Clstn3 calsyntenin 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clstn3provided by MGI
Official Full Name: calsyntenin 3provided by MGI
Primary source: MGI:MGI:2178323
See related: Ensembl:ENSMUSG00000008153 AllianceGenome:MGI:2178323
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: Cs3; CSTN3; Cst-3; Clstn3b; alc-beta
Summary: Enables cell-cell adhesion mediator activity; enzyme inhibitor activity; and neurexin family protein binding activity. Involved in several processes, including cold-induced thermogenesis; regulation of synapse assembly; and synapse assembly. Acts upstream of or within several processes, including chemical synaptic transmission; positive regulation of protein localization to synapse; and positive regulation of synapse assembly. Located in cell surface; postsynaptic density; and postsynaptic membrane. Part of protein-containing complex. Is active in several cellular components, including GABA-ergic synapse; lipid droplet; and postsynaptic density membrane. Is expressed in brain; central nervous system; cerebellum; dentate gyrus subgranular zone; and testis. Orthologous to human CLSTN3 (calsyntenin 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in cerebellum adult (RPKM 97.0), cortex adult (RPKM 62.3) and 8 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 F2; 6 59.15 cM

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (124407715..124441743, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (124430756..124464784, complement)

Chromosome 6 - NC_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

CircAFF2 Promotes Neuronal Cell Injury in Intracerebral Hemorrhage by Regulating the miR-488/CLSTN3 Axis.
Title: CircAFF2 Promotes Neuronal Cell Injury in Intracerebral Hemorrhage by Regulating the miR-488/CLSTN3 Axis.
CLSTN3beta enforces adipocyte multilocularity to facilitate lipid utilization.
Title: CLSTN3β enforces adipocyte multilocularity to facilitate lipid utilization.
CLSTN3 gene variant associates with obesity risk and contributes to dysfunction in white adipose tissue.
Title: CLSTN3 gene variant associates with obesity risk and contributes to dysfunction in white adipose tissue.
Deletion of Calsyntenin-3, an atypical cadherin, suppresses inhibitory synapses but increases excitatory parallel-fiber synapses in cerebellum.
Title: Deletion of Calsyntenin-3, an atypical cadherin, suppresses inhibitory synapses but increases excitatory parallel-fiber synapses in cerebellum.
Calsyntenin-3 interacts with the sodium-dependent vitamin C transporter-2 to regulate vitamin C uptake.
Title: Calsyntenin-3 interacts with the sodium-dependent vitamin C transporter-2 to regulate vitamin C uptake.
Neural regulation of energy and bone homeostasis by the synaptic adhesion molecule Calsyntenin-3.
Title: Neural regulation of energy and bone homeostasis by the synaptic adhesion molecule Calsyntenin-3.
thermogenic adipocytes express a previously unknown, mammal-specific protein of the endoplasmic reticulum, termed calsyntenin 3beta; genetic loss or gain of expression of calsyntenin 3beta in adipocytes reduces or enhances functional sympathetic innervation, respectively, in adipose tissue; ablation of calsyntenin 3beta predisposes mice on a high-fat diet to obesity
Title: Innervation of thermogenic adipose tissue via a calsyntenin 3β-S100b axis.
The C-terminal fragment but not full-length Cst-3 accumulated in dystrophic neurites surrounding amyloidbeta plaques in Tg2576 mouse and Alzheimer disease brains.
Title: Calsyntenin-3 C-terminal fragment accumulates in dystrophic neurites surrounding aβ plaques in tg2576 mouse and Alzheimer disease brains: its neurotoxic role in mediating dystrophic neurite formation.

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Variation

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Alleles

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

Endonuclease-mediated (3) 1 citation
Gene trapped (1)
Targeted (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6Mit331 (e-PCR), detects polymorphism
- UniSTS:130885

EC185RR (e-PCR), detects polymorphism
- UniSTS:142948

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables cell-cell adhesion mediator activity	IDA Inferred from Direct Assay more info	PubMed
enables cell-cell adhesion mediator activity	IEA Inferred from Electronic Annotation more info
enables cell-cell adhesion mediator activity	ISO Inferred from Sequence Orthology more info
enables enzyme inhibitor activity	IDA Inferred from Direct Assay more info	PubMed
enables neurexin family protein binding	IDA Inferred from Direct Assay more info	PubMed
enables neurexin family protein binding	IEA Inferred from Electronic Annotation more info
enables neurexin family protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in L-ascorbic acid metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in L-ascorbic acid metabolic process	ISO Inferred from Sequence Orthology more info
involved_in adaptive thermogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cold-induced thermogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in excitatory synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in inhibitory synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in motor learning	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of excitatory synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of lipid droplet fusion	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of lipid storage	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of inhibitory synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of lipid catabolic process	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of protein localization to synapse	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of synapse assembly	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of synapse assembly	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of synaptic transmission	IGI Inferred from Genetic Interaction more info	PubMed
involved_in protein secretion	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of cell growth	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of excitatory synapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of presynapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of presynapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in sympathetic neuron projection extension	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within synapse assembly	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synaptic transmission, GABAergic	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within synaptic transmission, glutamatergic	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in GABA-ergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
is_active_in cell surface	IBA Inferred from Biological aspect of Ancestor more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	IEA Inferred from Electronic Annotation more info
is_active_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IEP Inferred from Expression Pattern more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in lipid droplet	IDA Inferred from Direct Assay more info	PubMed
located_in lipid droplet	IEA Inferred from Electronic Annotation more info
is_active_in organelle membrane contact site	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic density membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic density membrane	IEP Inferred from Expression Pattern more info	PubMed
is_active_in postsynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic membrane	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: calsyntenin-3

Names: alcadein-beta; calsyntenin 3beta

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_001346656.1 → NP_001333585.1 calsyntenin-3 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 2, which has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

BC041781

Consensus CDS

CCDS85156.1

UniProtKB/TrEMBL

D3Z601

Related

ENSMUSP00000108142.2, ENSMUST00000112523.8
NM_153508.4 → NP_705728.1 calsyntenin-3 isoform 1 precursor

See identical proteins and their annotated locations for NP_705728.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK032336, AV341395, CJ152135, CJ287099

Consensus CDS

CCDS20519.1

UniProtKB/Swiss-Prot

A0A4P8DYG6, Q544R0, Q99JH7

Related

ENSMUSP00000008297.5, ENSMUST00000008297.5

Conserved Domains (1) summary

cd11304
Location:32 → 140

Cadherin_repeat; Cadherin tandem repeat domain