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    Syt6 synaptotagmin VI [ Mus musculus (house mouse) ]

    Gene ID: 54524, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Syt6provided by MGI
    Official Full Name
    synaptotagmin VIprovided by MGI
    Primary source
    MGI:MGI:1859544
    See related
    Ensembl:ENSMUSG00000027849 AllianceGenome:MGI:1859544
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    sytVI; 3110037A08Rik
    Summary
    Enables calcium-dependent protein binding activity; phospholipid binding activity; and protein dimerization activity. Involved in acrosome reaction. Located in cytoplasmic side of plasma membrane; cytosol; and perinuclear endoplasmic reticulum. Is expressed in several structures, including alimentary system; genitourinary system; integumental system; nervous system; and sensory organ. Orthologous to human SYT6 (synaptotagmin 6). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in frontal lobe adult (RPKM 13.3), CNS E18 (RPKM 5.5) and 6 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Syt6 in Genome Data Viewer
    Location:
    3 F2.2; 3 45.45 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (103482561..103552883)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (103575245..103645567)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 25199 Neighboring gene predicted gene, 34049 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:103445250-103445524 Neighboring gene STARR-seq mESC enhancer starr_08600 Neighboring gene autophagy related 4A, pseudogene Neighboring gene predicted gene, 57719 Neighboring gene uncharacterized LOC108168889

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Lymph node mapping in patients with bladder cancer undergoing radical cystectomy and lymph node dissection to the level of the inferior mesenteric artery. Jensen JB, et al. BJU Int, 2010 Jul. PMID 20002670
    2. Synaptotagmins 3 and 7 mediate the majority of asynchronous release from synapses in the cerebellum and hippocampus. Weingarten DJ, et al. Cell Rep, 2024 Aug 27. PMID 39116209, Free PMC Article
    3. A novel alternatively spliced variant of synaptotagmin VI lacking a transmembrane domain. Implications for distinct functions of the two isoforms. Fukuda M, et al. J Biol Chem, 1999 Oct 29. PMID 10531344
    4. Synaptotagmin-3 drives AMPA receptor endocytosis, depression of synapse strength, and forgetting. Awasthi A, et al. Science, 2019 Jan 4. PMID 30545844
    5. IgSF molecule MDGA1 is involved in radial migration and positioning of a subset of cortical upper-layer neurons. Ishikawa T, et al. Dev Dyn, 2011 Jan. PMID 21104742

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (1) 

    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 MGI

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables calcium-dependent protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables clathrin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylserine binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    NOT enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables syntaxin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in acrosomal vesicle exocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in acrosome reaction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chemical synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in postsynaptic dense core vesicle exocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of calcium ion-dependent 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
    located_in cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in exocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in synaptic membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    synaptotagmin-6

    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_001276676.3 → NP_001263605.1  synaptotagmin-6 isoform 2

      See identical proteins and their annotated locations for NP_001263605.1

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      Q05BE2, Q8C8S6
      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    2. NM_001276677.3 → NP_001263606.1  synaptotagmin-6 isoform 3

      See identical proteins and their annotated locations for NP_001263606.1

      Status: VALIDATED

      Source sequence(s)
      AC123057
      Consensus CDS
      CCDS71296.1
      UniProtKB/TrEMBL
      Q6P1H9, Q8C8S6
      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    3. NM_001276679.2 → NP_001263608.1  synaptotagmin-6 isoform 3

      See identical proteins and their annotated locations for NP_001263608.1

      Status: VALIDATED

      Source sequence(s)
      AC123057
      Consensus CDS
      CCDS71296.1
      UniProtKB/TrEMBL
      Q6P1H9, Q8C8S6
      Related
      ENSMUSP00000112486.2, ENSMUST00000118117.8
      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    4. NM_001276680.2 → NP_001263609.1  synaptotagmin-6 isoform 4

      See identical proteins and their annotated locations for NP_001263609.1

      Status: VALIDATED

      Source sequence(s)
      AC123057
      Consensus CDS
      CCDS71297.1
      UniProtKB/TrEMBL
      Q3UY13
      Related
      ENSMUSP00000113287.2, ENSMUST00000118563.3
      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cl14603
      Location:279 → 314
      C2; C2 domain

