022 protein C-terminus binding
GO:0017075 syntaxin-1 binding
GO:0019905 syntaxin binding
GO:0030276 clathrin binding
GO:0030348 syntaxin-3 binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity
GO:0048306 calcium-dependent protein binding
GO:0050750 low-density lipoprotein particle receptor binding

Biological Process:
GO:0005513 detection of calcium ion
GO:0006906 vesicle fusion
GO:0007268 chemical synaptic transmission
GO:0007269 neurotransmitter secretion
GO:0007420 brain development
GO:0014047 glutamate secretion
GO:0014059 regulation of dopamine secretion
GO:0016079 synaptic vesicle exocytosis
GO:0017157 regulation of exocytosis
GO:0017158 regulation of calcium ion-dependent exocytosis
GO:0030154 cell differentiation
GO:0031340 positive regulation of vesicle fusion
GO:0045956 positive regulation of calcium ion-dependent exocytosis
GO:0048278 vesicle docking
GO:0048488 synaptic vesicle endocytosis
GO:0048791 calcium ion-regulated exocytosis of neurotransmitter
GO:0050806 positive regulation of synaptic transmission
GO:0051260 protein homooligomerization
GO:0051291 protein heterooligomerization
GO:0051592 response to calcium ion
GO:0051966 regulation of synaptic transmission, glutamatergic
GO:0061024 membrane organization
GO:0071277 cellular response to calcium ion
GO:0098746 fast, calcium ion-dependent exocytosis of neurotransmitter
GO:1903305 regulation of regulated secretory pathway
GO:1903861 positive regulation of dendrite extension

Cellular Component:
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030141 secretory granule
GO:0030285 integral component of synaptic vesicle membrane
GO:0030424 axon
GO:0030658 transport vesicle membrane
GO:0030665 clathrin-coated vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031045 dense core granule
GO:0031201 SNARE complex
GO:0031410 cytoplasmic vesicle
GO:0042584 chromaffin granule membrane
GO:0042734 presynaptic membrane
GO:0043005 neuron projection
GO:0043229 intracellular organelle
GO:0044306 neuron projection terminus
GO:0045202 synapse
GO:0060076 excitatory synapse
GO:0060201 clathrin-sculpted acetylcholine transport vesicle membrane
GO:0060203 clathrin-sculpted glutamate transport vesicle membrane
GO:0061202 clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane
GO:0070083 clathrin-sculpted monoamine transport vesicle membrane


-  Descriptions from all associated GenBank mRNAs
  AK094616 - Homo sapiens cDNA FLJ37297 fis, clone BRAMY2015503, highly similar to Synaptotagmin-1.
JA482081 - Sequence 64 from Patent WO2011072091.
JE980373 - Sequence 64 from Patent EP2862929.
AK126908 - Homo sapiens cDNA FLJ44960 fis, clone BRAWH2012866, highly similar to Synaptotagmin-1.
JA482080 - Sequence 63 from Patent WO2011072091.
JE980372 - Sequence 63 from Patent EP2862929.
BX647240 - Homo sapiens mRNA; cDNA DKFZp686E2449 (from clone DKFZp686E2449).
BC041373 - Homo sapiens cDNA clone IMAGE:5273902, containing frame-shift errors.
BC058917 - Homo sapiens synaptotagmin I, mRNA (cDNA clone MGC:65084 IMAGE:6187902), complete cds.
CR627387 - Homo sapiens mRNA; cDNA DKFZp781D2042 (from clone DKFZp781D2042).
JA482082 - Sequence 65 from Patent WO2011072091.
JE980374 - Sequence 65 from Patent EP2862929.
AK308743 - Homo sapiens cDNA, FLJ98784.
M55047 - Human synaptotagmin mRNA, complete cds.
AB384875 - Synthetic construct DNA, clone: pF1KB3935, Homo sapiens SYT1 gene for synaptotagmin-1, complete cds, without stop codon, in Flexi system.
KJ897632 - Synthetic construct Homo sapiens clone ccsbBroadEn_07026 SYT1 gene, encodes complete protein.
BC051915 - Homo sapiens cDNA clone IMAGE:6191772, partial cds.
JD154847 - Sequence 135871 from Patent EP1572962.
AK123228 - Homo sapiens cDNA FLJ41234 fis, clone BRAMY2030915.
JD279959 - Sequence 260983 from Patent EP1572962.
JD130146 - Sequence 111170 from Patent EP1572962.
JD346000 - Sequence 327024 from Patent EP1572962.
JD181707 - Sequence 162731 from Patent EP1572962.
JD069091 - Sequence 50115 from Patent EP1572962.
JD207360 - Sequence 188384 from Patent EP1572962.
JD099336 - Sequence 80360 from Patent EP1572962.
JD344510 - Sequence 325534 from Patent EP1572962.
JD303716 - Sequence 284740 from Patent EP1572962.
JD394091 - Sequence 375115 from Patent EP1572962.
JD218889 - Sequence 199913 from Patent EP1572962.
JD088986 - Sequence 70010 from Patent EP1572962.
JD118815 - Sequence 99839 from Patent EP1572962.
JD132062 - Sequence 113086 from Patent EP1572962.
U19921 - Human synaptotagmin I mRNA, 3' UTR.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P21579 (Reactome details) participates in the following event(s):

