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    CLSTN3 calsyntenin 3 [ Homo sapiens (human) ]

    Gene ID: 9746, updated on 3-Dec-2024

    Summary

    Official Symbol
    CLSTN3provided by HGNC
    Official Full Name
    calsyntenin 3provided by HGNC
    Primary source
    HGNC:HGNC:18371
    See related
    Ensembl:ENSG00000139182 MIM:611324; AllianceGenome:HGNC:18371
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CSTN3; CDHR14; alcbeta
    Summary
    Enables cell-cell adhesion mediator activity and neurexin family protein binding activity. Involved in L-ascorbic acid metabolic process and regulation of synapse assembly. Predicted to be located in several cellular components, including Golgi membrane; dendrite; and postsynaptic density. Predicted to be part of protein-containing complex. Predicted to be active in several cellular components, including GABA-ergic synapse; lipid droplet; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 35.5), kidney (RPKM 13.1) and 23 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:
    12p13.31
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7129093..7158945)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7142174..7172097)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7282967..7311541)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:7260830-7262029 Neighboring gene complement C1r subcomponent like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7265863-7266364 Neighboring gene C1RL antisense RNA 1 Neighboring gene RNA, U6 small nuclear 485, pseudogene Neighboring gene retinol binding protein 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7283265-7283766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4199 Neighboring gene Sharpr-MPRA regulatory region 5519 Neighboring gene uncharacterized LOC124902869 Neighboring gene MPRA-validated peak1553 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7340767-7341268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7341269-7341768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7342139-7342855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7342856-7343571 Neighboring gene peroxisomal biogenesis factor 5

    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

    Clone Names

    • KIAA0726, MGC131797, MGC138488

    Gene Ontology Provided by GOA

    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables enzyme inhibitor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables neurexin family protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables neurexin family protein binding ISS
    Inferred from Sequence or Structural Similarity
    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 adaptive thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in excitatory synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inhibitory synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of excitatory synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of lipid droplet fusion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of lipid storage ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of inhibitory synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of lipid catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of protein localization to synapse IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of synapse assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of synaptic transmission IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cell growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of excitatory synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of presynapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synapse assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in sympathetic neuron projection extension ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in synapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in synaptic transmission, GABAergic IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in synaptic transmission, glutamatergic IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in GABA-ergic synapse IEA
    Inferred from Electronic Annotation
    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 dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lipid droplet IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in lipid droplet ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in organelle membrane contact site ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in postsynaptic membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of protein-containing complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    calsyntenin-3
    Names
    alc-beta
    alcadein beta
    cadherin-related family member 14

    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_014718.4NP_055533.2  calsyntenin-3 precursor

      See identical proteins and their annotated locations for NP_055533.2

      Status: VALIDATED

      Source sequence(s)
      AA864252, AC018653, AJ277460, DA092023
      Consensus CDS
      CCDS8575.1
      UniProtKB/Swiss-Prot
      A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9
      UniProtKB/TrEMBL
      B4DRB1, B7Z9U4
      Related
      ENSP00000266546.6, ENST00000266546.11
      Conserved Domains (1) summary
      cd11304
      Location:32140
      Cadherin_repeat; Cadherin tandem repeat domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      7129093..7158945
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429921.1XP_047285877.1  calsyntenin-3 isoform X2

      UniProtKB/Swiss-Prot
      A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9
      UniProtKB/TrEMBL
      B4DRB1, B7Z9U4
      Related
      ENST00000537408.1
    2. XM_047429919.1XP_047285875.1  calsyntenin-3 isoform X1

      UniProtKB/TrEMBL
      B4DRB1, B7Z9U4
    3. XM_047429920.1XP_047285876.1  calsyntenin-3 isoform X2

      UniProtKB/Swiss-Prot
      A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9
      UniProtKB/TrEMBL
      B4DRB1, B7Z9U4

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_021160008.1 Reference GRCh38.p14 PATCHES

      Range
      56779..86631
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332547.1XP_054188522.1  calsyntenin-3 isoform X2

      UniProtKB/Swiss-Prot
      A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9
      UniProtKB/TrEMBL
      B4DRB1, B7Z9U4
    2. XM_054332546.1XP_054188521.1  calsyntenin-3 isoform X1

      UniProtKB/TrEMBL
      B4DRB1, B7Z9U4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      7142174..7172097
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373906.1XP_054229881.1  calsyntenin-3 isoform X2

      UniProtKB/Swiss-Prot
      A0A3B3IRF8, D3DUT6, O94831, Q2T9J5, Q5UE57, Q9BQT9
      UniProtKB/TrEMBL
      B4DRB1, B7Z9U4
    2. XM_054373905.1XP_054229880.1  calsyntenin-3 isoform X1

      UniProtKB/TrEMBL
      B4DRB1, B7Z9U4