SYT11 synaptotagmin 11 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYT11provided by HGNC
Official Full Name: synaptotagmin 11provided by HGNC
Primary source: HGNC:HGNC:19239
See related: Ensembl:ENSG00000132718 MIM:608741; AllianceGenome:HGNC:19239
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SYT12; sytXI
Summary: 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]
Annotation information: Note: In 2002, the HUGO Gene Nomenclature Committee (HGNC) changed the official nomenclature of this locus to be standard with mouse and rat official nomenclature. Therefore, the gene previously known as "synaptotagmin XI" (SYT11, GeneID 23208) became "synaptotagmin XII" (SYT12) and "synaptotagmin XII" (SYT12, GeneID 91683) became "synaptotagmin XI" (SYT11). [13 Feb 2013]
Expression: Biased expression in brain (RPKM 160.9), adrenal (RPKM 11.8) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 1q22

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (155859567..155885199)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (154998435..155023315)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (155829358..155854990)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Palmitoylation of the Parkinson's disease-associated protein synaptotagmin-11 links its turnover to alpha-synuclein homeostasis.
Title: Palmitoylation of the Parkinson's disease-associated protein synaptotagmin-11 links its turnover to α-synuclein homeostasis.
Impad1 and Syt11 work in an epistatic pathway that regulates EMT-mediated vesicular trafficking to drive lung cancer invasion and metastasis.
Title: Impad1 and Syt11 work in an epistatic pathway that regulates EMT-mediated vesicular trafficking to drive lung cancer invasion and metastasis.
The highly expressed calcium-insensitive synaptotagmin-11 and synaptotagmin-13 modulate insulin secretion.
Title: The highly expressed calcium-insensitive synaptotagmin-11 and synaptotagmin-13 modulate insulin secretion.
Synaptotagmin 11 scaffolds MKK7-JNK signaling process to promote stem-like molecular subtype gastric cancer oncogenesis.
Title: Synaptotagmin 11 scaffolds MKK7-JNK signaling process to promote stem-like molecular subtype gastric cancer oncogenesis.
Association analysis of SYT11, FGF20, GCH1 rare variants in Parkinson's disease.
Title: Association analysis of SYT11, FGF20, GCH1 rare variants in Parkinson's disease.
The rs3129882/rs4248166 in HLA-DRA and rs34372695 in SYT11 are not associated with sporadic Parkinson's disease in Central Chinese population.
Title: The rs3129882/rs4248166 in HLA-DRA and rs34372695 in SYT11 are not associated with sporadic Parkinson's disease in Central Chinese population.
Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue.
Title: Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue.
Targeted sequencing of Parkinson's disease loci genes highlights SYT11, FGF20 and other associations.
Title: Targeted sequencing of Parkinson's disease loci genes highlights SYT11, FGF20 and other associations.
ATP13A2 and SYT11 form a functional network in the regulation of the autophagy-lysosome pathway, which may contribute to forms of Parkinson's Disease-associated neurodegeneration.
Title: The Parkinson's disease-associated genes ATP13A2 and SYT11 regulate autophagy via a common pathway.
parkin deficiency induces synaptotagmin-11 accumulation and PD-like neurotoxicity in mouse models, which is reversed by SYT11 knockdown in the SNpc or knockout of SYT11 restricted to dopaminergic neuron
Title: Synaptotagmin-11 is a critical mediator of parkin-linked neurotoxicity and Parkinson's disease-like pathology.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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
Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies. EBI GWAS Catalog EBI GWAS CatalogPubMed
Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH25308 (e-PCR)
- UniSTS:7170

RH78173 (e-PCR)
- UniSTS:53788

IB1251 (e-PCR)
- UniSTS:56894

RH16657 (e-PCR)
- UniSTS:13136

D7S2133E (e-PCR)
- UniSTS:151132

D1S1849E (e-PCR)
- UniSTS:150956

GDB:335751 (e-PCR)
- UniSTS:156601

SHGC-148333 (e-PCR)
- UniSTS:176331

A002N39 (e-PCR)
- UniSTS:56017

D15S1390 (e-PCR)
- UniSTS:474340

Clone Names

KIAA0080, MGC10881, MGC17226, DKFZp781D015

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables beta-tubulin binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
NOT 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
NOT enables calcium-dependent phospholipid binding	ISS Inferred from Sequence or Structural Similarity more info
enables clathrin binding	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylserine binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables translation initiation factor binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium ion regulated lysosome exocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium ion-regulated exocytosis of neurotransmitter	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of vesicle localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in learning	ISS Inferred from Sequence or Structural Similarity more info
involved_in memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cytokine production	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of dopamine secretion	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of interleukin-6 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of microglial cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of neurotransmitter secretion	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of phagocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of tumor necrosis factor production	ISS Inferred from Sequence or Structural Similarity more info
involved_in plasma membrane repair	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein localization to phagocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of defense response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in regulation of phagosome maturation	IC Inferred by Curator more info
involved_in regulation of synaptic vesicle endocytosis	IEA Inferred from Electronic Annotation more info
involved_in vesicle fusion	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
located_in axon	ISS Inferred from Sequence or Structural Similarity more info
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	ISS Inferred from Sequence or Structural Similarity more info
located_in dopaminergic synapse	IEA Inferred from Electronic Annotation more info
located_in early phagosome	ISS Inferred from Sequence or Structural Similarity more info
located_in excitatory synapse	ISS Inferred from Sequence or Structural Similarity more info
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in inhibitory synapse	ISS Inferred from Sequence or Structural Similarity more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in phagocytic cup	IEA Inferred from Electronic Annotation more info
located_in phagocytic vesicle	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic density	ISS Inferred from Sequence or Structural Similarity more info
located_in presynapse	ISS Inferred from Sequence or Structural Similarity more info
located_in presynaptic active zone membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in recycling endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in recycling endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
NOT located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in synaptic vesicle	TAS Traceable Author Statement more info	PubMed
located_in trans-Golgi network	ISS Inferred from Sequence or Structural Similarity more info
located_in vesicle	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: synaptotagmin-11

Names: synaptotagmin 12; synaptotagmin XI

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)

NM_152280.5 → NP_689493.3 synaptotagmin-11

See identical proteins and their annotated locations for NP_689493.3

Status: REVIEWED

Source sequence(s)

AA824539, AL139128, BC004291, DA239014

Consensus CDS

CCDS1122.1

UniProtKB/Swiss-Prot

Q14998, Q5W0D4, Q68CT5, Q8IXU3, Q96SU2, Q9BT88

Related

ENSP00000357307.4, ENST00000368324.5

Conserved Domains (2) summary

cd08388
Location:158 → 283

C2A_Synaptotagmin-4-11; C2A domain first repeat present in Synaptotagmins 4 and 11

cd08404
Location:292 → 429

C2B_Synaptotagmin-4; C2 domain second repeat present in Synaptotagmin 4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

155859567..155885199

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017000759.3 → XP_016856248.1 synaptotagmin-11 isoform X1
XM_005245014.4 → XP_005245071.1 synaptotagmin-11 isoform X2

Conserved Domains (2) summary

cd08388
Location:158 → 283

C2A_Synaptotagmin-4-11; C2A domain first repeat present in Synaptotagmins 4 and 11

cd08404
Location:292 → 428

C2B_Synaptotagmin-4; C2 domain second repeat present in Synaptotagmin 4