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SYT3 synaptotagmin 3 [ Homo sapiens (human) ]

Gene ID: 84258, updated on 11-Apr-2024

Summary

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Official Symbol
SYT3provided by HGNC
Official Full Name
synaptotagmin 3provided by HGNC
Primary source
HGNC:HGNC:11511
See related
Ensembl:ENSG00000213023 MIM:600327; AllianceGenome:HGNC:11511
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
SytIII
Summary
Predicted to enable several functions, including phospholipid binding activity; protein dimerization activity; and syntaxin binding activity. Involved in positive regulation of dendrite extension. Located in endosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 3.3), testis (RPKM 0.5) and 3 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
19q13.33
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (50621977..50658105, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (53710730..53746830, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (51125234..51143138, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904747 Neighboring gene leucine rich repeat containing 4B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:51055019-51055930 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10973 Neighboring gene CRISPRi-validated cis-regulatory element chr19.5650 Neighboring gene small NF90 (ILF3) associated RNA F Neighboring gene Sharpr-MPRA regulatory region 12037 Neighboring gene Sharpr-MPRA regulatory region 12891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14994 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10974 Neighboring gene chromosome 19 open reading frame 81 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:51165023-51165681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:51165682-51166339 Neighboring gene SH3 and multiple ankyrin repeat domains 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10976 Neighboring gene C-type lectin domain containing 11A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. The C terminus of SNAP25 is essential for Ca(2+)-dependent binding of synaptotagmin to SNARE complexes. Gerona RR, et al. J Biol Chem, 2000 Mar 3. PMID 10692432
  2. Control of plasma membrane lipid homeostasis by the extended synaptotagmins. Saheki Y, et al. Nat Cell Biol, 2016 May. PMID 27065097, Free PMC Article
  3. Sr2+ binding to the Ca2+ binding site of the synaptotagmin 1 C2B domain triggers fast exocytosis without stimulating SNARE interactions. Shin OH, et al. Neuron, 2003 Jan 9. PMID 12526776
  4. Synaptotagmin genes on mouse chromosomes 1, 7, and 10 and human chromosome 19. Jones JM, et al. Mamm Genome, 1995 Mar. PMID 7749232
  5. SYNCRIP, a cytoplasmic counterpart of heterogeneous nuclear ribonucleoprotein R, interacts with ubiquitous synaptotagmin isoforms. Mizutani A, et al. J Biol Chem, 2000 Mar 31. PMID 10734137

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • DKFZp761O132

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SNARE binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 NAS
Non-traceable Author Statement
more info
 PubMed 
enables clathrin binding IBA
Inferred from Biological aspect of Ancestor
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 
Process Evidence Code Pubs
involved_in calcium-ion regulated exocytosis 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 
Component Evidence Code Pubs
located_in endosome IDA
Inferred from Direct Assay
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 transport vesicle membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
synaptotagmin-3
Names
synaptotagmin III

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.

mRNA and Protein(s)

  1. NM_001160328.2 → NP_001153800.1  synaptotagmin-3

    See identical proteins and their annotated locations for NP_001153800.1

    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 protein.
    Source sequence(s)
    AC008743
    Consensus CDS
    CCDS12798.1
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1
    Related
    ENSP00000468982.1, ENST00000593901.5
    Conserved Domains (2) summary
    cd08385
    Location:299 → 424
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:433 → 567
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  2. NM_001160329.2 → NP_001153801.1  synaptotagmin-3

    See identical proteins and their annotated locations for NP_001153801.1

    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 protein.
    Source sequence(s)
    AC008743
    Consensus CDS
    CCDS12798.1
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1
    Related
    ENSP00000469398.1, ENST00000600079.6
    Conserved Domains (2) summary
    cd08385
    Location:299 → 424
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:433 → 567
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

  3. NM_001424344.1 → NP_001411273.1  synaptotagmin-3

    Status: VALIDATED

    Source sequence(s)
    AC008743
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1

  4. NM_001424345.1 → NP_001411274.1  synaptotagmin-3

    Status: VALIDATED

    Source sequence(s)
    AC008743
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1

  5. NM_001424346.1 → NP_001411275.1  synaptotagmin-3

    Status: VALIDATED

    Source sequence(s)
    AC008743
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1

  6. NM_001424347.1 → NP_001411276.1  synaptotagmin-3

    Status: VALIDATED

    Source sequence(s)
    CP068259
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1

  7. NM_001424348.1 → NP_001411277.1  synaptotagmin-3

    Status: VALIDATED

    Source sequence(s)
    CP068259
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1

  8. NM_001424349.1 → NP_001411278.1  synaptotagmin-3

    Status: VALIDATED

    Source sequence(s)
    CP068259
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1

  9. NM_001424350.1 → NP_001411279.1  synaptotagmin-3

    Status: VALIDATED

    Source sequence(s)
    CP068259
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1

  10. NM_032298.3 → NP_115674.1  synaptotagmin-3

    See identical proteins and their annotated locations for NP_115674.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC008743
    Consensus CDS
    CCDS12798.1
    UniProtKB/Swiss-Prot
    Q8N5Z1, Q8N640, Q9BQG1
    Related
    ENSP00000340914.3, ENST00000338916.8
    Conserved Domains (2) summary
    cd08385
    Location:299 → 424
    C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
    cd08403
    Location:433 → 567
    C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    50621977..50658105 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    53710730..53746830 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BQG1.1 GenPept UniProtKB/Swiss-Prot:Q9BQG1

Gene LinkOut

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