Syt11 synaptotagmin 11 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Syt11provided by RGD
Official Full Name: synaptotagmin 11provided by RGD
Primary source: RGD:62042
See related: EnsemblRapid:ENSRNOG00000020279 AllianceGenome:RGD:62042
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: Predicted to enable several functions, including beta-tubulin binding activity; calcium ion sensor activity; and ubiquitin protein ligase binding activity. Involved in negative regulation of cellular component organization and negative regulation of dopamine secretion. Located in several cellular components, including inhibitory synapse; postsynaptic density; and synaptic vesicle. Is active in several cellular components, including Schaffer collateral - CA1 synapse; presynaptic active zone membrane; and synaptic vesicle membrane. Orthologous to human SYT11 (synaptotagmin 11). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 1190.7) and Adrenal (RPKM 48.6) See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (176503845..176530354, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (174206032..174232540, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (188112301..188138180, complement)

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 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?

propose that Syt11 functions to ensure precision in vesicle retrieval, mainly by limiting the sites of membrane invagination at the early stage of endocytosis
Title: Synaptotagmin-11 inhibits clathrin-mediated and bulk endocytosis.
Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain were identified using high-resolution crystal structures. have identified
Title: Crystallographic identification of Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

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

BF388304 (e-PCR)
- UniSTS:244918

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables SNARE binding	IEA Inferred from Electronic Annotation more info
enables SNARE binding	ISO Inferred from Sequence Orthology more info
enables beta-tubulin binding	IEA Inferred from Electronic Annotation more info
enables beta-tubulin binding	ISO Inferred from Sequence Orthology more info
NOT enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
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 identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology 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 translation initiation factor binding	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in autophagy	ISO Inferred from Sequence Orthology more info
involved_in autophagy	ISS Inferred from Sequence or Structural Similarity more info
involved_in calcium ion regulated lysosome exocytosis	IEA Inferred from Electronic Annotation more info
involved_in calcium ion regulated lysosome exocytosis	ISO Inferred from Sequence Orthology more info
involved_in calcium-dependent activation of synaptic vesicle fusion	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of vesicle localization	IEA Inferred from Electronic Annotation more info
involved_in establishment of vesicle localization	ISO Inferred from Sequence Orthology more info
involved_in establishment of vesicle localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in learning	IEA Inferred from Electronic Annotation more info
involved_in learning	ISO Inferred from Sequence Orthology more info
involved_in learning	ISS Inferred from Sequence or Structural Similarity more info
involved_in memory	IEA Inferred from Electronic Annotation more info
involved_in memory	ISO Inferred from Sequence Orthology more info
involved_in memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of clathrin coat assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of clathrin-dependent endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of cytokine production	ISO Inferred from Sequence Orthology 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	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of dopamine secretion	IEA Inferred from Electronic Annotation more info
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	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of interleukin-6 production	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interleukin-6 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of membrane invagination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of microglial cell activation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of microglial cell activation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of microglial cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of phagocytosis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of phagocytosis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of phagocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of synaptic vesicle endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of tumor necrosis factor production	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
involved_in plasma membrane repair	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein localization to phagocytic vesicle	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein localization to phagocytic vesicle	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 defense response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in regulation of defense response to bacterium	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic vesicle endocytosis	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic vesicle endocytosis	ISO Inferred from Sequence Orthology more info
involved_in response to wounding	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cell body	IDA Inferred from Direct Assay more info	PubMed
located_in clathrin-coated vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in dendrite	ISO Inferred from Sequence Orthology more info
located_in dendrite	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	IDA Inferred from Direct Assay more info	PubMed
located_in dopaminergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in dopaminergic synapse	ISO Inferred from Sequence Orthology more info
located_in early phagosome	IEA Inferred from Electronic Annotation more info
located_in early phagosome	ISO Inferred from Sequence Orthology more info
located_in early phagosome	ISS Inferred from Sequence or Structural Similarity more info
located_in excitatory synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in exocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in inhibitory synapse	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in lysosome	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	IEA Inferred from Electronic Annotation 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 perikaryon	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in phagocytic cup	IEA Inferred from Electronic Annotation more info
located_in phagocytic cup	ISO Inferred from Sequence Orthology more info
located_in phagocytic vesicle	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 postsynapse	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	ISO Inferred from Sequence Orthology more info
located_in postsynaptic density	ISS Inferred from Sequence or Structural Similarity more info
located_in presynapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynaptic active zone membrane	IDA Inferred from Direct Assay more info	PubMed
located_in presynaptic active zone membrane	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome	IEA Inferred from Electronic Annotation more info
located_in recycling endosome	ISO Inferred from Sequence Orthology 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
located_in synaptic vesicle	IDA Inferred from Direct Assay more info	PubMed
NOT located_in synaptic vesicle	ISO Inferred from Sequence Orthology more info
NOT located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
is_active_in synaptic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
located_in terminal bouton	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network	IEA Inferred from Electronic Annotation more info
located_in trans-Golgi network	ISO Inferred from Sequence Orthology more info
located_in trans-Golgi network	ISS Inferred from Sequence or Structural Similarity more info
located_in vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in vesicle	ISO Inferred from Sequence Orthology 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 XI; 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_031667.3 → NP_113855.2 synaptotagmin-11

See identical proteins and their annotated locations for NP_113855.2

Status: VALIDATED

Source sequence(s)

BC094518, JAXUCZ010000002

UniProtKB/TrEMBL

A0A8I6APP2, Q505J5

Related

ENSRNOP00000027474.4, ENSRNOT00000027474.5

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 → 427

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

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

176503845..176530354 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006232748.3 → XP_006232810.1 synaptotagmin-11 isoform X1

See identical proteins and their annotated locations for XP_006232810.1

UniProtKB/Swiss-Prot

O08835, Q925B6

UniProtKB/TrEMBL

A0A8I6APP2, A6J6A4

Related

ENSRNOP00000091028.2, ENSRNOT00000107218.2

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 → 428

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