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    CDH20 cadherin 20 [ Homo sapiens (human) ]

    Gene ID: 28316, updated on 28-Oct-2024

    Summary

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    Official Symbol
    CDH20provided by HGNC
    Official Full Name
    cadherin 20provided by HGNC
    Primary source
    HGNC:HGNC:1760
    See related
    Ensembl:ENSG00000101542 MIM:605807; AllianceGenome:HGNC:1760
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    Cdh7; CDH7L3
    Summary
    This gene is a type II classical cadherin from the cadherin superfamily and one of three cadherin 7-like genes located in a cluster on chromosome 18. The encoded membrane protein is a calcium dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Since disturbance of intracellular adhesion is a prerequisite for invasion and metastasis of tumor cells, cadherins are considered prime candidates for tumor suppressor genes. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 10.7) and fat (RPKM 4.1) See more
    Orthologs
    mouse all
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    Genomic context

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    See CDH20 in Genome Data Viewer
    Location:
    18q21.33
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (61333430..61555779)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (61536681..61759001)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (59000663..59223012)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ARF like GTPase 14 effector protein pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:58352137-58352638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:58352639-58353138 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:58471303-58472038 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 31 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:58647560-58648273 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:58931179-58931678 Neighboring gene NANOG hESC enhancer GRCh37_chr18:58936564-58937065 Neighboring gene RNA, U6 small nuclear 116, pseudogene Neighboring gene ribosomal protein L30 pseudogene 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:59221319-59221826 Neighboring gene uncharacterized LOC124904314 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:59273512-59274711 Neighboring gene LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated pseudogene 1

    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. Characterization of three novel human cadherin genes (CDH7, CDH19, and CDH20) clustered on chromosome 18q22-q23 and with high homology to chicken cadherin-7. Kools P, et al. Genomics, 2000 Sep 15. PMID 10995570
    2. Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping. McDonough CW, et al. Hum Genet, 2009 Dec. PMID 19690890, Free PMC Article
    3. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. Khanna R, et al. FEBS J, 2018 Jun. PMID 29676528
    4. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping.
    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
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ37047

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables beta-catenin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cadherin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in adherens junction organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-cell adhesion mediated by cadherin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-cell junction assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catenin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    cadherin-20
    Names
    cadherin 20, type 2

    NCBI Reference Sequences (RefSeq)

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    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_031891.4 → NP_114097.2  cadherin-20 preproprotein

      See identical proteins and their annotated locations for NP_114097.2

      Status: REVIEWED

      Source sequence(s)
      AC006203, AC025656, AC090409
      Consensus CDS
      CCDS11977.1
      UniProtKB/Swiss-Prot
      Q495S3, Q9HBT6
      UniProtKB/TrEMBL
      A8K2C5
      Related
      ENSP00000262717.3, ENST00000262717.9
      Conserved Domains (3) summary
      cd11304
      Location:394 → 490
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:85 → 163
      CA; Cadherin repeats
      pfam01049
      Location:643 → 794
      Cadherin_C; Cadherin cytoplasmic region

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      61333430..61555779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024451165.2 → XP_024306933.1  cadherin-20 isoform X1

      UniProtKB/Swiss-Prot
      Q495S3, Q9HBT6
      UniProtKB/TrEMBL
      A8K2C5
      Related
      ENSP00000444767.1, ENST00000536675.2
      Conserved Domains (3) summary
      cd11304
      Location:394 → 490
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:85 → 163
      CA; Cadherin repeats
      pfam01049
      Location:643 → 794
      Cadherin_C; Cadherin cytoplasmic region

    RNA

    1. XR_001753187.2 RNA Sequence

    2. XR_001753186.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      61536681..61759001
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318533.1 → XP_054174508.1  cadherin-20 isoform X1

      UniProtKB/Swiss-Prot
      Q495S3, Q9HBT6

    RNA

    1. XR_008484998.1 RNA Sequence

    2. XR_008484997.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HBT6.2 GenPept UniProtKB/Swiss-Prot:Q9HBT6

    Gene LinkOut

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

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