Clstn1 calsyntenin 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Clstn1provided by MGI
Official Full Name: calsyntenin 1provided by MGI
Primary source: MGI:MGI:1929895
See related: Ensembl:ENSMUSG00000039953 AllianceGenome:MGI:1929895
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: Cst-1; Cstn1; 1810034E21Rik
Summary: Predicted to enable X11-like protein binding activity; amyloid-beta binding activity; and kinesin binding activity. Involved in neurotransmitter receptor transport to postsynaptic membrane; regulation of synapse maturation; and vesicle-mediated transport in synapse. Acts upstream of or within positive regulation of synapse assembly; positive regulation of synaptic transmission; and regulation of cell growth. Located in several cellular components, including cell surface; postsynaptic density; and postsynaptic membrane. Is active in glutamatergic synapse and postsynaptic endosome. Is expressed in alimentary system; central nervous system; dorsal root ganglion; olfactory epithelium; and retina. Orthologous to human CLSTN1 (calsyntenin 1). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Broad expression in cortex adult (RPKM 93.0), frontal lobe adult (RPKM 80.3) and 23 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 E2; 4 79.91 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (149670536..149733356)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (149585111..149648899)

Chromosome 4 - NC_000070.7 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: 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?

Axonal transport of Frizzled5 by Alcadein alpha-containing vesicles is associated with kinesin-1.
Title: Axonal transport of Frizzled5 by Alcadein α-containing vesicles is associated with kinesin-1.
Amyloidogenic processing of amyloid beta protein precursor (APP) is enhanced in the brains of alcadein alpha-deficient mice.
Title: Amyloidogenic processing of amyloid β protein precursor (APP) is enhanced in the brains of alcadein α-deficient mice.
These results indicate that regulated intramembrane proteolysis of Alca by gamma-secretase regulates APP trafficking and the production of Abeta in vivo.
Title: Cytoplasmic fragment of Alcadein α generated by regulated intramembrane proteolysis enhances amyloid β-protein precursor (APP) transport into the late secretory pathway and facilitates APP cleavage.
these results highlight a key role for calsyntenin-1 in the transport of NMDA receptors to synaptic targets, which is necessary for the maturation of neuronal circuits during early development.
Title: Calsyntenin-1 regulates targeting of dendritic NMDA receptors and dendritic spine maturation in CA1 hippocampal pyramidal cells during postnatal development.
Alcalpha is efficiently processed in part to minimize the inappropriate peripheral retention of kinesin-1
Title: Constitutive cleavage of the single-pass transmembrane protein alcadeinα prevents aberrant peripheral retention of Kinesin-1.
Immunoisolated calsyntenin-1 organelles from murine brain homogenates; determined their proteome by MS. Found calsyntenin-1 organelles are endowed with components of the endosomal trafficking machinery and contained the beta-amyloid precursor protein (APP).
Title: Molecular characterization of a trafficking organelle: dissecting the axonal paths of calsyntenin-1 transport vesicles.
Phosphorylation of KLC1 at serine 460 modulates binding and trafficking of calsyntenin-1.
Title: Phosphorylation of kinesin light chain 1 at serine 460 modulates binding and trafficking of calsyntenin-1.
Calsyntenin-1 links a certain type of vesicular and tubulovesicular organelles to the Kinesin-1 motor.
Title: Calsyntenin-1 docks vesicular cargo to kinesin-1.
The novel cargo Alcadein induces vesicle association of kinesin-1 motor components and activates axonal transport.
Title: The novel cargo Alcadein induces vesicle association of kinesin-1 motor components and activates axonal transport.

