Clstn1 calsyntenin 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Clstn1provided by RGD
Official Full Name: calsyntenin 1provided by RGD
Primary source: RGD:1306458
See related: EnsemblRapid:ENSRNOG00000016398 AllianceGenome:RGD:1306458
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable X11-like protein binding activity; amyloid-beta binding activity; and kinesin binding activity. Predicted to be involved in several processes, including neurotransmitter receptor transport to postsynaptic membrane; positive regulation of synaptic transmission; and regulation of synapse organization. Predicted to act upstream of or within regulation of cell growth. Is active in several cellular components, including GABA-ergic synapse; postsynaptic density membrane; and spine apparatus membrane. Orthologous to human CLSTN1 (calsyntenin 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 811.2), Lung (RPKM 341.7) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (165314128..165377627)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (160031235..160094585)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (166533262..166601686)

Chromosome 5 - NC_086023.1 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?

Calsyntenin-1 expression and function in brain tissue of lithium-pilocarpine rat seizure models.
Title: Calsyntenin-1 expression and function in brain tissue of lithium-pilocarpine rat seizure models.
findings show that amyloid precursor protein (APP) and calsyntenin-1 are co-transported through axons, that loss of calsyntenin-1 disrupts axonal transport of APP and that calsyntenin-1 loss also leads to altered APP processing and increased production of Abeta
Title: Calsyntenin-1 mediates axonal transport of the amyloid precursor protein and regulates Aβ production.
Results indicate that calsyntenins function outside the nervous system and potentially are modulators of endocrine function.
Title: Calsyntenins are secretory granule proteins in anterior pituitary gland and pancreatic islet alpha cells.
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.

Submit: New GeneRIF Correction

General gene information

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Markers

RH127701 (e-PCR)
- UniSTS:211011

AI237764 (e-PCR)
- UniSTS:249936

RH15907 (e-PCR)
- UniSTS:78774

BF411685 (e-PCR)
- UniSTS:247780

AW533824 (e-PCR)
- UniSTS:246014

Gene Ontology Provided by RGD

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	IEA Inferred from Electronic Annotation more info
enables kinesin binding	IEA Inferred from Electronic Annotation more info
enables kinesin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in neurotransmitter receptor transport to postsynaptic membrane	IEA Inferred from Electronic Annotation more info
involved_in neurotransmitter receptor transport to postsynaptic membrane	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of synapse assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of synapse assembly	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of synaptic transmission	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in regulation of synapse maturation	IEA Inferred from Electronic Annotation more info
involved_in regulation of synapse maturation	ISO Inferred from Sequence Orthology more info
involved_in vesicle-mediated transport in synapse	IEA Inferred from Electronic Annotation more info
involved_in vesicle-mediated transport in synapse	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IDA Inferred from Direct Assay 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	IEA Inferred from Electronic Annotation more info
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular region	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic density membrane	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic endosome	IEA Inferred from Electronic Annotation more info
is_active_in postsynaptic endosome	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic membrane	IEA Inferred from Electronic Annotation more info
located_in postsynaptic membrane	ISO Inferred from Sequence Orthology more info
is_active_in spine apparatus membrane	IDA Inferred from Direct Assay more info	PubMed

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_001007092.1 → NP_001007093.1 calsyntenin-1 precursor

See identical proteins and their annotated locations for NP_001007093.1

Status: PROVISIONAL

Source sequence(s)

AY569014

UniProtKB/Swiss-Prot

Q6Q0N0

UniProtKB/TrEMBL

A0A8I6AMV4

Related

ENSRNOP00000047223.4, ENSRNOT00000045063.5

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 ...

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_086023.1 Reference GRCr8

Range

165314128..165377627

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039110100.2 → XP_038966028.1 calsyntenin-1 isoform X1

UniProtKB/TrEMBL

A0A8I6AMV4, A0A8I6GFE6, A6IUB8

Related

ENSRNOP00000086858.1, ENSRNOT00000119851.2

Conserved Domains (2) summary

cd11304
Location:168 → 258

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:365 → 477

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_039110102.2 → XP_038966030.1 calsyntenin-1 isoform X3

UniProtKB/TrEMBL

A0A8I6AMV4, A0A8L2QPW4

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_039110101.2 → XP_038966029.1 calsyntenin-1 isoform X2

UniProtKB/TrEMBL

A0A8I6AC41, A0A8I6AMV4

Related

ENSRNOP00000089605.1, ENSRNOT00000113486.2

Conserved Domains (2) summary

cd11304
Location:41 → 149

Cadherin_repeat; Cadherin tandem repeat domain

cl22861
Location:355 → 467

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 ...