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    SYT9 synaptotagmin 9 [ Homo sapiens (human) ]

    Gene ID: 143425, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SYT9provided by HGNC
    Official Full Name
    synaptotagmin 9provided by HGNC
    Primary source
    HGNC:HGNC:19265
    See related
    Ensembl:ENSG00000170743 MIM:613528; AllianceGenome:HGNC:19265
    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
    Predicted to enable several functions, including SNARE binding activity; calcium ion binding activity; and phospholipid binding activity. Predicted to be involved in calcium-ion regulated exocytosis. Predicted to be located in clathrin-coated endocytic vesicle membrane. Predicted to be active in hippocampal mossy fiber to CA3 synapse; plasma membrane; and secretory vesicle. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in brain (RPKM 1.0), adrenal (RPKM 0.5) and 7 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYT9 in Genome Data Viewer
    Location:
    11p15.4
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (7238778..7469043)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (7297482..7527410)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (7273135..7490274)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NLR family pyrin domain containing 14 Neighboring gene RBMX like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3108 Neighboring gene NANOG hESC enhancer GRCh37_chr11:7296267-7296768 Neighboring gene microRNA 302e Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4359 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:7438930-7440129 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4360 Neighboring gene Sharpr-MPRA regulatory region 13298 Neighboring gene NANOG hESC enhancer GRCh37_chr11:7472795-7473306 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4362 Neighboring gene SYT9 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:7506414-7506918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4364 Neighboring gene leucine-rich repeat extensin-like protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4371 Neighboring gene MPRA-validated peak1190 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4373 Neighboring gene olfactomedin like 1 Neighboring gene PPFIA binding protein 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:7584372-7584873 Neighboring gene uncharacterized LOC105376535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:7595102-7595926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:7595927-7596750 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:7599169-7599403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4374

    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 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 Zika virus infection remodels the expression of the synaptotagmin-9 secretory protein. Leiva S, et al. Biol Chem, 2024 Mar 25. PMID 37677740
    2. A genetic variant in a homocysteine metabolic gene that increases the risk of congenital cardiac septal defects in Han Chinese populations. Xie HH, et al. IUBMB Life, 2017 Sep. PMID 28834160
    3. Ca2+-dependent synaptotagmin binding to SNAP-25 is essential for Ca2+-triggered exocytosis. Zhang X, et al. Neuron, 2002 May 16. PMID 12062043
    4. Synaptotagmin IX, a possible linker between the perinuclear endocytic recycling compartment and the microtubules. Haberman Y, et al. J Cell Sci, 2003 Nov 1. PMID 12966166
    5. Regulated exocytosis contributes to protein kinase C potentiation of vanilloid receptor activity. Morenilla-Palao C, et al. J Biol Chem, 2004 Jun 11. PMID 15066994

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Zika virus infection remodels the expression of the synaptotagmin-9 secretory protein.
      Title: The Zika virus infection remodels the expression of the synaptotagmin-9 secretory protein.
    2. The intronic SYT9 variant rs11041321, which exhibits a significant genome-wide association with circulating homocysteine, was associated with the occurrence of congenital cardiac septal defects (CCSDs). This finding helps to characterize the unexpected role of SYT9 in homocysteine metabolism and the development of CCSDs, which further highlighted the interplay of diet, genetics, and human birth defects
      Title: A genetic variant in a homocysteine metabolic gene that increases the risk of congenital cardiac septal defects in Han Chinese populations.
    3. SYT9 expression is significantly downregulated in human masticatory mucosa during wound healing
      Title: Human gingiva transcriptome during wound healing.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    EBI GWAS Catalog

    Description
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    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

    Clone Names

    • FLJ45896

    Gene Ontology Provided by GOA

    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 identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol-4,5-bisphosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in calcium-dependent activation of synaptic vesicle fusion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of vesicle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    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 hippocampal mossy fiber to CA3 synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    synaptotagmin-9
    Names
    synaptotagmin IX
    sytIX

    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_175733.4 → NP_783860.1  synaptotagmin-9

      See identical proteins and their annotated locations for NP_783860.1

      Status: VALIDATED

      Source sequence(s)
      AC027804, AC060799, AC107884
      Consensus CDS
      CCDS7778.1
      UniProtKB/Swiss-Prot
      Q86SS6
      UniProtKB/TrEMBL
      B2RCA8
      Related
      ENSP00000324419.6, ENST00000318881.11
      Conserved Domains (2) summary
      cd08403
      Location:354 → 487
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
      cl14603
      Location:221 → 345
      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      7238778..7469043
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011519902.3 → XP_011518204.1  synaptotagmin-9 isoform X3

      UniProtKB/TrEMBL
      B2RCA8
      Conserved Domains (2) summary
      cd08403
      Location:322 → 455
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
      cl14603
      Location:189 → 313
      C2; C2 domain

    2. XM_047426379.1 → XP_047282335.1  synaptotagmin-9 isoform X6

    3. XM_011519901.3 → XP_011518203.1  synaptotagmin-9 isoform X2

      UniProtKB/TrEMBL
      B2RCA8
      Conserved Domains (2) summary
      cd08403
      Location:354 → 487
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
      cl14603
      Location:221 → 345
      C2; C2 domain

    4. XM_011519900.3 → XP_011518202.1  synaptotagmin-9 isoform X1

      UniProtKB/TrEMBL
      B2RCA8
      Conserved Domains (2) summary
      cd08403
      Location:354 → 487
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
      cl14603
      Location:221 → 345
      C2; C2 domain

    5. XM_011519904.3 → XP_011518206.1  synaptotagmin-9 isoform X5

      UniProtKB/TrEMBL
      B2RCA8
      Conserved Domains (2) summary
      cd08403
      Location:354 → 487
      C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
      cl14603
      Location:221 → 345
      C2; C2 domain

    6. XM_047426378.1 → XP_047282334.1  synaptotagmin-9 isoform X4

    7. XM_047426380.1 → XP_047282336.1  synaptotagmin-9 isoform X7

    8. XM_011519907.3 → XP_011518209.1  synaptotagmin-9 isoform X9

      UniProtKB/TrEMBL
      E9PDN4, H0YCQ9, Q8NCP8
      Conserved Domains (1) summary
      cl14603
      Location:221 → 345
      C2; C2 domain

    9. XM_011519906.3 → XP_011518208.1  synaptotagmin-9 isoform X8

      UniProtKB/TrEMBL
      E9PDN4, H0YCQ9
      Related
      ENSP00000432141.2, ENST00000524820.6
      Conserved Domains (1) summary
      cl14603
      Location:221 → 345
      C2; C2 domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      7297482..7527410
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367700.1 → XP_054223675.1  synaptotagmin-9 isoform X3

    2. XM_054367703.1 → XP_054223678.1  synaptotagmin-9 isoform X6

    3. XM_054367699.1 → XP_054223674.1  synaptotagmin-9 isoform X2

    4. XM_054367698.1 → XP_054223673.1  synaptotagmin-9 isoform X1

    5. XM_054367701.1 → XP_054223676.1  synaptotagmin-9 isoform X4

    6. XM_054367702.1 → XP_054223677.1  synaptotagmin-9 isoform X5

    7. XM_054367704.1 → XP_054223679.1  synaptotagmin-9 isoform X7

    8. XM_054367706.1 → XP_054223681.1  synaptotagmin-9 isoform X9

    9. XM_054367705.1 → XP_054223680.1  synaptotagmin-9 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86SS6.1 GenPept UniProtKB/Swiss-Prot:Q86SS6

    Gene LinkOut

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

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