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Variation

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Alleles

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

Endonuclease-mediated (2)
Gene trapped (1)
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW742791 (e-PCR)
- UniSTS:207726

AW537209 (e-PCR)
- UniSTS:179708

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables X11-like protein binding	IEA Inferred from Electronic Annotation more info
enables X11-like protein binding	ISO Inferred from Sequence Orthology more info
enables amyloid-beta binding	IEA Inferred from Electronic Annotation more info
enables amyloid-beta binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	NAS Non-traceable Author Statement more info	PubMed
enables kinesin binding	IEA Inferred from Electronic Annotation more info
enables kinesin 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 chemical synaptic transmission	NAS Non-traceable Author Statement more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within intracellular calcium ion homeostasis	TAS Traceable Author Statement more info	PubMed
involved_in neurotransmitter receptor transport to postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in neurotransmitter receptor transport to postsynaptic membrane	IEP Inferred from Expression Pattern more info	PubMed
involved_in neurotransmitter receptor transport to postsynaptic membrane	IMP Inferred from Mutant Phenotype 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	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
acts_upstream_of_or_within regulation of cell growth	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of synapse maturation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synapse maturation	IEP Inferred from Expression Pattern more info	PubMed
involved_in regulation of synapse maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport in synapse	IDA Inferred from Direct Assay more info	PubMed
involved_in vesicle-mediated transport in synapse	IEP Inferred from Expression Pattern more info	PubMed
involved_in vesicle-mediated transport in synapse	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	ISO Inferred from Sequence Orthology more info
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 endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IDA Inferred from Direct Assay more info	PubMed
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 glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in neuron projection	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic density membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic endosome	IDA Inferred from Direct Assay 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
is_active_in spine apparatus membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: calsyntenin-1

Names: alc-alpha; alcadein alpha

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_001290989.1 → NP_001277918.1 calsyntenin-1 isoform 2 precursor

See identical proteins and their annotated locations for NP_001277918.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.

Source sequence(s)

AK034544, AW060392, BQ177451, CB525309, CJ066764, CO433558, CX566257

Consensus CDS

CCDS71522.1

UniProtKB/Swiss-Prot

Q9EPL2

Related

ENSMUSP00000101316.2, ENSMUST00000105691.8

Conserved Domains (2) summary

cd11304
Location:41 → 149

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:355 → 468

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
NM_023051.5 → NP_075538.1 calsyntenin-1 isoform 1 precursor

See identical proteins and their annotated locations for NP_075538.1

Status: VALIDATED

Description

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

Source sequence(s)

AK034544, AW060392, BQ177451, BY231070, CB525309, CJ066764, CO433558, CX566257

Consensus CDS

CCDS18963.1

UniProtKB/Swiss-Prot

A2A800, B2KFP1, B2KFP2, Q69ZV9, Q7TS67, Q8K103, Q9EPL2

Related

ENSMUSP00000036962.7, ENSMUST00000039144.7

Conserved Domains (2) summary

cd11304
Location:168 → 258

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:365 → 478

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000070.7 Reference GRCm39 C57BL/6J

Range

149670536..149733356

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036164295.1 → XP_036020188.1 calsyntenin-1 isoform X3

Conserved Domains (1) summary

COG1874
Location:48 → 145

GanA; Beta-galactosidase GanA [Carbohydrate transport and metabolism]
XM_030253693.2 → XP_030109553.1 calsyntenin-1 isoform X3

Conserved Domains (1) summary

COG1874
Location:48 → 145

GanA; Beta-galactosidase GanA [Carbohydrate transport and metabolism]
XM_006539094.5 → XP_006539157.1 calsyntenin-1 isoform X2

See identical proteins and their annotated locations for XP_006539157.1

Conserved Domains (2) summary

cd11304
Location:41 → 149

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:355 → 515

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_006539093.5 → XP_006539156.1 calsyntenin-1 isoform X1

See identical proteins and their annotated locations for XP_006539156.1

Conserved Domains (2) summary

cd11304
Location:168 → 258

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:365 → 525

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_030253692.1 → XP_030109552.1 calsyntenin-1 isoform X3

Conserved Domains (1) summary

COG1874
Location:48 → 145

GanA; Beta-galactosidase GanA [Carbohydrate transport and metabolism]