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SYT2 synaptotagmin 2 [ Homo sapiens (human) ]

Gene ID: 127833, updated on 1-Mar-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
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Genomic context

See SYT2 in Genome Data Viewer
Location:
1q32.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202590596..202710454, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201852402..201972645, complement)
105.20220307 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 calcium ion binding 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 clathrin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables inositol 1,3,4,5 tetrakisphosphate binding ISS
Inferred from Sequence or Structural Similarity
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 syntaxin binding IBA
Inferred from Biological aspect of Ancestor
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 cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to calcium ion IBA
Inferred from Biological aspect of Ancestor
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 dopamine secretion IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in synaptic vesicle endocytosis 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)

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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_2023_10

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