Syt11 synaptotagmin XI [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Syt11provided by MGI
Official Full Name: synaptotagmin XIprovided by MGI
Primary source: MGI:MGI:1859547
See related: Ensembl:ENSMUSG00000068923 AllianceGenome:MGI:1859547
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 1500004A13Rik; 3632445O20Rik; 5430404N14Rik; 6530420C11Rik
Summary: Enables several functions, including SNARE binding activity; beta-tubulin binding activity; and identical protein binding activity. Involved in several processes, including learning or memory; negative regulation of cytokine production; and regulation of endocytosis. Located in several cellular components, including cytoplasmic vesicle; postsynaptic density; and trans-Golgi network. Is active in dopaminergic synapse. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Orthologous to human SYT11 (synaptotagmin 11). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in cortex adult (RPKM 100.4), cerebellum adult (RPKM 98.9) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F1; 3 38.96 cM

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (88652006..88682466, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (88744699..88775159, complement)

Chromosome 3 - NC_000069.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Synaptotagmin-11 facilitates assembly of a presynaptic signaling complex in post-Golgi cargo vesicles.
Title: Synaptotagmin-11 facilitates assembly of a presynaptic signaling complex in post-Golgi cargo vesicles.
Synaptotagmin-11 regulates immune functions of microglia in vivo.
Title: Synaptotagmin-11 regulates immune functions of microglia in vivo.
Synaptotagmin-11 Inhibits Synaptic Vesicle Endocytosis via Endophilin A1.
Title: Synaptotagmin-11 Inhibits Synaptic Vesicle Endocytosis via Endophilin A1.
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.
Parkin-dependent and -independent degradation of synaptotagmin-11 in neurons and astrocytes.
Title: Parkin-dependent and -independent degradation of synaptotagmin-11 in neurons and astrocytes.
Synaptotagmin-11 regulates the functions of caveolae and responds to mechanical stimuli in astrocytes.
Title: Synaptotagmin-11 regulates the functions of caveolae and responds to mechanical stimuli in astrocytes.
Syt11 is an essential component of a neuronal vesicular trafficking pathway that differs from the well-characterized synaptic vesicle trafficking pathway but is also essential for life.
Title: Synaptotagmin-11 mediates a vesicle trafficking pathway that is essential for development and synaptic plasticity.
The results of this study proposed that Syt11 suppresses microglial activation under both physiological and pathological conditions through the inhibition of cytokine secretion and phagocytosis.
Title: Synaptotagmin-11 inhibits cytokine secretion and phagocytosis in microglia.
These results identify the lysosomes and Syt XI as the sub-cellular and molecular regulators, respectively of astrocyte cell membrane repair.
Title: Injured astrocytes are repaired by Synaptotagmin XI-regulated lysosome exocytosis.
Syt XI is directly degraded by the zinc metalloprotease GP63 and excluded from Leishmania parasitophorous vacuoles by the promastigotes surface glycolipid lipophosphoglycan.
Title: Leishmania promastigotes induce cytokine secretion in macrophages through the degradation of synaptotagmin XI.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Targeted (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

