This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that are known calcium sensors and mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. The encoded protein is also a substrate for ubiquitin-E3-ligase parkin. The gene has previously been referred to as synaptotagmin XII but has been re... See more...

Aliases for SYT11 Gene

Aliases for SYT11 Gene

  • Synaptotagmin 11 2 3 5
  • Synaptotagmin XI 2 3 4
  • Synaptotagmin-11 3 4
  • SytXI 3 4
  • Synaptotagmin 12 3
  • KIAA0080 4
  • SYT12 3

External Ids for SYT11 Gene

Previous GeneCards Identifiers for SYT11 Gene

  • GC01U990248
  • GC01P151576
  • GC01P152607
  • GC01P153046
  • GC01P152642
  • GC01P154095
  • GC01P127190

Summaries for SYT11 Gene

Entrez Gene Summary for SYT11 Gene

  • This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that are known calcium sensors and mediate calcium-dependent regulation of membrane trafficking in synaptic transmission. The encoded protein is also a substrate for ubiquitin-E3-ligase parkin. The gene has previously been referred to as synaptotagmin XII but has been renamed synaptotagmin XI to be consistent with mouse and rat official nomenclature. [provided by RefSeq, Apr 2010]

GeneCards Summary for SYT11 Gene

SYT11 (Synaptotagmin 11) is a Protein Coding gene. Diseases associated with SYT11 include Parkinson Disease, Late-Onset. Among its related pathways are Parkinsons Disease Pathway and Chks in Checkpoint Regulation. Gene Ontology (GO) annotations related to this gene include calcium ion binding and syntaxin binding. An important paralog of this gene is SYT4.

UniProtKB/Swiss-Prot Summary for SYT11 Gene

  • Synaptotagmin family member involved in vesicular and membrane trafficking which does not bind Ca(2+). Inhibits clathrin-mediated and bulk endocytosis, functions to ensure precision in vesicle retrieval. Plays an important role in dopamine transmission by regulating endocytosis and the vesicle-recycling process. Essential component of a neuronal vesicular trafficking pathway that differs from the synaptic vesicle trafficking pathway but is crucial for development and synaptic plasticity. In macrophages and microglia, inhibits the conventional cytokine secretion, of at least IL6 and TNF, and phagocytosis. In astrocytes, regulates lysosome exocytosis, mechanism required for the repair of injured astrocyte cell membrane (By similarity). Required for the ATP13A2-mediated regulation of the autophagy-lysosome pathway (PubMed:27278822).

Gene Wiki entry for SYT11 Gene

Additional gene information for SYT11 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYT11 Gene

Genomics for SYT11 Gene

GeneHancer (GH) Regulatory Elements for SYT11 Gene

Promoters and enhancers for SYT11 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYT11 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYT11

Top Transcription factor binding sites by QIAGEN in the SYT11 gene promoter:
  • AP-4
  • c-Myb
  • Pax-5
  • POU2F1
  • POU2F1a
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • RFX1
  • YY1

Genomic Locations for SYT11 Gene

Genomic Locations for SYT11 Gene
chr1:155,859,469-155,885,199
(GRCh38/hg38)
Size:
25,731 bases
Orientation:
Plus strand
chr1:155,829,260-155,854,990
(GRCh37/hg19)
Size:
25,731 bases
Orientation:
Plus strand

Genomic View for SYT11 Gene

Genes around SYT11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYT11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYT11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYT11 Gene

Proteins for SYT11 Gene

  • Protein details for SYT11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BT88-SYT11_HUMAN
    Recommended name:
    Synaptotagmin-11
    Protein Accession:
    Q9BT88
    Secondary Accessions:
    • Q14998
    • Q5W0D4
    • Q68CT5
    • Q8IXU3
    • Q96SU2

    Protein attributes for SYT11 Gene

    Size:
    431 amino acids
    Molecular mass:
    48297 Da
    Quaternary structure:
    • Homodimer. Can also form heterodimers. Interacts with PRKN (PubMed:12925569). Interacts (via C2 2 domain) with AGO2 and SND1; the interaction with SND1 is direct. Interacts with KIF1A; the interaction increases in presence of calcium (By similarity).
    SequenceCaution:
    • Sequence=BAA07527.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

neXtProt entry for SYT11 Gene

Post-translational modifications for SYT11 Gene

  • Ubiquitinated, at least by PRKN, and targeted to the proteasome complex for degradation (PubMed:12925569, PubMed:27278822). Ubiquitination is inhibited by ATP13A2 (PubMed:27278822).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYT11 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SYT11 Gene

Domains & Families for SYT11 Gene

Gene Families for SYT11 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SYT11 Gene

