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    SYT2 synaptotagmin 2 [ Homo sapiens (human) ]

    Gene ID: 127833, updated on 10-Dec-2024

    Summary

    Official Symbol
    SYT2provided by HGNC
    Official Full Name
    synaptotagmin 2provided by HGNC
    Primary source
    HGNC:HGNC:11510
    See related
    Ensembl:ENSG00000143858 MIM:600104; AllianceGenome:HGNC:11510
    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
    CMS7; CMS7A; CMS7B; MYSPC; SytII
    Summary
    This gene encodes a synaptic vesicle membrane protein. The encoded protein is thought to function as a calcium sensor in vesicular trafficking and exocytosis. Mutations in this gene are associated with myasthenic syndrome, presynaptic, congenital, with or without motor neuropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
    Expression
    Broad expression in brain (RPKM 1.4), adrenal (RPKM 1.3) and 17 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SYT2 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202590596..202710454, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201852402..201972645, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202559724..202679582, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 1 regulatory subunit 12B Neighboring gene ribosomal protein S27 pseudogene 8 Neighboring gene Sharpr-MPRA regulatory region 4568 Neighboring gene Sharpr-MPRA regulatory region 13016 Neighboring gene small nucleolar RNA SNORA70 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202536800-202537472 Neighboring gene Sharpr-MPRA regulatory region 13308 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:202557917-202559116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202560242-202561068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202591842-202592466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202606743-202607308 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202611908-202612840 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202626482-202626641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202627175-202627676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202640443-202640943 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202645972-202646140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202671295-202671794 Neighboring gene lysine demethylase 5B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202764986-202765486 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202765487-202765987 Neighboring gene COX7C pseudogene 2 Neighboring gene solute carrier family 25 member 39 pseudogene 1

    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

    EBI GWAS Catalog

    Description
    A possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ42519

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables calcium ion sensor activity IBA
    Inferred from Biological aspect of Ancestor
    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 inositol 1,3,4,5 tetrakisphosphate binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in calcium-dependent activation of synaptic vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of dendrite extension IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of calcium ion-dependent exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of synaptic vesicle exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    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
     
    is_active_in dense core granule IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in exocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    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
     
    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-2
    Names
    synaptotagmin II

    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.

    Genomic

    1. NG_041776.1 RefSeqGene

      Range
      4970..124828
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136504.1NP_001129976.1  synaptotagmin-2

      See identical proteins and their annotated locations for NP_001129976.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC118556, AK094430, BC100815
      Consensus CDS
      CCDS1427.1
      UniProtKB/Swiss-Prot
      Q496K5, Q8N9I0, Q8NBE5
      Related
      ENSP00000356236.1, ENST00000367267.5
      Conserved Domains (2) summary
      cd08385
      Location:139261
      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. NM_177402.5NP_796376.2  synaptotagmin-2

      See identical proteins and their annotated locations for NP_796376.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the more prevalent variant. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC104463, AC118556, BC100815, DA098279
      Consensus CDS
      CCDS1427.1
      UniProtKB/Swiss-Prot
      Q496K5, Q8N9I0, Q8NBE5
      Related
      ENSP00000356237.4, ENST00000367268.5
      Conserved Domains (2) summary
      cd08385
      Location:139261
      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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      202590596..202710454 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509192.3XP_011507494.1  synaptotagmin-2 isoform X3

      See identical proteins and their annotated locations for XP_011507494.1

      Conserved Domains (3) summary
      cd08385
      Location:142264
      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
      cd21964
      Location:4113
      Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins
    2. XM_017000312.2XP_016855801.1  synaptotagmin-2 isoform X3

      Conserved Domains (3) summary
      cd08385
      Location:142264
      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
      cd21964
      Location:4113
      Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins
    3. XM_017000313.2XP_016855802.1  synaptotagmin-2 isoform X4

      UniProtKB/Swiss-Prot
      Q496K5, Q8N9I0, Q8NBE5
      Conserved Domains (2) summary
      cd08385
      Location:139261
      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. XM_017000311.3XP_016855800.1  synaptotagmin-2 isoform X3

      Conserved Domains (3) summary
      cd08385
      Location:142264
      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
      cd21964
      Location:4113
      Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins
    5. XM_017000310.3XP_016855799.1  synaptotagmin-2 isoform X2

    6. XM_017000309.3XP_016855798.1  synaptotagmin-2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      201852402..201972645 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334403.1XP_054190378.1  synaptotagmin-2 isoform X3

    2. XM_054334402.1XP_054190377.1  synaptotagmin-2 isoform X3

    3. XM_054334404.1XP_054190379.1  synaptotagmin-2 isoform X4

      UniProtKB/Swiss-Prot
      Q496K5, Q8N9I0, Q8NBE5
    4. XM_054334401.1XP_054190376.1  synaptotagmin-2 isoform X3

    5. XM_054334400.1XP_054190375.1  synaptotagmin-2 isoform X2

    6. XM_054334399.1XP_054190374.1  synaptotagmin-2 isoform X1