UniSTS:225059 (e-PCR)
- UniSTS:225059

BE113851 (e-PCR)
- UniSTS:246819

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

AI851970 (e-PCR)
- UniSTS:164209

Syt11 (e-PCR), detects polymorphism
- UniSTS:507259

AF123611 (e-PCR)
- UniSTS:178861

Gene Ontology Provided by MGI

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

Process	Evidence Code	Pubs
involved_in autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in autophagy	ISO Inferred from Sequence Orthology more info
involved_in calcium ion regulated lysosome exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium-dependent activation of synaptic vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of vesicle localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in learning	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in memory	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of clathrin coat assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of clathrin-dependent endocytosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cytokine production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of dopamine secretion	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of dopamine secretion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of endocytosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interleukin-6 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of interleukin-6 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of membrane invagination	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of microglial cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of phagocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of phagocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of synaptic vesicle endocytosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of tumor necrosis factor production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in plasma membrane repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to phagocytic vesicle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of calcium ion-dependent exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of defense response to bacterium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of phagosome maturation	IC Inferred by Curator more info	PubMed
involved_in regulation of phagosome maturation	TAS Traceable Author Statement more info	PubMed
involved_in regulation of synaptic vesicle endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synaptic vesicle endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to wounding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle fusion	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
is_active_in Schaffer collateral - CA1 synapse	ISO Inferred from Sequence Orthology more info
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IEA Inferred from Electronic Annotation more info
located_in axon	ISO Inferred from Sequence Orthology more info
located_in cell body	ISO Inferred from Sequence Orthology more info
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
located_in dendritic spine	ISO Inferred from Sequence Orthology more info
is_active_in dopaminergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in dopaminergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in early phagosome	IDA Inferred from Direct Assay more info	PubMed
located_in excitatory synapse	ISO Inferred from Sequence Orthology more info
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in inhibitory synapse	ISO Inferred from Sequence Orthology more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in phagocytic cup	IDA Inferred from Direct Assay more info	PubMed
located_in phagocytic vesicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynapse	ISO Inferred from Sequence Orthology more info
located_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic density	ISO Inferred from Sequence Orthology more info
located_in presynapse	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic active zone membrane	ISO Inferred from Sequence Orthology more info
located_in presynaptic active zone membrane	ISO Inferred from Sequence Orthology more info
located_in recycling endosome	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle	ISO Inferred from Sequence Orthology more info
is_active_in synaptic vesicle membrane	ISO Inferred from Sequence Orthology more info
located_in terminal bouton	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed
located_in vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in vesicle	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: synaptotagmin-11

Names: sytXI

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_018804.3 → NP_061274.2 synaptotagmin-11

See identical proteins and their annotated locations for NP_061274.2

Status: VALIDATED

Source sequence(s)

BC054526, BU056967, BY295190, CD776044, CV561059

Consensus CDS

CCDS38484.1

UniProtKB/Swiss-Prot

Q7TQG8, Q9R0N3

UniProtKB/TrEMBL

Q3TYC4

Related

ENSMUSP00000088464.5, ENSMUST00000090945.5

Conserved Domains (2) summary

cd08388
Location:157 → 282

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

cd08404
Location:291 → 428

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

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

88652006..88682466 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006501350.4 → XP_006501413.1 synaptotagmin-11 isoform X2

See identical proteins and their annotated locations for XP_006501413.1

UniProtKB/TrEMBL

Q3TPH5, Q3TYC4

Conserved Domains (2) summary

cd08388
Location:157 → 282

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

cd08404
Location:291 → 427

C2B_Synaptotagmin-4; C2 domain second repeat present in Synaptotagmin 4
XM_006501348.1 → XP_006501411.1 synaptotagmin-11 isoform X1

See identical proteins and their annotated locations for XP_006501411.1

UniProtKB/Swiss-Prot

Q7TQG8, Q9R0N3

UniProtKB/TrEMBL

Q3TYC4

Related

ENSMUSP00000103129.2, ENSMUST00000107505.8

Conserved Domains (2) summary

cd08388
Location:157 → 282

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

cd08404
Location:291 → 428

C2B_Synaptotagmin-4; C2 domain second repeat present in Synaptotagmin 4
XM_030252576.1 → XP_030108436.1 synaptotagmin-11 isoform X1

UniProtKB/Swiss-Prot

Q7TQG8, Q9R0N3

UniProtKB/TrEMBL

Q3TYC4

Conserved Domains (2) summary

cd08388
Location:157 → 282

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

cd08404
Location:291 → 428

C2B_Synaptotagmin-4; C2 domain second repeat present in Synaptotagmin 4
XM_036163052.1 → XP_036018945.1 synaptotagmin-11 isoform X2

UniProtKB/TrEMBL

Q3TPH5, Q3TYC4

Related

ENSMUSP00000138284.2, ENSMUST00000183267.2

Conserved Domains (2) summary

cd08388
Location:157 → 282

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

cd08404
Location:291 → 427

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