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SYT1 synaptotagmin 1 [ Homo sapiens (human) ]

Gene ID: 6857, updated on 12-Oct-2019

Summary

Official Symbol
SYT1provided by HGNC
Official Full Name
synaptotagmin 1provided by HGNC
Primary source
HGNC:HGNC:11509
See related
Ensembl:ENSG00000067715 MIM:185605
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
P65; SYT; BAGOS; SVP65
Summary
The synaptotagmins are integral membrane proteins of synaptic vesicles thought to serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis. Calcium binding to synaptotagmin-1 participates in triggering neurotransmitter release at the synapse (Fernandez-Chacon et al., 2001 [PubMed 11242035]).[supplied by OMIM, Jul 2010]
Expression
Biased expression in brain (RPKM 173.4) and adrenal (RPKM 11.7) See more
Orthologs

Genomic context

See SYT1 in Genome Data Viewer
Location:
12q21.2
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (78863982..79452008)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (79257773..79845788)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L11 pseudogene 3 Neighboring gene v-ral simian leukemia viral oncogene homolog A (ras related) pseudogene Neighboring gene uncharacterized LOC105369863 Neighboring gene RE1 silencing transcription factor pseudogene Neighboring gene microRNA 1252 Neighboring gene NOP56 ribonucleoprotein pseudogene 3 Neighboring gene pro-apoptotic WT1 regulator

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
BAKER-GORDON SYNDROME
MedGen: C4748715 OMIM: 618218 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Pathways from BioSystems

  • Acetylcholine Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Acetylcholine Neurotransmitter Release Cycle, organism-specific biosystemAcetylcholine neurotransmitter release cycle involves syntheis of choline, loading of clathrin scultpted synaptic vesicles, docking and priming of the acetyl choline loaded synaptic vesicles and then...
  • Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystemRecruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-...
  • Clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Clathrin-mediated endocytosis, organism-specific biosystemClathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Dopamine Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Dopamine Neurotransmitter Release Cycle, organism-specific biosystemDopamine neurotransmitter cycle occurs in dopaminergic neurons. Dopamine is synthesized and loaded into the clathrin sculpted monoamine transport vesicles. The vesicles are docked, primed and fused w...
  • Effects of Botulinum toxin, organism-specific biosystem (from Pathway Interaction Database)
    Effects of Botulinum toxin, organism-specific biosystem
    Effects of Botulinum toxin
  • GABA synthesis, release, reuptake and degradation, organism-specific biosystem (from REACTOME)
    GABA synthesis, release, reuptake and degradation, organism-specific biosystemGABA is a major inhibitory neurotransmitter in the mammalian central nervous system. GABA modulates neuronal excitability throughout the nervous system. Disruption of GABA neurotransmission leads to ...
  • Glutamate Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Glutamate Neurotransmitter Release Cycle, organism-specific biosystemCommunication at the synapse involves the release of glutamate from the presynaptic neuron and its binding to glutamate receptors on the postsynaptic cell to generate a series of events that lead to ...
  • Infectious disease, organism-specific biosystem (from REACTOME)
    Infectious disease, organism-specific biosystem
    Infectious disease
  • Interactions of neurexins and neuroligins at synapses, organism-specific biosystem (from REACTOME)
    Interactions of neurexins and neuroligins at synapses, organism-specific biosystemNeurexins (NRXNs) and neuroligins (NLGNs) are best characterized synaptic cell-adhesion molecules. They are part of excitatory glutamatergic and inhibitory GABAergic synapses in mammalian brain, medi...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Neuronal System, organism-specific biosystem (from REACTOME)
    Neuronal System, organism-specific biosystemThe human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication a...
  • Neurotoxicity of clostridium toxins, organism-specific biosystem (from REACTOME)
    Neurotoxicity of clostridium toxins, organism-specific biosystemClostridial neurotoxins, when taken up by human neurons, block synaptic transmission by cleaving proteins required for the fusion of synaptic vesicles with the plasma membrane. They are remarkably ef...
  • Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Neurotransmitter Release Cycle, organism-specific biosystemNeurotransmitter is stored in the synaptic vesicle in the pre-synaptic terminal prior to its release in the synaptic cleft upon depolarization of the pre-synaptic membrane. The release of the neurotr...
  • Norepinephrine Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Norepinephrine Neurotransmitter Release Cycle, organism-specific biosystemNoradrenalin release cycle consists of reacidification of the empty clathrin sculpted monoamine transport vesicle, loading of dopamine into reacidified clathrin coated monamine transport vesicle, con...
  • Protein-protein interactions at synapses, organism-specific biosystem (from REACTOME)
    Protein-protein interactions at synapses, organism-specific biosystemSynapses constitute highly specialized sites of asymmetric cell-cell adhesion and intercellular communication. Its formation involves the recruitment of presynaptic and postsynaptic molecules at newl...
  • Serotonin Neurotransmitter Release Cycle, organism-specific biosystem (from REACTOME)
    Serotonin Neurotransmitter Release Cycle, organism-specific biosystemSerotonin is synthesized in the serotonergic neurons in the central nervous system and the enterochrommaffin cells of the gastroinetstinal system. Serotonin is loaded into the clathrin sculpted monoa...
  • Synaptic Vesicle Pathway, organism-specific biosystem (from WikiPathways)
    Synaptic Vesicle Pathway, organism-specific biosystemPathway depicting synaptic transmission of neurotransmitters from the presynaptic nerve terminal to the synaptic cleft upon depolarization. Synaptotagmin mediated transport along the nerve cell cytos...
  • Synaptic vesicle cycle, organism-specific biosystem (from KEGG)
    Synaptic vesicle cycle, organism-specific biosystemCommunication between neurons is mediated by the release of neurotransmitter from synaptic vesicles (SVs). At the nerve terminal, SVs cycle through repetitive episodes of exocytosis and endocytosis. ...
  • Synaptic vesicle cycle, conserved biosystem (from KEGG)
    Synaptic vesicle cycle, conserved biosystemCommunication between neurons is mediated by the release of neurotransmitter from synaptic vesicles (SVs). At the nerve terminal, SVs cycle through repetitive episodes of exocytosis and endocytosis. ...
  • Toxicity of botulinum toxin type B (BoNT/B), organism-specific biosystem (from REACTOME)
    Toxicity of botulinum toxin type B (BoNT/B), organism-specific biosystemBotulinum toxin type B (BoNT/B), a disulfide-bonded heavy chain (HC) - light chain (LC) heterodimer, enters the gut typically as a result of consuming contaminated food (Hatheway 1995), as a complex ...
  • Toxicity of botulinum toxin type G (BoNT/G), organism-specific biosystem (from REACTOME)
    Toxicity of botulinum toxin type G (BoNT/G), organism-specific biosystemBotulinum toxin type G (BoNT/G) is rarely if ever associated with human disease (Hatheway 1995) and a pathway by which it might enter the circulation from the human gut has not been described. Nevert...
  • Transmission across Chemical Synapses, organism-specific biosystem (from REACTOME)
    Transmission across Chemical Synapses, organism-specific biosystemChemical synapses are specialized junctions that are used for communication between neurons, neurons and muscle or gland cells. The synapse involves a pre-synaptic neuron and a post-synaptic neuron,...
  • Uptake and actions of bacterial toxins, organism-specific biosystem (from REACTOME)
    Uptake and actions of bacterial toxins, organism-specific biosystemThe toxic effects of many bacteria on their human hosts are mediated by proteins released from the bacteria that enter human cells and disrupt critical cellular functions (Henkel et al. 2010). All of...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp781D2042

