U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Clstn3 calsyntenin 3 [ Mus musculus (house mouse) ]

    Gene ID: 232370, updated on 9-Dec-2024

    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, Dec 2024]
    Expression
    Biased expression in cerebellum adult (RPKM 97.0), cortex adult (RPKM 62.3) and 8 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Clstn3 in Genome Data Viewer
    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_000072.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700027F06 gene Neighboring gene RIKEN cDNA D830015G05 gene Neighboring gene peroxisomal biogenesis factor 5 Neighboring gene STARR-positive B cell enhancer ABC_E3680 Neighboring gene predicted gene, 44096 Neighboring gene complement component 1, r subcomponent-like Neighboring gene complement component 1, r subcomponent A

    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)

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0726

    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

    Preferred Names
    calsyntenin-3
    Names
    alcadein-beta
    calsyntenin 3beta

    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_001346656.1NP_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
    2. NM_153508.4NP_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:32140
      Cadherin_repeat; Cadherin tandem repeat domain

    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_000072.7 Reference GRCm39 C57BL/6J

      Range
      124407715..124441743 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)