R-HSA-5250986 BoNT/G HC:LC binds SYT1 and GT1b on the target cell surface
R-HSA-210430 release of L-Glutamate at the synapse
R-HSA-372529 Release of acetylcholine at the synapse
R-HSA-374899 Release of noradrenaline at the synapse
R-HSA-380869 Release of docked dopamine loaded synaptic vesicle
R-HSA-380901 Release of docked serotonin loaded synaptic vesicle
R-HSA-888589 Release of GABA at the synapse
R-HSA-5244397 BoNT/B HC:LC binds SYT1 or 2 and GT1b on the target cell surface
R-HSA-6794348 NRXNs bind SYTs
R-HSA-264615 Loading of acetylcholine in synaptic vesicle
R-HSA-372505 Acetylcholine synaptic vesicle docking and priming
R-HSA-374922 Noradrenalin synaptic vesicle docking and priming
R-HSA-380574 Dopamine synaptic vesicle docking and priming
R-HSA-380905 Serotonin loaded synaptic vesicle docking and priming
R-HSA-210426 Glutamate synaptic vesicle docking and priming
R-HSA-210444 L-Glutamate loading of synaptic vesicle
R-HSA-917744 GABA loaded synaptic vesicle Docking and Priming
R-HSA-8863463 STON2 binds SYT proteins
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-5250989 Toxicity of botulinum toxin type G (BoNT/G)
R-HSA-210500 Glutamate Neurotransmitter Release Cycle
R-HSA-264642 Acetylcholine Neurotransmitter Release Cycle
R-HSA-181430 Norepinephrine Neurotransmitter Release Cycle
R-HSA-212676 Dopamine Neurotransmitter Release Cycle
R-HSA-181429 Serotonin Neurotransmitter Release Cycle
R-HSA-888590 GABA synthesis, release, reuptake and degradation
R-HSA-5250958 Toxicity of botulinum toxin type B (BoNT/B)
R-HSA-168799 Neurotoxicity of clostridium toxins
R-HSA-112310 Neurotransmitter release cycle
R-HSA-6794361 Neurexins and neuroligins
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-5339562 Uptake and actions of bacterial toxins
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-5663205 Infectious disease
R-HSA-112316 Neuronal System
R-HSA-199991 Membrane Trafficking
R-HSA-1643685 Disease
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000261205.1, ENST00000261205.2, ENST00000261205.3, ENST00000261205.4, ENST00000261205.5, ENST00000261205.6, ENST00000261205.7, ENST00000261205.8, NM_005639, P21579, Q6AI31, SVP65, SYT, SYT1 , SYT1_HUMAN, uc317gnr.1, uc317gnr.2
UCSC ID: ENST00000261205.9_7
RefSeq Accession: NM_005639.3
Protein: P21579 (aka SYT1_HUMAN)

-  Gene Model Information
  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.