Gene Ontology Provided by GOA

Function Evidence Code Pubs
1-phosphatidylinositol binding TAS
Traceable Author Statement
more info
PubMed 
SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SNARE binding ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion sensor activity IEA
Inferred from Electronic Annotation
more info
 
calcium-dependent phospholipid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium-dependent phospholipid binding ISS
Inferred from Sequence or Structural Similarity
more info
 
calcium-dependent phospholipid binding TAS
Traceable Author Statement
more info
PubMed 
calcium-dependent protein binding IEA
Inferred from Electronic Annotation
more info
 
calmodulin binding IEA
Inferred from Electronic Annotation
more info
 
clathrin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
low-density lipoprotein particle receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-4,5-bisphosphate binding IEA
Inferred from Electronic Annotation
more info
 
phosphatidylserine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein C-terminus binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
syntaxin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
syntaxin-1 binding ISS
Inferred from Sequence or Structural Similarity
more info
 
syntaxin-1 binding TAS
Traceable Author Statement
more info
PubMed 
syntaxin-3 binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
brain development IEA
Inferred from Electronic Annotation
more info
 
calcium ion regulated exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion-regulated exocytosis of neurotransmitter IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium-dependent activation of synaptic vesicle fusion IEA
Inferred from Electronic Annotation
more info
 
cellular response to calcium ion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to calcium ion ISS
Inferred from Sequence or Structural Similarity
more info
 
chemical synaptic transmission TAS
Traceable Author Statement
more info
PubMed 
detection of calcium ion TAS
Traceable Author Statement
more info
PubMed 
fast, calcium ion-dependent exocytosis of neurotransmitter ISS
Inferred from Sequence or Structural Similarity
more info
 
glutamate secretion TAS
Traceable Author Statement
more info
 
membrane organization TAS
Traceable Author Statement
more info
 
neurotransmitter secretion TAS
Traceable Author Statement
more info
PubMed 
positive regulation of calcium ion-dependent exocytosis of neurotransmitter ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of dendrite extension IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
 
