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    CDH4 cadherin 4, type 1, R-cadherin (retinal) [ Homo sapiens ]

    Gene ID: 1002, updated on 19-May-2012
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    Summary

    Official Symbol
    CDH4provided by HGNC
    Official Full Name
    cadherin 4, type 1, R-cadherin (retinal)provided by HGNC
    Primary source
    HGNC:1763
    See related
    Ensembl:ENSG00000179242; HPRD:04304; MIM:603006; Vega:OTTHUMG00000032890
    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
    CAD4; RCAD; FLJ22202; FLJ40547; MGC126700; MGC138355
    Summary
    This gene is a classical cadherin from the cadherin superfamily. The encoded protein is a calcium-dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Based on studies in chicken and mouse, this cadherin is thought to play an important role during brain segmentation and neuronal outgrowth. In addition, a role in kidney and muscle development is indicated. Of particular interest are studies showing stable cis-heterodimers of cadherins 2 and 4 in cotransfected cell lines. Previously thought to interact in an exclusively homophilic manner, this is the first evidence of cadherin heterodimerization. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
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    Genomic context

    Location :
    20q13.3
    Sequence :
    Chromosome: 20; NC_000020.10 (59827559..60512299)
    See CDH4 in Epigenomics, MapViewer

    Chromosome 20 - NC_000020.10Genomic Context describing neighboring genes Neighboring gene microRNA 548ag-2 Neighboring gene uncharacterized LOC100506470 Neighboring gene uncharacterized LOC100128310 Neighboring gene microRNA 1257 Neighboring gene ribosomal protein L17 pseudogene 48 Neighboring gene TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Chromodomain helicase DNA-binding protein 4 (CHD4) regulates homologous recombination DNA repair, and its deficiency sensitizes cells to poly(ADP-ribose) polymerase (PARP) inhibitor treatment. Pan MR, et al. J Biol Chem, 2012 Feb 24. PMID 22219182.
    2. CDH4 as a novel putative tumor suppressor gene epigenetically silenced by promoter hypermethylation in nasopharyngeal carcinoma. Du C, et al. Cancer Lett, 2011 Oct 1. PMID 21665361.
    3. GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. Aouizerat BE, et al. BMC Cardiovasc Disord, 2011 Jun 10. PMID 21658281.
    4. Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study. Han MR, et al. BMC Neurol, 2010 Oct 8. PMID 20932310.
    5. Joint influence of small-effect genetic variants on human longevity. Yashin AI, et al. Aging (Albany NY), 2010 Sep. PMID 20834067.

    See all (30) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. Findings identify an important role of CHD4 in controlling homologous recombination repair to maintain genome stability and establish the potential therapeutic implications of targeting CHD4 deficiency in tumors.
      Title: Chromodomain helicase DNA-binding protein 4 (CHD4) regulates homologous recombination DNA repair, and its deficiency sensitizes cells to poly(ADP-ribose) polymerase (PARP) inhibitor treatment.
    2. a novel putative tumor suppressor gene that can be frequently and tumor-specifically inactivated by its promoter methylation in nasopharyngeal carcinoma
      Title: CDH4 as a novel putative tumor suppressor gene epigenetically silenced by promoter hypermethylation in nasopharyngeal carcinoma.
    3. 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.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    5. the degradation of E-cadherin in response to expression of R-cadherin is due to competition for p120(ctn)
      Title: Expression of inappropriate cadherins by epithelial tumor cells promotes endocytosis and degradation of E-cadherin via competition for p120(ctn).
    6. R-cadherin induces cell motility when expressed in epithelial cells, and this increased motility is dependent upon Rho GTPase activity.
      Title: R-cadherin influences cell motility via Rho family GTPases.
    7. CDH4 may act as a tumor suppressor gene in human gastrointestinal tumors and can potentially be used as an early diagnostic marker for gastrointestinal tumorigenesis
      Title: Frequent aberrant methylation of the CDH4 gene promoter in human colorectal and gastric cancer.
    Submit: New GeneRIF Correction
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

    Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.

    Genome-wide association reveals genetic effects on human A 42 and ? protein levels in cerebrospinal fluids: a case control study.

    GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease.

    Joint influence of small-effect genetic variants on human longevity.

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    P55283 P19022 CDH2    HPRD  PubMed  
    BioGRID:107437 BioGRID:107435 CDH2    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:107437 BioGRID:123213 CDK5RAP3    BioGRID  PubMed Affinity Capture-MS; Affinity Capture-Western; Co-fractionation 
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    General gene information

    Markers

    Genotypes

    Homology

    Pathways from BioSystems

    • Adherens junctions interactions, organism-specific biosystem (from REACTOME)
      Adherens junctions interactions, organism-specific biosystemThe adherens junctions (AJ) are multiprotein complexes that promote homotypic cell adhesion in nearly all types of tissue by linking membrane and cytoskeletal components at discrete contact regions (...
    • CDO in myogenesis, organism-specific biosystem (from REACTOME)
      CDO in myogenesis, organism-specific biosystemCDO/Cdon (cell-adhesion-molecule-related/downregulated by oncogenes) is a type I transmembrane multifunctional co-receptor consisting of five immunoglobulin and three fibronectin type III (FNIII) rep...
    • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
      Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
      Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell junction organization, organism-specific biosystem (from REACTOME)
      Cell junction organization, organism-specific biosystem
      Cell junction organization
    • Cell-Cell communication, organism-specific biosystem (from REACTOME)
      Cell-Cell communication, organism-specific biosystemCell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell cont...
    • Cell-cell junction organization, organism-specific biosystem (from REACTOME)
      Cell-cell junction organization, organism-specific biosystemEpithelial cell-cell contacts consist of three major adhesion systems: adherens junctions (AJs), tight junctions (TJs), and desmosomes. These adhesion systems differ in their function and compositio...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • Myogenesis, organism-specific biosystem (from REACTOME)
      Myogenesis, organism-specific biosystemMyogenesis, the formation of muscle tissue, is a complex process involving steps of cell proliferation mediated by growth factor signaling, cell differentiation, reorganization of cells to form myotu...

