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CLSTN1 calsyntenin 1 [ Homo sapiens (human) ]

Gene ID: 22883, updated on 22-Jan-2020

Summary

Official Symbol
CLSTN1provided by HGNC
Official Full Name
calsyntenin 1provided by HGNC
Primary source
HGNC:HGNC:17447
See related
Ensembl:ENSG00000171603 MIM:611321
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CST-1; CSTN1; CDHR12; PIK3CD; ALC-ALPHA; XB31alpha; alcalpha1; alcalpha2
Summary
This gene is a member of the calsyntenin family, a subset of the cadherin superfamily. The encoded transmembrane protein, also known as alcadein-alpha, is thought to bind to kinesin-1 motors to mediate the axonal anterograde transport of certain types of vesicle. Amyloid precursor protein (APP) is trafficked via these vesicles and so this protein is being investigated to see how it might contribute to the mechanisms underlying Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]
Expression
Ubiquitous expression in brain (RPKM 135.7), skin (RPKM 44.9) and 23 other tissues See more
Orthologs

Genomic context

See CLSTN1 in Genome Data Viewer
Location:
1p36.22
Exon count:
19
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (9728926..9824526, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (9789079..9884550, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta Neighboring gene PIK3CD antisense RNA 2 Neighboring gene ribosomal protein L26 pseudogene 7 Neighboring gene mitotic spindle organizing protein 1 pseudogene 1 Neighboring gene uncharacterized LOC105376717 Neighboring gene catenin beta interacting protein 1 Neighboring gene leucine zipper and CTNNBIP1 domain containing Neighboring gene nicotinamide nucleotide adenylyltransferase 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ32258, KIAA0911

Gene Ontology Provided by GOA

Function Evidence Code Pubs
X11-like protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
amyloid-beta binding IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
kinesin binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cell adhesion TAS
Traceable Author Statement
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
neurotransmitter receptor transport to postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
positive regulation of synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cell growth IEA
Inferred from Electronic Annotation
more info
 
regulation of synapse maturation IEA
Inferred from Electronic Annotation
more info
 
vesicle-mediated transport in synapse IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of spine apparatus membrane IEA
Inferred from Electronic Annotation
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
postsynaptic endosome IEA
Inferred from Electronic Annotation
more info
 
postsynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
calsyntenin-1
Names
alcadein-alpha
alzheimer-related cadherin-like protein
cadherin-related family member 12
non-classical cadherin XB31alpha

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001009566.3NP_001009566.1  calsyntenin-1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001009566.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL357140, AL691449
    Consensus CDS
    CCDS30580.1
    UniProtKB/Swiss-Prot
    O94985
    Related
    ENSP00000366513.4, ENST00000377298.9
    Conserved Domains (2) summary
    cd11304
    Location:168258
    Cadherin_repeat; Cadherin tandem repeat domain
    cl22861
    Location:365477
    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 ...
  2. NM_001302883.1NP_001289812.1  calsyntenin-1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001289812.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in a shorter isoform (3) that is missing an internal segment compared to isoform 1.
    Source sequence(s)
    AB020718, AL357140, BI335759
    UniProtKB/Swiss-Prot
    O94985
    UniProtKB/TrEMBL
    B4E3Q1
    Related
    ENSP00000401934.1, ENST00000435891.5
    Conserved Domains (2) summary
    cd11304
    Location:168258
    Cadherin_repeat; Cadherin tandem repeat domain
    cl22861
    Location:365525
    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 ...
  3. NM_014944.4NP_055759.3  calsyntenin-1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_055759.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in a shorter isoform (2) that is missing an internal segment compared to isoform 1.
    Source sequence(s)
    AB020718, AL357140, BI335759
    Consensus CDS
    CCDS105.1
    UniProtKB/Swiss-Prot
    O94985
    Related
    ENSP00000354997.4, ENST00000361311.4
    Conserved Domains (2) summary
    cd11304
    Location:41149
    Cadherin_repeat; Cadherin tandem repeat domain
    cl22861
    Location:355467
    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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    9728926..9824526 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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