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    CLSTN2 calsyntenin 2 [ Homo sapiens (human) ]

    Gene ID: 64084, updated on 9-Dec-2024

    Summary

    Official Symbol
    CLSTN2provided by HGNC
    Official Full Name
    calsyntenin 2provided by HGNC
    Primary source
    HGNC:HGNC:17448
    See related
    Ensembl:ENSG00000158258 MIM:611323; AllianceGenome:HGNC:17448
    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
    CS2; CSTN2; CDHR13; ALC-GAMMA; alcagamma
    Summary
    Predicted to enable calcium ion binding activity. Predicted to be involved in positive regulation of synapse assembly and positive regulation of synaptic transmission. Predicted to be located in several cellular components, including Golgi membrane; endoplasmic reticulum membrane; and postsynaptic density. Predicted to be active in cell surface; glutamatergic synapse; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in ovary (RPKM 37.4), brain (RPKM 15.7) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CLSTN2 in Genome Data Viewer
    Location:
    3q23
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (139935185..140577397)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (142682539..143324729)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (139654027..140296239)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene nicotinamide nucleotide adenylyltransferase 3 Neighboring gene RNA, 7SL, cytoplasmic 724, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14769 Neighboring gene Sharpr-MPRA regulatory region 1318 Neighboring gene MPRA-validated peak4849 silencer Neighboring gene tRNA methyltransferase subunit 11-2 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20616 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:139917505-139918704 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:139922884-139923456 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:139923457-139924028 Neighboring gene uncharacterized LOC124909440 Neighboring gene NANOG hESC enhancer GRCh37_chr3:139984181-139984682 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:140017275-140017955 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:140059844-140060451 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:140060452-140061058 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:140105082-140106281 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:140141804-140143003 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:140143411-140144295 Neighboring gene uncharacterized LOC124900599 Neighboring gene uncharacterized LOC105374132 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:140185495-140186694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:140240291-140240792 Neighboring gene CLSTN2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20618 Neighboring gene uncharacterized LOC102724068 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:140307280-140307869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:140401669-140402169 Neighboring gene tripartite motif containing 42

    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?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
    EBI GWAS Catalog
    A meta-analysis of Hodgkin lymphoma reveals 19p13.3 TCF3 as a novel susceptibility locus.
    EBI GWAS Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium.
    EBI GWAS Catalog
    Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits.
    EBI GWAS Catalog
    GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease.
    EBI GWAS Catalog
    Oligoclonal band status in Scandinavian multiple sclerosis patients is associated with specific genetic risk alleles.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ39113, FLJ39499, MGC119560

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in associative learning IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inhibitory synapse assembly 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
     
    Component Evidence Code Pubs
    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
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    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
     

    General protein information

    Preferred Names
    calsyntenin-2
    Names
    alcadein gamma
    cadherin-related family member 13

    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_022131.3NP_071414.2  calsyntenin-2 precursor

      See identical proteins and their annotated locations for NP_071414.2

      Status: VALIDATED

      Source sequence(s)
      AC048346, AJ278018, AK315308, BC004871, BC103506
      Consensus CDS
      CCDS3112.1
      UniProtKB/Swiss-Prot
      B2RCW5, D3DNF4, Q3SX54, Q3ZB76, Q5UE56, Q96HZ2, Q9BSS0, Q9H4D0
      Related
      ENSP00000402460.2, ENST00000458420.7
      Conserved Domains (1) summary
      cd11304
      Location:165256
      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      139935185..140577397
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007022.3XP_016862511.1  calsyntenin-2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      142682539..143324729
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347514.1XP_054203489.1  calsyntenin-2 isoform X1