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    Syt5 synaptotagmin 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 54309, updated on 11-Apr-2024

    Summary

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    Official Symbol
    Syt5provided by RGD
    Official Full Name
    synaptotagmin 5provided by RGD
    Primary source
    RGD:3806
    See related
    Ensembl:ENSRNOG00000018217 AllianceGenome:RGD:3806
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    SytIX
    Summary
    Enables calcium-dependent phospholipid binding activity; clathrin binding activity; and syntaxin binding activity. Predicted to be involved in cellular response to calcium ion; regulation of secretion by cell; and synaptic vesicle cycle. Predicted to be located in neuronal cell body; perinuclear region of cytoplasm; and proximal neuron projection. Predicted to be active in axon; plasma membrane; and secretory vesicle. Predicted to be integral component of neuronal dense core vesicle membrane. Orthologous to human SYT5 (synaptotagmin 5). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 245.8), Lung (RPKM 34.5) and 1 other tissue See more
    Orthologs
    human mouse all
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    Genomic context

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    See Syt5 in Genome Data Viewer
    Location:
    1q12
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (78320034..78327750)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (69277351..69285071)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (72859806..72867934)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene transmembrane protein 86B Neighboring gene protein tyrosine phosphatase, receptor type, H Neighboring gene uncharacterized LOC108349515 Neighboring gene dynein, axonemal, assembly factor 3 Neighboring gene troponin I3, cardiac type

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Synaptotagmin V and IX isoforms control Ca2+ -dependent insulin exocytosis. Iezzi M, et al. J Cell Sci, 2004 Jul 1. PMID 15190121
    2. Synaptotagmin V: a novel synaptotagmin isoform expressed in rat brain. Craxton M, et al. FEBS Lett, 1995 Mar 20. PMID 7698322
    3. Structural analysis of Ca(2+)-binding pocket of synaptotagmin 5 C2A domain. Qiu X, et al. Int J Biol Macromol, 2017 Feb. PMID 27793683
    4. Synaptotagmins I and IX function redundantly in regulated exocytosis but not endocytosis in PC12 cells. Lynch KL, et al. J Cell Sci, 2007 Feb 15. PMID 17264148
    5. Classical protein kinase C(s) regulates targeting of synaptotagmin IX to the endocytic recycling compartment. Haberman Y, et al. J Cell Sci, 2005 Apr 15. PMID 15784685

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Syt1 and Syt5 function redundantly in regulated exocytosis but not endocytosis in PC12 cells.
      Title: Synaptotagmins I and IX function redundantly in regulated exocytosis but not endocytosis in PC12 cells.
    2. Syt V is a dense-core vesicle-specific Syt isoform that controls a specific type of Ca2+-regulated secretion
      Title: Synaptotagmin V is targeted to dense-core vesicles that undergo calcium-dependent exocytosis in PC12 cells.
    3. We show that targeting of Syt IX to the ERC involves constitutive trafficking to the plasma membrane followed by internalization and transport to the ERC.
      Title: Classical protein kinase C(s) regulates targeting of synaptotagmin IX to the endocytic recycling compartment.
    4. Syt V and Syt IX are directly involved in the Ca2+ -dependent stimulation of exocytosis [Synaptotagmin IX]
      Title: Synaptotagmin V and IX isoforms control Ca2+ -dependent insulin exocytosis.
    5. Syt IX is involved in regulating transport from the endocytic recycling compartment to the cell surface-( Synaptotagmin IX (Syt IX)
      Title: Synaptotagmin IX, a possible linker between the perinuclear endocytic recycling compartment and the microtubules.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC105442

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables SNARE binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    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 phospholipid binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables clathrin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables clathrin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-4,5-bisphosphate binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylserine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylserine binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables syntaxin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in calcium ion-regulated exocytosis of neurotransmitter IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in calcium-ion regulated exocytosis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of calcium ion-dependent exocytosis ISO
    Inferred from Sequence Orthology
    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
    		  
    is_active_in dense core granule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dense core granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in exocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in neuron projection ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in neuronal cell body ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in neuronal dense core vesicle membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in proximal neuron projection ISO
    Inferred from Sequence Orthology
    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 IX
    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_019350.2 → NP_062223.1  synaptotagmin-5

      See identical proteins and their annotated locations for NP_062223.1

      Status: PROVISIONAL

      Source sequence(s)
      BC092198
      UniProtKB/Swiss-Prot
      P47861, Q56A28
      UniProtKB/TrEMBL
      A6KNM3
      Related
      ENSRNOP00000024547.4, ENSRNOT00000024547.5
      Conserved Domains (3) summary
      cd08385
      Location:108 → 230
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08402
      Location:240 → 374
      C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
      cl41733
      Location:6 → 76
      Syt1_2_N; N-terminal domain of synaptotagmin-1 and -2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      78320034..78327750
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006228287.5 → XP_006228349.1  synaptotagmin-5 isoform X1

      UniProtKB/TrEMBL
      A6KNM3
      Conserved Domains (2) summary
      cd08385
      Location:108 → 230
      C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10
      cd08402
      Location:239 → 373
      C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P47861.1 GenPept UniProtKB/Swiss-Prot:P47861

    Gene LinkOut

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

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