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    CNTN3 contactin 3 [ Homo sapiens (human) ]

    Gene ID: 5067, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CNTN3provided by HGNC
    Official Full Name
    contactin 3provided by HGNC
    Primary source
    HGNC:HGNC:2173
    See related
    Ensembl:ENSG00000113805 MIM:601325; AllianceGenome:HGNC:2173
    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
    PCS; PANG; BIG-1
    Summary
    Predicted to be involved in cell adhesion. Predicted to be located in extracellular region and plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in brain (RPKM 2.7), prostate (RPKM 1.8) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CNTN3 in Genome Data Viewer
    Location:
    3p12.3
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (74262568..74614659, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (74304615..74656673, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (74311719..74663810, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene heat shock protein 90 alpha family class B member 5, pseudogene Neighboring gene aldo-keto reductase family 1 member B1 pseudogene 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:74648227-74649426 Neighboring gene uncharacterized LOC105377166 Neighboring gene uncharacterized LOC105377167 Neighboring gene uncharacterized LOC105377168

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Down-regulation of the brain-specific cell-adhesion molecule contactin-3 in tuberous sclerosis complex during the early postnatal period. Korotkov A, et al. J Neurodev Disord, 2022 Jan 15. PMID 35030990, Free PMC Article
    2. Identification of a genetic variant associated with abdominal aortic aneurysms on chromosome 3p12.3 by genome wide association. Elmore JR, et al. J Vasc Surg, 2009 Jun. PMID 19497516
    3. PANG, a gene encoding a neuronal glycoprotein, is ectopically activated by intracisternal A-type particle long terminal repeats in murine plasmacytomas. Connelly MA, et al. Proc Natl Acad Sci U S A, 1994 Feb 15. PMID 8108413, Free PMC Article
    4. SLC1A1, SLC16A9, and CNTN3 Are Potential Biomarkers for the Occurrence of Colorectal Cancer. Zhou J, et al. Biomed Res Int, 2020. PMID 32566650, Free PMC Article
    5. Human NB-2 of the contactin subgroup molecules: chromosomal localization of the gene (CNTN5) and distinct expression pattern from other subgroup members. Kamei Y, et al. Genomics, 2000 Oct 1. PMID 11013081

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Down-regulation of the brain-specific cell-adhesion molecule contactin-3 in tuberous sclerosis complex during the early postnatal period.
      Title: Down-regulation of the brain-specific cell-adhesion molecule contactin-3 in tuberous sclerosis complex during the early postnatal period.
    2. SLC1A1, SLC16A9, and CNTN3 Are Potential Biomarkers for the Occurrence of Colorectal Cancer.
      Title: SLC1A1, SLC16A9, and CNTN3 Are Potential Biomarkers for the Occurrence of Colorectal Cancer.
    3. BIG1 and BIG2 have roles in endomembrane organization
      Title: Specific functions of BIG1 and BIG2 in endomembrane organization.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Identification of a genetic variant associated with abdominal aortic aneurysms on chromosome 3p12.3 by genome wide association.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of smoking behaviours among Bangladeshi adults.
    EBI GWAS Catalog
    The genetic architecture of economic and political preferences.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1496

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    contactin-3
    Names
    brain-derived immunoglobulin superfamily protein 1
    contactin 3 (plasmacytoma associated)
    plasmacytoma-associated neuronal glycoprotein

    NCBI Reference Sequences (RefSeq)

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    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_001393376.1 → NP_001380305.1  contactin-3 precursor

      Status: VALIDATED

      Source sequence(s)
      AC016945, AC016950, AC024222, AC128653, AC128656
      Consensus CDS
      CCDS33790.1
      UniProtKB/Swiss-Prot
      B9EK50, Q9H039, Q9P232
      Conserved Domains (3) summary
      cd00063
      Location:598 → 695
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd00096
      Location:498 → 504
      Ig; Ig strand A [structural motif]
      cl11960
      Location:498 → 598
      Ig; Immunoglobulin domain

    2. NM_020872.3 → NP_065923.1  contactin-3 precursor

      See identical proteins and their annotated locations for NP_065923.1

      Status: VALIDATED

      Source sequence(s)
      AC016945, AC016950, AC024222, AC128653, AC128656
      Consensus CDS
      CCDS33790.1
      UniProtKB/Swiss-Prot
      B9EK50, Q9H039, Q9P232
      Related
      ENSP00000263665.6, ENST00000263665.7
      Conserved Domains (3) summary
      cd00063
      Location:598 → 695
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd00096
      Location:498 → 504
      Ig; Ig strand A [structural motif]
      cl11960
      Location:498 → 598
      Ig; Immunoglobulin 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
      74262568..74614659 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533768.3 → XP_011532070.1  contactin-3 isoform X1

      Conserved Domains (4) summary
      smart00410
      Location:419 → 496
      IG_like; Immunoglobulin like
      cd00063
      Location:598 → 695
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam07679
      Location:318 → 403
      I-set; Immunoglobulin I-set domain
      cl11960
      Location:227 → 315
      Ig; Immunoglobulin domain

    2. XM_017006508.2 → XP_016861997.1  contactin-3 isoform X2

    3. XM_017006509.1 → XP_016861998.1  contactin-3 isoform X3

      Conserved Domains (3) summary
      smart00410
      Location:64 → 152
      IG_like; Immunoglobulin like
      cd00063
      Location:156 → 253
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cl11960
      Location:73 → 156
      Ig; Immunoglobulin domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      74304615..74656673 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346680.1 → XP_054202655.1  contactin-3 isoform X1

    2. XM_054346681.1 → XP_054202656.1  contactin-3 isoform X2

    3. XM_054346682.1 → XP_054202657.1  contactin-3 isoform X3

    4. XM_054346683.1 → XP_054202658.1  contactin-3 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P232.3 GenPept UniProtKB/Swiss-Prot:Q9P232

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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