Blocks:
  • C2 domain
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYT11 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ50786, highly similar to Synaptotagmin-11 (B4DK40_HUMAN)
  • Synaptotagmin XI (SYT11_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BT88

UniProtKB/Swiss-Prot:

SYT11_HUMAN :
  • The second C2 domain/C2B is required for the inhibitory role in both clathrin-mediated and bulk endocytosis. The transmembrane domain and the first C2 domain/C2A are critical for the inhibitory role in clathrin-mediated endocytosis or bulk endocytosis, respectively.
  • Belongs to the synaptotagmin family.
Domain:
  • The second C2 domain/C2B is required for the inhibitory role in both clathrin-mediated and bulk endocytosis. The transmembrane domain and the first C2 domain/C2A are critical for the inhibitory role in clathrin-mediated endocytosis or bulk endocytosis, respectively.
  • Unlike in other synaptotagmin family members, the first C2 domain/C2A does not bind Ca(2+) neither mediates Ca(2+)-dependent phospholipid binding. An aspartate-to-serine substitution in this domain inactivates Ca(2+)/phospho-lipid binding.
Family:
  • Belongs to the synaptotagmin family.
genes like me logo Genes that share domains with SYT11: view

Function for SYT11 Gene

Molecular function for SYT11 Gene

UniProtKB/Swiss-Prot Function:
Synaptotagmin family member involved in vesicular and membrane trafficking which does not bind Ca(2+). Inhibits clathrin-mediated and bulk endocytosis, functions to ensure precision in vesicle retrieval. Plays an important role in dopamine transmission by regulating endocytosis and the vesicle-recycling process. Essential component of a neuronal vesicular trafficking pathway that differs from the synaptic vesicle trafficking pathway but is crucial for development and synaptic plasticity. In macrophages and microglia, inhibits the conventional cytokine secretion, of at least IL6 and TNF, and phagocytosis. In astrocytes, regulates lysosome exocytosis, mechanism required for the repair of injured astrocyte cell membrane (By similarity). Required for the ATP13A2-mediated regulation of the autophagy-lysosome pathway (PubMed:27278822).

Phenotypes From GWAS Catalog for SYT11 Gene

Gene Ontology (GO) - Molecular Function for SYT11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000149 SNARE binding IBA 21873635
GO:0001786 phosphatidylserine binding IBA 21873635
GO:0005509 NOT calcium ion binding IBA,ISS --
GO:0005515 protein binding IPI 16189514
GO:0005544 NOT calcium-dependent phospholipid binding ISS,IBA --
genes like me logo Genes that share ontologies with SYT11: view
genes like me logo Genes that share phenotypes with SYT11: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYT11

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYT11 Gene

Localization for SYT11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYT11 Gene

Cytoplasmic vesicle membrane; Single-pass membrane protein. Perikaryon. Golgi apparatus, trans-Golgi network membrane; Single-pass membrane protein. Recycling endosome membrane; Single-pass membrane protein. Lysosome membrane; Single-pass membrane protein. Cytoplasmic vesicle, phagosome. Cell projection, axon. Cell projection, dendrite. Cell junction, synapse, postsynaptic density. Recycling endosome membrane; Single-pass membrane protein. Cytoplasmic vesicle, clathrin-coated vesicle membrane; Single-pass membrane protein. Perikaryon. Note=Localized in vesicles that travels in axonal and dendritic shafts in both anterograde and retrograde directions. In macrophages and microglia, recruited in phagosomes at early stages of phagocytosis (By similarity). Found in the core of the Lewy bodies in the brain of sporadic Parkinson disease patients (PubMed:12925569). {ECO:0000250 UniProtKB:Q9R0N3, ECO:0000269 PubMed:12925569}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYT11 gene
Compartment Confidence
plasma membrane 4
endosome 4
lysosome 4
golgi apparatus 4
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
nucleus 1

Gene Ontology (GO) - Cellular Components for SYT11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001891 phagocytic cup IEA --
GO:0005623 cell IEA --
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome ISS,IEA --
GO:0005802 trans-Golgi network ISS --
genes like me logo Genes that share ontologies with SYT11: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SYT11 Gene

Pathways & Interactions for SYT11 Gene

genes like me logo Genes that share pathways with SYT11: view

Pathways by source for SYT11 Gene

1 Qiagen pathway for SYT11 Gene
  • Parkinson's Disease Pathway

Gene Ontology (GO) - Biological Process for SYT11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001778 plasma membrane repair IEA,ISS --
GO:0006914 autophagy IMP 27278822
GO:0007612 learning ISS --
GO:0007613 memory ISS --
GO:0009611 response to wounding IEA --
genes like me logo Genes that share ontologies with SYT11: view

