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    SYT1 synaptotagmin 1 [ Homo sapiens (human) ]

    Gene ID: 6857, updated on 11-Apr-2024

    Summary

    Official Symbol
    SYT1provided by HGNC
    Official Full Name
    synaptotagmin 1provided by HGNC
    Primary source
    HGNC:HGNC:11509
    See related
    Ensembl:ENSG00000067715 MIM:185605; AllianceGenome:HGNC:11509
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    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
    This gene encodes a member of the synaptotagmin protein family. The synaptotagmins are integral membrane proteins of synaptic vesicles that serve as calcium sensors in the process of vesicular trafficking and exocytosis. The encoded protein participates in triggering neurotransmitter release at the synapse in response to calcium binding. Mutations in this gene are associated with Baker-Gordon syndrome. [provided by RefSeq, Jan 2023]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Biased expression in brain (RPKM 173.4) and adrenal (RPKM 11.7) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    12q21.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (78863982..79452008)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (78842458..79430647)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (79257762..79845788)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L11 pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:79045498-79046127 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:79152976-79154175 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:79187167-79188366 Neighboring gene MPRA-validated peak1851 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr12:79229192-79229693 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79233792-79234605 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79234606-79235418 Neighboring gene RAS like proto-oncogene A pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4680 Neighboring gene uncharacterized LOC105369863 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:79438588-79439174 Neighboring gene uncharacterized LOC124902973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6685 Neighboring gene Sharpr-MPRA regulatory region 15006 Neighboring gene RE1 silencing transcription factor pseudogene Neighboring gene MPRA-validated peak1855 silencer Neighboring gene MPRA-validated peak1856 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:79774873-79775471 Neighboring gene microRNA 1252 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79906476-79906976 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79906977-79907477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:79926619-79927119 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79933315-79933826 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79933827-79934340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:79936391-79936902 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79938953-79939466 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:79941058-79941786 Neighboring gene NOP56 ribonucleoprotein pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:80048601-80049285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4681 Neighboring gene PPP1R12A antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4682 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
    Infantile hypotonia-oculomotor anomalies-hyperkinetic movements-developmental delay syndrome
    MedGen: C4748715 OMIM: 618218 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • DKFZp781D2042

    Gene Ontology Provided by GOA

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

    General protein information

    Preferred Names
    synaptotagmin-1
    Names
    synaptotagmin I
    sytI

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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: REVIEWED

      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, Q6AI31
      UniProtKB/TrEMBL
      A0A994J5A7
      Related
      ENSP00000376932.3, ENST00000393240.7
      Conserved Domains (3) 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
      cd21963
      Location:6113
      Syt1_N; N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins
    2. NM_001135806.2NP_001129278.1  synaptotagmin-1 isoform 1

      See identical proteins and their annotated locations for NP_001129278.1

      Status: REVIEWED

      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, Q6AI31
      UniProtKB/TrEMBL
      A0A994J5A7
      Related
      ENSP00000447575.1, ENST00000552744.5
      Conserved Domains (3) 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
      cd21963
      Location:6113
      Syt1_N; N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins
    3. NM_001291901.2NP_001278830.1  synaptotagmin-1 isoform 2

      See identical proteins and their annotated locations for NP_001278830.1

      Status: REVIEWED

      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
      A0A994J5A7, J3KQA0
      Related
      ENSP00000391056.2, ENST00000457153.6
      Conserved Domains (3) 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
      cd21963
      Location:6113
      Syt1_N; N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins
    4. NM_001415938.1NP_001402867.1  synaptotagmin-1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC027288, AC073572, AC073606, AC078917
      UniProtKB/Swiss-Prot
      P21579, Q6AI31
    5. NM_001415939.1NP_001402868.1  synaptotagmin-1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC027288, AC073572, AC073606, AC073616, AC078917
      UniProtKB/Swiss-Prot
      P21579, Q6AI31
    6. NM_001415940.1NP_001402869.1  synaptotagmin-1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC027288, AC073572, AC073606, AC073616, AC078917, AC090709
      UniProtKB/Swiss-Prot
      P21579, Q6AI31
      Related
      ENSP00000516009.1, ENST00000704714.1
    7. NM_001415941.1NP_001402870.1  synaptotagmin-1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC027288, AC073572, AC073606, AC073616, AC078917
      UniProtKB/TrEMBL
      J3KQA0
      Related
      ENSP00000515996.1, ENST00000704699.1
    8. NM_001415942.1NP_001402871.1  synaptotagmin-1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC027288, AC073572, AC073616, AC078917
      UniProtKB/TrEMBL
      J3KQA0
    9. NM_001415943.1NP_001402872.1  synaptotagmin-1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC027288, AC073572, AC073606, AC073616, AC078917, AC090709
      UniProtKB/TrEMBL
      J3KQA0
    10. NM_005639.3NP_005630.1  synaptotagmin-1 isoform 1

      See identical proteins and their annotated locations for NP_005630.1

      Status: REVIEWED

      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, Q6AI31
      UniProtKB/TrEMBL
      A0A994J5A7
      Related
      ENSP00000261205.4, ENST00000261205.9
      Conserved Domains (3) 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
      cd21963
      Location:6113
      Syt1_N; N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

    1. XM_047429479.1XP_047285435.1  synaptotagmin-1 isoform X1

      UniProtKB/Swiss-Prot
      P21579, Q6AI31
    2. XM_047429484.1XP_047285440.1  synaptotagmin-1 isoform X2

      UniProtKB/TrEMBL
      J3KQA0
    3. XM_047429480.1XP_047285436.1  synaptotagmin-1 isoform X1

      UniProtKB/Swiss-Prot
      P21579, Q6AI31
    4. XM_047429482.1XP_047285438.1  synaptotagmin-1 isoform X1

      UniProtKB/Swiss-Prot
      P21579, Q6AI31
    5. XM_047429483.1XP_047285439.1  synaptotagmin-1 isoform X1

      UniProtKB/Swiss-Prot
      P21579, Q6AI31
    6. XM_047429481.1XP_047285437.1  synaptotagmin-1 isoform X1

      UniProtKB/Swiss-Prot
      P21579, Q6AI31

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      78842458..79430647
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373100.1XP_054229075.1  synaptotagmin-1 isoform X1

      UniProtKB/Swiss-Prot
      P21579, Q6AI31
    2. XM_054373098.1XP_054229073.1  synaptotagmin-1 isoform X1

      UniProtKB/Swiss-Prot
      P21579, Q6AI31
    3. XM_054373101.1XP_054229076.1  synaptotagmin-1 isoform X2

      UniProtKB/TrEMBL
      J3KQA0
    4. XM_054373099.1XP_054229074.1  synaptotagmin-1 isoform X1

      UniProtKB/Swiss-Prot
      P21579, Q6AI31