Syt6 synaptotagmin 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Syt6provided by RGD
Official Full Name: synaptotagmin 6provided by RGD
Primary source: RGD:62012
See related: EnsemblRapid:ENSRNOG00000019163 AllianceGenome:RGD:62012
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 syntaxin binding activity. Involved in presynaptic dense core vesicle exocytosis. Is active in glutamatergic synapse. Is integral component of synaptic membrane. Orthologous to human SYT6 (synaptotagmin 6). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 283.0) and Brain (RPKM 42.4) See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (193781051..193840741)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (191093009..191152283)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (206064181..206119034)

Chromosome 2 - NC_086020.1 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?

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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	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	ISO Inferred from Sequence Orthology more info
enables calcium-dependent phospholipid binding	ISO Inferred from Sequence Orthology more info
enables calcium-dependent protein binding	ISO Inferred from Sequence Orthology more info
enables clathrin binding	IBA Inferred from Biological aspect of Ancestor more info
enables clathrin binding	IEA Inferred from Electronic Annotation more info
enables clathrin binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables phosphatidylserine binding	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylserine binding	ISO Inferred from Sequence Orthology more info
NOT enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
NOT enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables syntaxin binding	IDA Inferred from Direct Assay more info	PubMed
enables syntaxin binding	IEA Inferred from Electronic Annotation more info
enables syntaxin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in acrosomal vesicle exocytosis	IEA Inferred from Electronic Annotation more info
involved_in acrosomal vesicle exocytosis	ISO Inferred from Sequence Orthology more info
involved_in acrosome reaction	ISO Inferred from Sequence Orthology more info
involved_in calcium-ion regulated exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in postsynaptic dense core vesicle exocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in postsynaptic dense core vesicle exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasmic side of plasma membrane	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic side of plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in perinuclear endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynapse	IEA Inferred from Electronic Annotation more info
is_active_in synaptic membrane	EXP Inferred from Experiment more info	PubMed
is_active_in synaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: synaptotagmin-6

Names: synaptotagmin VI; sytVI

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_022191.3 → NP_071527.1 synaptotagmin-6

See identical proteins and their annotated locations for NP_071527.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/Swiss-Prot

Q4KLI6, Q62746

UniProtKB/TrEMBL

A0A8I6ABK1, A6K3L5

Related

ENSRNOP00000025953.7, ENSRNOT00000025953.7

Conserved Domains (2) summary

cd08385
Location:231 → 355

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

cd08403
Location:364 → 497

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10

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_086020.1 Reference GRCr8

Range

193781051..193840741

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039103020.2 → XP_038958948.1 synaptotagmin-6 isoform X1

UniProtKB/TrEMBL

A0A8L2QEQ5

Related

ENSRNOP00000081725.2, ENSRNOT00000094540.2

Conserved Domains (2) summary

cd08385
Location:231 → 355

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

cd08403
Location:364 → 497

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
XM_039103022.2 → XP_038958950.1 synaptotagmin-6 isoform X3

UniProtKB/TrEMBL

A0A8L2QEQ5

Conserved Domains (2) summary

cd08385
Location:146 → 270

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

cd08403
Location:279 → 412

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
XM_063282441.1 → XP_063138511.1 synaptotagmin-6 isoform X4

UniProtKB/TrEMBL

A0A0G2JW68, A0A8L2QEQ5
XM_039103023.2 → XP_038958951.1 synaptotagmin-6 isoform X3

UniProtKB/TrEMBL

A0A8L2QEQ5

Conserved Domains (2) summary

cd08385
Location:146 → 270

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

cd08403
Location:279 → 412

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10
XM_039103021.2 → XP_038958949.1 synaptotagmin-6 isoform X2

UniProtKB/TrEMBL

A0A8I6ABK1

Conserved Domains (2) summary

cd08385
Location:237 → 361

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

cd08403
Location:370 → 503

C2B_Synaptotagmin-3-5-6-9-10; C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10