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SYT9 synaptotagmin 9 [ Homo sapiens (human) ]

Gene ID: 143425, updated on 27-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
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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
  • 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)

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 metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-4,5-bisphosphate binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylserine 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 chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
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 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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