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    Clstn1 calsyntenin 1 [ Mus musculus (house mouse) ]

    Gene ID: 65945, updated on 9-Dec-2024

    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, Dec 2024]
    Expression
    Broad expression in cortex adult (RPKM 93.0), frontal lobe adult (RPKM 80.3) and 23 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Clstn1 in Genome Data Viewer
    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_000070.7Genomic Context describing neighboring genes Neighboring gene catenin beta interacting protein 1 Neighboring gene microRNA 5616 Neighboring gene predicted gene 13066 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:149032165-149032348 Neighboring gene phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta Neighboring gene microRNA 7023 Neighboring gene STARR-positive B cell enhancer mm9_chr4:149063846-149064146 Neighboring gene STARR-positive B cell enhancer ABC_E9249 Neighboring gene STARR-positive B cell enhancer ABC_E2730 Neighboring gene STARR-positive B cell enhancer mm9_chr4:149084694-149084994 Neighboring gene transmembrane protein 201

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Gene trapped (1) 
    • Targeted (5)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    Preferred Names
    calsyntenin-1
    Names
    alc-alpha
    alcadein alpha

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001290989.1NP_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:41149
      Cadherin_repeat; Cadherin tandem repeat domain
      cl22861
      Location:355468
      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_023051.5NP_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:168258
      Cadherin_repeat; Cadherin tandem repeat domain
      cl22861
      Location:365478
      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

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      149670536..149733356
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Conserved Domains (1) summary
      COG1874
      Location:48145
      GanA; Beta-galactosidase GanA [Carbohydrate transport and metabolism]
    2. XM_030253693.2XP_030109553.1  calsyntenin-1 isoform X3

      Conserved Domains (1) summary
      COG1874
      Location:48145
      GanA; Beta-galactosidase GanA [Carbohydrate transport and metabolism]
    3. XM_006539094.5XP_006539157.1  calsyntenin-1 isoform X2

      See identical proteins and their annotated locations for XP_006539157.1

      Conserved Domains (2) summary
      cd11304
      Location:41149
      Cadherin_repeat; Cadherin tandem repeat domain
      cl22861
      Location:355515
      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 ...
    4. XM_006539093.5XP_006539156.1  calsyntenin-1 isoform X1

      See identical proteins and their annotated locations for XP_006539156.1

      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 ...
    5. XM_030253692.1XP_030109552.1  calsyntenin-1 isoform X3

      Conserved Domains (1) summary
      COG1874
      Location:48145
      GanA; Beta-galactosidase GanA [Carbohydrate transport and metabolism]