    5. NM_001276681.2 → NP_001263610.1  synaptotagmin-6 isoform 3

      See identical proteins and their annotated locations for NP_001263610.1

      Status: VALIDATED

      Source sequence(s)
      AC123057
      Consensus CDS
      CCDS71296.1
      UniProtKB/TrEMBL
      Q6P1H9, Q8C8S6
      Related
      ENSMUSP00000113373.2, ENSMUST00000117221.9
      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    6. NM_001428812.1 → NP_001415741.1  synaptotagmin-6 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      Q8C8S6

    7. NM_001428813.1 → NP_001415742.1  synaptotagmin-6 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      A0A5F8MPS8

    8. NM_001428814.1 → NP_001415743.1  synaptotagmin-6 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      Q05BE2, Q8C8S6

    9. NM_001428815.1 → NP_001415744.1  synaptotagmin-6 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      Q05BE2, Q8C8S6

    10. NM_001428816.1 → NP_001415745.1  synaptotagmin-6 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      Q05BE2, Q8C8S6

    11. NM_001428817.1 → NP_001415746.1  synaptotagmin-6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      Q6P1H9, Q8C8S6

    12. NM_001428818.1 → NP_001415747.1  synaptotagmin-6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      Q6P1H9, Q8C8S6

    13. NM_001428819.1 → NP_001415748.1  synaptotagmin-6 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC123057
      UniProtKB/TrEMBL
      Q6P1H9, Q8C8S6

    14. NM_018800.6 → NP_061270.2  synaptotagmin-6 isoform 1

      See identical proteins and their annotated locations for NP_061270.2

      Status: VALIDATED

      Source sequence(s)
      AC123057
      Consensus CDS
      CCDS38575.1
      UniProtKB/Swiss-Prot
      E9QJV2, Q9QUK7, Q9R0N8
      UniProtKB/TrEMBL
      Q8C8S6
      Related
      ENSMUSP00000088196.5, ENSMUST00000090697.11
      Conserved Domains (2) summary
      cd08385
      Location:231 → 355
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:364 → 497
      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_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000069.7 Reference GRCm39 C57BL/6J

      Range
      103482561..103552883
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036163165.1 → XP_036019058.1  synaptotagmin-6 isoform X4

      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    2. XM_006501704.5 → XP_006501767.1  synaptotagmin-6 isoform X1

      Related
      ENSMUSP00000159100.2, ENSMUST00000239027.2
      Conserved Domains (2) summary
      cd08385
      Location:231 → 355
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:364 → 497
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    3. XM_006501705.3 → XP_006501768.1  synaptotagmin-6 isoform X2

      Conserved Domains (2) summary
      cd08385
      Location:231 → 355
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:364 → 497
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    4. XM_006501707.4 → XP_006501770.1  synaptotagmin-6 isoform X3

      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    5. XM_006501706.3 → XP_006501769.1  synaptotagmin-6 isoform X3

      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    6. XM_006501708.3 → XP_006501771.1  synaptotagmin-6 isoform X3

      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    7. XM_030252690.2 → XP_030108550.1  synaptotagmin-6 isoform X3

      UniProtKB/TrEMBL
      Q05BE2, Q8C8S6
      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    8. XM_036163164.1 → XP_036019057.1  synaptotagmin-6 isoform X3

      UniProtKB/TrEMBL
      Q05BE2, Q8C8S6
      Conserved Domains (2) summary
      cd08385
      Location:146 → 270
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08403
      Location:279 → 412
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

    RNA

    1. XR_375547.5 RNA Sequence

      Related
      ENSMUST00000132325.10

    2. XR_375546.4 RNA Sequence

    3. XR_003954362.2 RNA Sequence

    4. XR_003954361.1 RNA Sequence

    5. XR_003954360.2 RNA Sequence

    6. XR_004941361.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9R0N8.2 GenPept UniProtKB/Swiss-Prot:Q9R0N8

    Gene LinkOut

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

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