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    SYT5 synaptotagmin 5 [ Homo sapiens (human) ]

    Gene ID: 6861, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SYT5provided by HGNC
    Official Full Name
    synaptotagmin 5provided by HGNC
    Primary source
    HGNC:HGNC:11513
    See related
    Ensembl:ENSG00000129990 MIM:600782; AllianceGenome:HGNC:11513
    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
    Summary
    Synaptotagmins, such as SYT5, are a family of type III membrane proteins characterized by cytoplasmic repeats related to protein kinase C (see MIM 176960) regulatory (C2) domains, which are thought to bind calcium. Synaptotagmins may act both as negative regulators of vesicle fusion, allowing fusion in the presence of calcium, and as calcium receptors or sensor molecules (summary by Hudson and Birnbaum, 1995 [PubMed 7597049]).[supplied by OMIM, Feb 2011]
    Expression
    Biased expression in brain (RPKM 20.3) and adrenal (RPKM 2.1) See more
    Orthologs
    mouse all
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    Genomic context

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    See SYT5 in Genome Data Viewer
    Location:
    19q13.42; 11p
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (55171196..55180289, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (58265259..58274351, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55682564..55691657, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:55672120-55673046 Neighboring gene DNAAF3 antisense RNA 1 Neighboring gene dynein axonemal assembly factor 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:55677361-55677592 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15078 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:55691190-55691602 Neighboring gene protein tyrosine phosphatase receptor type H Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:55701037-55701536 Neighboring gene uncharacterized LOC124904771

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Cloning, expression, purification, crystallization and preliminary X-ray diffraction crystallographic study of human synaptotagmin 5 C2A domain. Qiu X, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2011 Nov 1. PMID 22102235, Free PMC Article
    2. Evidence for the association of synaptotagmin with glutathione S-transferases: implications for a novel function in human breast cancer. Sreenath AS, et al. Clin Biochem, 2005 May. PMID 15820774
    3. Identification of a nonneuronal isoform of synaptotagmin. Hudson AW, et al. Proc Natl Acad Sci U S A, 1995 Jun 20. PMID 7597049, Free PMC Article
    4. Human synaptotagmin V (SYT5): sequence, genomic structure, and chromosomal location. Craxton M, et al. Genomics, 1997 May 15. PMID 9177789
    5. Structural analysis of Ca(2+)-binding pocket of synaptotagmin 5 C2A domain. Qiu X, et al. Int J Biol Macromol, 2017 Feb. PMID 27793683

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ca(2+)-binding pocket of synaptotagmin 5 C2A domain
      Title: Structural analysis of Ca(2+)-binding pocket of synaptotagmin 5 C2A domain.
    2. crystals of synaptotagmin 5 belonged to the hexagonal space group P6(5), with unit-cell parameters a = b = 93.97, c = 28.05 A.
      Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction crystallographic study of human synaptotagmin 5 C2A domain.
    3. This protein has been found differentially expressed in thalami from patients with schizophrenia.
      Title: Proteome analysis of the thalamus and cerebrospinal fluid reveals glycolysis dysfunction and potential biomarkers candidates for schizophrenia.
    4. results suggest a novel putative functional role for the GST-synaptotagmin V complex in human breast cancers. As this association of GST M1-synaptotagmin was not seen in adjacent non-cancerous tissues, this can be used as a marker for breast cancers.
      Title: Evidence for the association of synaptotagmin with glutathione S-transferases: implications for a novel function in human breast cancer.
    Submit: New GeneRIF Correction

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 phosphatidylinositol-4,5-bisphosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein heterodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables syntaxin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in calcium-dependent activation of synaptic vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chemical synaptic transmission TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of calcium ion-dependent exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of calcium ion-dependent exocytosis IEA
    Inferred from Electronic Annotation
    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
    		  
    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
    		  
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in neuronal dense core vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in proximal neuron projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in recycling endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synaptic vesicle membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    synaptotagmin-5
    Names
    synaptotagmin V
    sytV

    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_001297774.2 → NP_001284703.1  synaptotagmin-5 isoform 2

      See identical proteins and their annotated locations for NP_001284703.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and contains multiple coding region differences, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC010327, AK295337, BM311004
      Consensus CDS
      CCDS74455.1
      UniProtKB/Swiss-Prot
      O00445
      Related
      ENSP00000465576.1, ENST00000590851.5
      Conserved Domains (2) summary
      cd08385
      Location:106 → 228
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cl14603
      Location:236 → 370
      C2; C2 domain

    2. NM_003180.3 → NP_003171.2  synaptotagmin-5 isoform 1

      See identical proteins and their annotated locations for NP_003171.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC010327, BC046157, BQ417474, DA529870
      Consensus CDS
      CCDS12919.1
      UniProtKB/Swiss-Prot
      B3KWJ8, B7Z300, O00445, Q86X72
      UniProtKB/TrEMBL
      Q05BS5
      Related
      ENSP00000346265.2, ENST00000354308.8
      Conserved Domains (2) summary
      cd08385
      Location:109 → 231
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cl14603
      Location:240 → 374
      C2; C2 domain

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      55171196..55180289 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439257.1 → XP_047295213.1  synaptotagmin-5 isoform X2

      UniProtKB/TrEMBL
      Q4FD32

    2. XM_017027175.2 → XP_016882664.1  synaptotagmin-5 isoform X1

      UniProtKB/Swiss-Prot
      B3KWJ8, B7Z300, O00445, Q86X72
      UniProtKB/TrEMBL
      Q05BS5
      Conserved Domains (2) summary
      cd08385
      Location:109 → 231
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cl14603
      Location:240 → 374
      C2; C2 domain

    3. XM_047439256.1 → XP_047295212.1  synaptotagmin-5 isoform X1

      UniProtKB/Swiss-Prot
      B3KWJ8, B7Z300, O00445, Q86X72

    4. XM_006723339.4 → XP_006723402.1  synaptotagmin-5 isoform X1

      See identical proteins and their annotated locations for XP_006723402.1

      UniProtKB/Swiss-Prot
      B3KWJ8, B7Z300, O00445, Q86X72
      UniProtKB/TrEMBL
      Q05BS5
      Related
      ENSP00000442896.1, ENST00000537500.5
      Conserved Domains (2) summary
      cd08385
      Location:109 → 231
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cl14603
      Location:240 → 374
      C2; C2 domain

    5. XM_006723341.4 → XP_006723404.1  synaptotagmin-5 isoform X3

      Conserved Domains (2) summary
      cd08385
      Location:106 → 228
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cl14603
      Location:237 → 371
      C2; C2 domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      58265259..58274351 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321845.1 → XP_054177820.1  synaptotagmin-5 isoform X1

      UniProtKB/Swiss-Prot
      B3KWJ8, B7Z300, O00445, Q86X72

    2. XM_054321847.1 → XP_054177822.1  synaptotagmin-5 isoform X1

      UniProtKB/Swiss-Prot
      B3KWJ8, B7Z300, O00445, Q86X72

    3. XM_054321846.1 → XP_054177821.1  synaptotagmin-5 isoform X1

      UniProtKB/Swiss-Prot
      B3KWJ8, B7Z300, O00445, Q86X72

    4. XM_054321849.1 → XP_054177824.1  synaptotagmin-5 isoform X3

    5. XM_054321848.1 → XP_054177823.1  synaptotagmin-5 isoform X2

      UniProtKB/TrEMBL
      Q4FD32
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O00445.2 GenPept UniProtKB/Swiss-Prot:O00445

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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