No data available for SIGNOR curated interactions for SYT11 Gene

Drugs & Compounds for SYT11 Gene

(1) Drugs for SYT11 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
genes like me logo Genes that share compounds with SYT11: view

Transcripts for SYT11 Gene

mRNA/cDNA for SYT11 Gene

1 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYT11

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYT11 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b · 3c ^ 4a · 4b
SP1: -
SP2:
SP3: -

Relevant External Links for SYT11 Gene

GeneLoc Exon Structure for
SYT11

Expression for SYT11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYT11 Gene

mRNA differential expression in normal tissues according to GTEx for SYT11 Gene

This gene is overexpressed in Brain - Cortex (x4.2) and Brain - Frontal Cortex (BA9) (x4.1).

Protein differential expression in normal tissues from HIPED for SYT11 Gene

This gene is overexpressed in Heart (36.2), Serum (20.1), and Frontal cortex (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SYT11 Gene



Protein tissue co-expression partners for SYT11 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYT11

SOURCE GeneReport for Unigene cluster for SYT11 Gene:

Hs.32984

Evidence on tissue expression from TISSUES for SYT11 Gene

  • Nervous system(5)
  • Bone marrow(4)
genes like me logo Genes that share expression patterns with SYT11: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYT11 Gene

Orthologs for SYT11 Gene

This gene was present in the common ancestor of animals.

Orthologs for SYT11 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SYT11 31 30
  • 99.61 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SYT11 31 30
  • 93.81 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SYT11 31
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SYT11 31 30
  • 91.01 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Syt11 30
  • 90.05 (n)
mouse
(Mus musculus)
Mammalia Syt11 17 31 30
  • 90 (n)
chicken
(Gallus gallus)
Aves SYT11 31 30
  • 78.63 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SYT11 31
  • 87 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii syt11a 31 30
  • 65.89 (n)
OneToMany
syt11b 31
  • 58 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Syt4 31
  • 36 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea snt-4 31
  • 32 (a)
OneToMany
Species where no ortholog for SYT11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for SYT11 Gene

ENSEMBL:
Gene Tree for SYT11 (if available)
TreeFam:
Gene Tree for SYT11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYT11: view image

Paralogs for SYT11 Gene

(19) SIMAP similar genes for SYT11 Gene using alignment to 2 proteins:

  • SYT11_HUMAN
  • B4DK40_HUMAN
genes like me logo Genes that share paralogs with SYT11: view

Variants for SYT11 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYT11 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs17853892 - p.Gly231Val
rs822522 - p.Gln48His

Additional dbSNP identifiers (rs#s) for SYT11 Gene

Structural Variations from Database of Genomic Variants (DGV) for SYT11 Gene

Variant ID Type Subtype PubMed ID
esv2664479 CNV deletion 23128226
esv2849680 CNV deletion 24192839
esv33869 CNV loss 17666407
esv3541067 CNV deletion 23714750
nsv1003170 CNV gain 25217958
nsv957176 CNV deletion 24416366

Variation tolerance for SYT11 Gene

Residual Variation Intolerance Score: 21% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.84; 17.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYT11 Gene

Human Gene Mutation Database (HGMD)
SYT11
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYT11

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYT11 Gene

Disorders for SYT11 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SYT11 Gene - From: DISEASES

Disorder Aliases PubMed IDs
parkinson disease, late-onset
  • pd
- elite association - COSMIC cancer census association via MalaCards
Search SYT11 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYT11

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SYT11: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYT11 Gene

Publications for SYT11 Gene

  1. The autosomal recessive juvenile Parkinson disease gene product, parkin, interacts with and ubiquitinates synaptotagmin XI. (PMID: 12925569) Huynh DP … Pulst SM (Human molecular genetics 2003) 3 4 23 54
  2. The Parkinson's disease-associated genes ATP13A2 and SYT11 regulate autophagy via a common pathway. (PMID: 27278822) Bento CF … Rubinsztein DC (Nature communications 2016) 3 4 54
  3. Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies. (PMID: 21292315) International Parkinson Disease Genomics Consortium … Wood NW (Lancet (London, England) 2011) 3 41 54
  4. Pharmacogenetics of antipsychotic response in the CATIE trial: a candidate gene analysis. (PMID: 19156168) Need AC … Goldstein DB (European journal of human genetics : EJHG 2009) 3 41 54
  5. Synaptotagmin XI as a candidate gene for susceptibility to schizophrenia. (PMID: 17192956) Inoue S … Oishi M (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2007) 3 23 54

Products for SYT11 Gene