Syt4 synaptotagmin 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Syt4provided by RGD
Official Full Name: synaptotagmin 4provided by RGD
Primary source: RGD:68397
See related: EnsemblRapid:ENSRNOG00000017333 AllianceGenome:RGD:68397
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables several functions, including phosphatidylserine binding activity; protein dimerization activity; and syntaxin binding activity. Involved in several processes, including dense core granule cytoskeletal transport; negative regulation of transport; and vesicle organization. Located in several cellular components, including astrocyte projection; neuronal cell body; and secretory vesicle. Biomarker of visual epilepsy. Orthologous to human SYT4 (synaptotagmin 4). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Restricted expression toward (RPKM 381.5) See more
Orthologs: human mouse all
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Genomic context

Location:: 18p12

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	18	NC_086036.1 (23311454..23320863, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	18	NC_051353.1 (23036973..23046380, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	18	NC_005117.4 (24172580..24181989, complement)

Chromosome 18 - NC_086036.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

neuronal activity increased dense core vesicle capture via JNK-dependent phosphorylation of the S135 site of Synaptotagmin-4
Title: Capture of Dense Core Vesicles at Synapses by JNK-Dependent Phosphorylation of Synaptotagmin-4.
The increased expression of Synaptotagmin IV in optic nerve crush eyes displays the possible neuroprotective effect of bone marrow mononuclear cell treatment
Title: Cell therapy modulates expression of Tax1-binding protein 1 and synaptotagmin IV in a model of optic nerve lesion.
Immunocytochemistry in rat chromaffin cells shows differential distribution of synaptotagmin-1, -4, -7, and -9.
Title: Differential distribution of synaptotagmin-1, -4, -7, and -9 in rat adrenal chromaffin cells.
These data support an inhibitory effect of syt IV on release of vesicles and their transmitter content
Title: Upregulation of synaptotagmin IV inhibits transmitter release in PC12 cells with targeted synaptotagmin I knockdown.
Rat and Drosophila synaptotagmin 4 have opposite effects during SNARE-catalyzed membrane fusion.
Title: Rat and Drosophila synaptotagmin 4 have opposite effects during SNARE-catalyzed membrane fusion.
The effects of syt IV on fusion pores are discussed in terms of structural models and kinetic mechanisms.
Title: Synaptotagmin IV modulation of vesicle size and fusion pores in PC12 cells.
Expression of Syt4 increases 9-fold at night in the rat pineal gland; treatment with dibutyryl cyclic AMP increases expresssion.
Title: Night/day changes in pineal expression of >600 genes: central role of adrenergic/cAMP signaling.
Given the neuroendocrine functions of the posterior pituitary, changes in Syt IV levels could be involved in endocrine transitions involving alterations in the release of the neuropeptides oxytocin and vasopressin
Title: Synaptotagmin IV: a multifunctional regulator of peptidergic nerve terminals.
Downregulation of Syt IV reduced Ca(2+)-triggered exocytosis of dense core vesicles. Syt I silencing, however, had no effect on vesicular release.
Title: Synaptotagmin IV regulates dense core vesicle (DCV) release in LbetaT2 cells.
Cells with overexpressed rat SytIV were unaltered in basal release probability, Ca2+ dependence of release, short-term plasticity, & fusion pore kinetics. Mutant Syt I (less Ca2+ affinity) reduced release probability & altered Ca2+ dependence of release.
Title: Synaptotagmin IV does not alter excitatory fast synaptic transmission or fusion pore kinetics in mammalian CNS neurons.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Syt4 (e-PCR), detects polymorphism
- UniSTS:507263

RH139264 (e-PCR)
- UniSTS:221350

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables SNARE binding	IDA Inferred from Direct Assay more info	PubMed
enables SNARE binding	IPI Inferred from Physical Interaction more info	PubMed
NOT enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion sensor activity	IBA Inferred from Biological aspect of Ancestor more info
NOT enables calcium-dependent phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium-dependent phospholipid binding	ISO Inferred from Sequence Orthology more info
enables clathrin binding	IDA Inferred from Direct Assay more info	PubMed
NOT enables phosphatidylserine binding	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylserine binding	IDA Inferred from Direct Assay more info	PubMed
NOT enables phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
NOT enables syntaxin binding	IDA Inferred from Direct Assay more info	PubMed
enables syntaxin binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin-1 binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin-3 binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in calcium-dependent activation of synaptic vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium-ion regulated exocytosis	NAS Non-traceable Author Statement more info	PubMed
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in dense core granule cytoskeletal transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dense core granule cytoskeletal transport	ISO Inferred from Sequence Orthology more info
involved_in memory	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of calcium ion-dependent exocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of catecholamine secretion	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of catecholamine secretion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of dense core granule exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of neurotransmitter secretion	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of protein secretion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of retrograde trans-synaptic signaling by neuropeptide	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of short-term neuronal synaptic plasticity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of synaptic vesicle exocytosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of vesicle fusion	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neurotransmitter secretion	ISO Inferred from Sequence Orthology more info
involved_in neurotransmitter secretion	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of dendrite extension	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of dense core granule exocytosis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of glutamate secretion	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
involved_in regulation of dopamine secretion	ISO Inferred from Sequence Orthology more info
involved_in regulation of endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of endocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of postsynaptic dense core vesicle exocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of trans-synaptic signaling by BDNF, modulating synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in regulation of vesicle fusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of vesicle fusion	ISO Inferred from Sequence Orthology more info
involved_in secretory granule maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in vesicle fusion with vesicle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in astrocyte projection	IDA Inferred from Direct Assay more info	PubMed
located_in astrocyte projection	ISO Inferred from Sequence Orthology more info
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IMP Inferred from Mutant Phenotype more info	PubMed
located_in axon	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in dense core granule	IDA Inferred from Direct Assay more info	PubMed
located_in dense core granule	ISO Inferred from Sequence Orthology more info
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in exocytic vesicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in microvesicle	ISO Inferred from Sequence Orthology more info
located_in neuron projection	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	ISO Inferred from Sequence Orthology more info
located_in neuron projection terminus	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in neuronal dense core vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal dense core vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuronal dense core vesicle membrane	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in secretory granule membrane	IDA Inferred from Direct Assay more info	PubMed
located_in somatodendritic compartment	ISO Inferred from Sequence Orthology more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
NOT located_in synaptic vesicle	ISO Inferred from Sequence Orthology more info
located_in synaptic vesicle	NAS Non-traceable Author Statement more info	PubMed
located_in vesicle	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: synaptotagmin-4

Names: synaptotagmin IV; sytIV

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_031693.2 → NP_113881.1 synaptotagmin-4

See identical proteins and their annotated locations for NP_113881.1

Status: VALIDATED

Source sequence(s)

BG666223, CB730279, CB786178, JAXUCZ010000018, U14398

UniProtKB/Swiss-Prot

P50232

UniProtKB/TrEMBL

A6J2N4, Q3S2E5

Related

ENSRNOP00000023593.4, ENSRNOT00000023594.7

Conserved Domains (2) summary

cd08388
Location:153 → 279

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

cd08404
Location:288 → 423

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