Syt2 synaptotagmin 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Syt2provided by RGD
Official Full Name: synaptotagmin 2provided by RGD
Primary source: RGD:3804
See related: EnsemblRapid:ENSRNOG00000004756 AllianceGenome:RGD:3804
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
Also known as: SYNII; RATSYNII
Summary: Enables calcium-dependent phospholipid binding activity and syntaxin binding activity. Predicted to be involved in positive regulation of dendrite extension and regulation of vesicle-mediated transport. Located in terminal bouton. Is active in synaptic vesicle membrane. Human ortholog(s) of this gene implicated in congenital myasthenic syndrome and congenital myasthenic syndrome 7. Orthologous to human SYT2 (synaptotagmin 2). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Restricted expression toward (RPKM 172.9) See more
Orthologs: human mouse all
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Genomic context

Location:: 13q13

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (48639634..48749814)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (46088046..46197976)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (51569248..51577824)

Chromosome 13 - NC_086031.1 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?

a point mutation on synaptotagmin, located outside of the BoNT/B-binding segment, inhibited GT1b binding and blocked GT1b-induced potentiation of BoNT/B binding to synaptotagmin-expressing cells.
Title: Gangliosides interact with synaptotagmin to form the high-affinity receptor complex for botulinum neurotoxin B.
Crystal structure of the rat Syt2 protein botulinum neurotoxin DC complex.
Title: Crystal structures of botulinum neurotoxin DC in complex with its protein receptors synaptotagmin I and II.
Data suggest that immature medial nucleus of the trapezoid body terminals may contain two populations of synaptic vesicles, one expressing VGLUT3 with synaptotagmin 2 and another expressing VGLUT3 with synaptotagmin 1.
Title: Synaptotagmins I and II in the developing rat auditory brainstem: Synaptotagmin I is transiently expressed in glutamate-releasing immature inhibitory terminals.
An overexpressed mutation in Syt2 leaves intrinsic calcium sensitivity of synaptic vesicles intact while it destabilizes the readily releasable pool of vesicles.
Title: Synaptotagmin has an essential function in synaptic vesicle positioning for synchronous release in addition to its role as a calcium sensor.
both synaptotagmins I and II can interact with the syntaxin/synaptosomal-associated protein of 25 kDa (SNAP-25) dimer
Title: Synaptotagmin interaction with the syntaxin/SNAP-25 dimer is mediated by an evolutionarily conserved motif and is sensitive to inositol hexakisphosphate.
Synaptotagmin II is critical for the delivery of internalized cargo for degradation. One consequence of Synaptotagmin II suppression is a delay in PKCalpha downregulation, resulting in its prolonged signaling.
Title: Suppression of Synaptotagmin II restrains phorbolester-induced downregulation of protein kinase Calpha by diverting the kinase from a degradative pathway to the recycling endocytic compartment.
the structure of a BoNT in complex with its protein receptor: the receptor-binding domain of botulinum neurotoxin serotype B (BoNT/B) bound to the luminal domain of synaptotagmin II, determined at 2.15 A resolution
Title: Botulinum neurotoxin B recognizes its protein receptor with high affinity and specificity.
syts I and II can function as protein receptors for Botulinum neurotoxin b and mediate its entry
Title: Synaptotagmins I and II mediate entry of botulinum neurotoxin B into cells.
The results indicated that Syt2 played a negative regulation in exocytosis of lysosomes in RBL-2H3 cells.
Title: The distribution of synaptotagmin II in RBL-2H3 and its regulation on exocytosis of lysosomes in RBL-2H3.

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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

D19Mgh6 (e-PCR)
- UniSTS:118479

D13Arb8 (e-PCR), detects polymorphism
- UniSTS:119251

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	TAS Traceable Author Statement more info	PubMed
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 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 inositol 1,3,4,5 tetrakisphosphate binding	ISO Inferred from Sequence Orthology more info
enables inositol 1,3,4,5 tetrakisphosphate binding	ISS Inferred from Sequence or Structural Similarity more info
enables phosphatidylserine binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin binding	IDA Inferred from Direct Assay 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-dependent activation of synaptic vesicle fusion	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of dendrite extension	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of dendrite extension	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 synaptic vesicle exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle exocytosis	TAS Traceable Author Statement more info	PubMed
involved_in vesicle-mediated transport	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	ISO Inferred from Sequence Orthology more info
located_in chromaffin granule membrane	IEA Inferred from Electronic Annotation 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
is_active_in neuromuscular junction	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
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in synaptic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in synaptic vesicle membrane	TAS Traceable Author Statement more info	PubMed
located_in terminal bouton	HDA more info	PubMed

General protein information

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Preferred Names: synaptotagmin-2

Names: synaptotagmin II; sytII

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_001429497.1 → NP_001416426.1 synaptotagmin-2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

A6ICC8, G3V6M3
NM_001429498.1 → NP_001416427.1 synaptotagmin-2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

A6ICC8, G3V6M3
NM_001429499.1 → NP_001416428.1 synaptotagmin-2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

A6ICC8, G3V6M3
NM_012665.3 → NP_036797.2 synaptotagmin-2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

A6ICC8, G3V6M3

Conserved Domains (3) summary

cd08385
Location:142 → 264

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08402
Location:274 → 409

C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1

cd21964
Location:4 → 116

Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086031.1 Reference GRCr8

Range

48639634..48749814

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039090349.2 → XP_038946277.1 synaptotagmin-2 isoform X1

Related

ENSRNOP00000006637.2, ENSRNOT00000006637.7

Conserved Domains (3) summary

cd08385
Location:142 → 264

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08402
Location:274 → 409

C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1

cd21964
Location:4 → 116

Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins
XM_039090348.2 → XP_038946276.2 synaptotagmin-2 isoform X1
XM_063272035.1 → XP_063128105.1 synaptotagmin-2 isoform X1
XM_039090350.2 → XP_038946278.1 synaptotagmin-2 isoform X1

Conserved Domains (3) summary

cd08385
Location:142 → 264

C2A_Synaptotagmin-1-5-6-9-10; C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10

cd08402
Location:274 → 409

C2B_Synaptotagmin-1; C2 domain second repeat present in Synaptotagmin 1

cd21964
Location:4 → 116

Syt2_N; N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins
XM_063272036.1 → XP_063128106.1 synaptotagmin-2 isoform X2