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Syt6 synaptotagmin VI [ Mus musculus (house mouse) ]

Gene ID: 54524, updated on 18-Apr-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 cytosol; perinuclear endoplasmic reticulum; and plasma membrane. Is extrinsic component of membrane and integral component of membrane. 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, Apr 2022]
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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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. Synaptotagmin-3 drives AMPA receptor endocytosis, depression of synapse strength, and forgetting. Awasthi A, et al. Science, 2019 Jan 4. PMID 30545844
  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. 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
  5. Synaptotagmin VI and VIII and syntaxin 2 are essential for the mouse sperm acrosome reaction. Hutt DM, et al. J Biol Chem, 2005 May 27. PMID 15774481

See all (32) 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 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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables calcium-dependent protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables clathrin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IBA
Inferred from Biological aspect of Ancestor
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 calcium-ion regulated exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in postsynaptic dense core vesicle exocytosis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
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 synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in synaptic membrane ISO
Inferred from Sequence Orthology
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

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

    Status: VALIDATED

    Source sequence(s)
    AC123057

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

    Status: VALIDATED

    Source sequence(s)
    AC123057

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

    Status: VALIDATED

    Source sequence(s)
    AC123057

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

    Status: VALIDATED

    Source sequence(s)
    AC123057

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

    Status: VALIDATED

    Source sequence(s)
    AC123057

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

    Status: VALIDATED

    Source sequence(s)
    AC123057

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

    Status: VALIDATED

    Source sequence(s)
    AC123057

  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

    UniProtKB/TrEMBL
    A0A5F8MPS8
    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

    UniProtKB/TrEMBL
    Q05BE2
    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

    UniProtKB/TrEMBL
    Q05BE2
    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

    UniProtKB/TrEMBL
    Q05BE2
    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

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