protein heterooligomerization IEA
Inferred from Electronic Annotation
more info
 
protein homooligomerization TAS
Traceable Author Statement
more info
PubMed 
regulation of calcium ion-dependent exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of dopamine secretion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of exocytosis TAS
Traceable Author Statement
more info
PubMed 
regulation of regulated secretory pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of synaptic transmission, glutamatergic ISS
Inferred from Sequence or Structural Similarity
more info
 
spontaneous neurotransmitter secretion IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synaptic vesicle exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synchronous neurotransmitter secretion IEA
Inferred from Electronic Annotation
more info
 
vesicle docking IEA
Inferred from Electronic Annotation
more info
 
vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell junction IEA
Inferred from Electronic Annotation
more info
 
chromaffin granule membrane IEA
Inferred from Electronic Annotation
more info
 
clathrin-coated vesicle membrane TAS
Traceable Author Statement
more info
 
clathrin-sculpted acetylcholine transport vesicle membrane TAS
Traceable Author Statement
more info
 
clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane TAS
Traceable Author Statement
more info
 
clathrin-sculpted glutamate transport vesicle membrane TAS
Traceable Author Statement
more info
 
clathrin-sculpted monoamine transport vesicle membrane TAS
Traceable Author Statement
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
dense core granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
excitatory synapse IEA
Inferred from Electronic Annotation
more info
 
exocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
hippocampal mossy fiber to CA3 synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron projection terminus IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle TAS
Traceable Author Statement
more info
PubMed 
synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synaptic vesicle membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
synaptotagmin-1
Names
synaptotagmin I
sytI

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001135805.2NP_001129277.1  synaptotagmin-1 isoform 1

    See identical proteins and their annotated locations for NP_001129277.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AC073606, AK094616, AK126908, BC041373, BM668697, DA174824
    Consensus CDS
    CCDS9017.1
    UniProtKB/Swiss-Prot
    P21579
    UniProtKB/TrEMBL
    A0A024RBE9
    Related
    ENSP00000376932.3, ENST00000393240.7
    Conserved Domains (2) summary
    cd08385
    Location:143265
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08402
    Location:274409
    C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
  2. NM_001135806.2NP_001129278.1  synaptotagmin-1 isoform 1

    See identical proteins and their annotated locations for NP_001129278.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    BC041373, BM668697, CR627387, DA174824
    Consensus CDS
    CCDS9017.1
    UniProtKB/Swiss-Prot
    P21579
    UniProtKB/TrEMBL
    A0A024RBE9
    Related
    ENSP00000447575.1, ENST00000552744.5
    Conserved Domains (2) summary
    cd08385
    Location:143265
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08402
    Location:274409
    C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
  3. NM_001291901.2NP_001278830.1  synaptotagmin-1 isoform 2

    See identical proteins and their annotated locations for NP_001278830.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC027288, AC073572, AC073606, AC078917
    Consensus CDS
    CCDS76582.1
    UniProtKB/TrEMBL
    J3KQA0
    Related
    ENSP00000391056.2, ENST00000457153.6
    Conserved Domains (2) summary
    cd08385
    Location:140262
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08402
    Location:271406
    C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
  4. NM_005639.3NP_005630.1  synaptotagmin-1 isoform 1

    See identical proteins and their annotated locations for NP_005630.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AC027288, AC073572, AC073606, AC073616, AC078917
    Consensus CDS
    CCDS9017.1
    UniProtKB/Swiss-Prot
    P21579
    UniProtKB/TrEMBL
    A0A024RBE9
    Related
    ENSP00000261205.4, ENST00000261205.9
    Conserved Domains (2) summary
    cd08385
    Location:143265
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08402
    Location:274409
    C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    78863982..79452008
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269113.3XP_005269170.1  synaptotagmin-1 isoform X2

    See identical proteins and their annotated locations for XP_005269170.1

    UniProtKB/TrEMBL
    J3KQA0
    Conserved Domains (2) summary
    cd08385
    Location:140262
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08402
    Location:271406
    C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
  2. XM_011538710.2XP_011537012.1  synaptotagmin-1 isoform X1

    See identical proteins and their annotated locations for XP_011537012.1

    UniProtKB/Swiss-Prot
    P21579
    UniProtKB/TrEMBL
    A0A024RBE9
    Conserved Domains (2) summary
    cd08385
    Location:143265
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08402
    Location:274409
    C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
  3. XM_006719576.1XP_006719639.1  synaptotagmin-1 isoform X2

    See identical proteins and their annotated locations for XP_006719639.1

    UniProtKB/TrEMBL
    J3KQA0
    Conserved Domains (2) summary
    cd08385
    Location:140262
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08402
    Location:271406
    C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
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