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    adherens junction organization TAS
    Traceable Author Statement
    more info
    		  
    axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    cell junction assembly TAS
    Traceable Author Statement
    more info
    		  
    cell-cell junction organization TAS
    Traceable Author Statement
    more info
    		  
    heterophilic cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    homophilic cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    positive regulation of axon extension IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    integral to plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
    		  
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    General protein information

    Preferred Names
    cadherin-4
    Names
    cadherin-4
    R-CAD
    R-cadherin
    retinal cadherin
    cadherin 4, type 1, preproprotein
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    NCBI Reference Sequences (RefSeq)

    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_001252338.1 → NP_001239267.1  cadherin-4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate exon in place of the first two exons compared to variant 1, and the alternate exon has an in-frame translation start site. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AK124724, AK308345, AL109911, BC101651, BM664894, L34059
      UniProtKB/TrEMBL
      B3KWB8
      UniProtKB/Swiss-Prot
      P55283
      Conserved Domains (4) summary
      pfam01049
      Location:726 – 876
      Blast Score: 349
      Cadherin_C; Cadherin cytoplasmic region
      cl07391
      Location:20 – 84
      Blast Score: 235
      Cadherin_pro; Cadherin prodomain like
      cd11304
      Location:244 – 351
      Blast Score: 265
      Cadherin_repeat; Cadherin tandem repeat domain.
      cl15786
      Location:136 – 236
      Blast Score: 184
      CA_like; Cadherin repeat-like domain.

    2. NM_001252339.1 → NP_001239268.1  cadherin-4 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an alternate exon in place of the first two exons compared to variant 1, but the alternate exon does not have an in-frame translation start site. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK124724, AL109911, BM664894, DC330816, L34059
      UniProtKB/TrEMBL
      B3KWB8
      UniProtKB/TrEMBL
      G3V1P8
      UniProtKB/Swiss-Prot
      P55283
      Conserved Domains (4) summary
      pfam01049
      Location:689 – 839
      Blast Score: 347
      Cadherin_C; Cadherin cytoplasmic region
      cl07391
      Location:1 – 47
      Blast Score: 160
      Cadherin_pro; Cadherin prodomain like
      cd11304
      Location:207 – 314
      Blast Score: 264
      Cadherin_repeat; Cadherin tandem repeat domain.
      cl15786
      Location:99 – 199
      Blast Score: 183
      CA_like; Cadherin repeat-like domain.

    3. NM_001794.3 → NP_001785.2  cadherin-4 isoform 1 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK124724, AL109911, BC101651, BM664894, L34059
      Consensus CDS
      CCDS13488.1
      UniProtKB/TrEMBL
      B3KWB8
      UniProtKB/Swiss-Prot
      P55283
      Related
      ENSP00000353656, OTTHUMP00000031444, ENST00000360469, OTTHUMT00000079965
      Conserved Domains (4) summary
      pfam01049
      Location:763 – 913
      Blast Score: 348
      Cadherin_C; Cadherin cytoplasmic region
      cl07391
      Location:30 – 121
      Blast Score: 329
      Cadherin_pro; Cadherin prodomain like
      cd11304
      Location:281 – 388
      Blast Score: 264
      Cadherin_repeat; Cadherin tandem repeat domain.
      cl15786
      Location:173 – 273
      Blast Score: 183
      CA_like; Cadherin repeat-like domain.

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000020.10 Reference GRCh37.p5 Primary Assembly

      Range
      59827559..60512299
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000152.1 Alternate HuRef

      Range
      57100643..57293394
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AL079336.27 None
    genomic AL109911.47 CAI19181.1
    genomic AL160412.14 None
    genomic AL162457.11 CAH73749.1
    genomic AL365229.13 CAI16510.1
    genomic AL365401.20 CAC26840.2
    genomic AL391316.7 None
    genomic AL450463.20 (100..27853) None
    genomic BX640515.3 (600..18481) None
    genomic CH471077.2 EAW75408.1
      EAW75409.1
      EAW75410.1
    mRNA AI422259.1 None
    mRNA AK025855.1 BAB15259.1
    mRNA AK091496.1 BAC03677.1
    mRNA AK092092.1 None
    mRNA AK124724.1 BAG54080.1
    mRNA AK308345.1 None
    mRNA AK315192.1 BAG37632.1
    mRNA BC101651.1 AAI01652.1
    mRNA BC112150.1 AAI12151.1
    mRNA BM664894.1 None
    mRNA DC330816.1 None
    mRNA L34059.1 AAA35627.1
    mRNA AL834206.1 CAD38893.2
    Protein Accession Links
    GenPept Link UniProtKB Link
    P55283.2 GenPept UniProtKB/Swiss-Prot:P55283
    Q8NB64 GenPept UniProtKB/TrEMBL:Q8NB64
    Q8ND09 GenPept UniProtKB/TrEMBL:Q8ND09
    Q9H6K0 GenPept UniProtKB/TrEMBL:Q9H6K0
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    Additional Links

    Gene LinkOut

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

    Chemical Information
    Medical
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