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    CDH4 cadherin 4 [ Homo sapiens (human) ]

    Gene ID: 1002, updated on 9-Dec-2024

    Summary

    Official Symbol
    CDH4provided by HGNC
    Official Full Name
    cadherin 4provided by HGNC
    Primary source
    HGNC:HGNC:1763
    See related
    Ensembl:ENSG00000179242 MIM:603006; AllianceGenome:HGNC:1763
    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; R-CAD
    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]
    Expression
    Biased expression in spleen (RPKM 3.2), brain (RPKM 3.1) and 6 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CDH4 in Genome Data Viewer
    Location:
    20q13.33
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (61252261..61940617)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (63037438..63731679)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (59827317..60515673)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:59676211-59677410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59688891-59689390 Neighboring gene long intergenic non-protein coding RNA 1718 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:59698201-59698846 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:59738200-59739399 Neighboring gene uncharacterized LOC105372701 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:59794837-59796036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59829421-59830113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59837300-59837811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59842714-59843244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59843245-59843775 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr20:59881901-59882407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59892319-59893194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59928779-59929522 Neighboring gene Sharpr-MPRA regulatory region 1887 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:59964898-59966097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59966867-59967466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59971133-59971634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59971635-59972134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59981242-59981742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59981743-59982243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60000424-60001315 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59999531-60000423 Neighboring gene uncharacterized LOC105372703 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60008559-60009148 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60009149-60009738 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:60011920-60013119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60023738-60024298 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60024299-60024857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60073706-60074206 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:60075832-60077031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60088606-60089115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60106507-60107008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60113444-60114423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60131355-60131856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60131857-60132356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60137997-60138897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60164799-60165300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60173673-60174405 Neighboring gene MPRA-validated peak4296 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr20:60193522-60194023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60204084-60204742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60203424-60204083 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:60231445-60231625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60237695-60238208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60237181-60237694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60263433-60263932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60274679-60275179 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:60284281-60284449 Neighboring gene uncharacterized LOC100128310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60321424-60321924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60321925-60322425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60328223-60329209 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60329210-60330195 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60332068-60332568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60332569-60333069 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60340987-60341560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60342316-60342816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60344183-60344683 Neighboring gene Sharpr-MPRA regulatory region 10002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60377656-60378176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60378177-60378697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60383971-60384684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60410329-60410830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60434505-60435006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60454167-60454667 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60453666-60454166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60466559-60467058 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60476138-60477031 Neighboring gene Sharpr-MPRA regulatory region 9437 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:60501357-60502556 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60507695-60508426 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60509158-60509888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60523619-60524118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60527344-60527916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60528727-60529226 Neighboring gene MPRA-validated peak4298 silencer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:60538354-60539553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60540456-60541084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60541085-60541714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60551058-60551558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60551559-60552059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60564347-60565309 Neighboring gene uncharacterized LOC105372704 Neighboring gene microRNA 1257 Neighboring gene TATA-box binding protein associated factor 4

    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
    Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.
    EBI GWAS Catalog
    Genetic determinants of plasma β₂-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.
    EBI GWAS Catalog
    Genome-wide association reveals genetic effects on human Aβ42 and τ protein levels in cerebrospinal fluids: a case control study.
    EBI GWAS Catalog
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    EBI GWAS Catalog
    Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies new susceptibility loci for migraine.
    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
    Joint influence of small-effect genetic variants on human longevity.
    EBI GWAS Catalog
    Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ22202, FLJ40547, MGC126700, MGC138355

    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 axon extension IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    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 adhesion TAS
    Traceable Author Statement
    more info
    PubMed 
    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 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules 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 positive regulation of axon extension 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
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    cadherin-4
    Names
    R-cadherin
    cadherin 4, type 1, R-cadherin (retinal)
    cadherin 4, type 1, preproprotein
    retinal cadherin

    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_001252338.2NP_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)
      AA213385, AK308345, AL109911, AL162457, KF511320
      UniProtKB/TrEMBL
      B2RCN5
      Conserved Domains (4) summary
      cd11304
      Location:244351
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:732874
      Cadherin_C; Cadherin cytoplasmic region
      cl07391
      Location:2082
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:136236
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    2. NM_001252339.3NP_001239268.1  cadherin-4 isoform 3

      See identical proteins and their annotated locations for NP_001239268.1

      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)
      AA213385, AK124724, AL109911, AL162457, DC330816, KF511320
      Consensus CDS
      CCDS58784.1
      UniProtKB/TrEMBL
      A0A087WX99
      Related
      ENSP00000443301.1, ENST00000543233.2
      Conserved Domains (4) summary
      cd11304
      Location:207314
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:695837
      Cadherin_C; Cadherin cytoplasmic region
      cl07391
      Location:245
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:99199
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    3. NM_001794.5NP_001785.2  cadherin-4 isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_001785.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA213385, AL109911, AL365229, BC101651, KF511320
      Consensus CDS
      CCDS13488.1
      UniProtKB/Swiss-Prot
      B3KWB8, G3V1P8, P55283, Q2M208, Q5VZ44, Q9BZ05
      UniProtKB/TrEMBL
      B2RCN5
      Related
      ENSP00000484928.1, ENST00000614565.5
      Conserved Domains (4) summary
      cd11304
      Location:281388
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:769911
      Cadherin_C; Cadherin cytoplasmic region
      pfam08758
      Location:30119
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:173273
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      61252261..61940617
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439812.1XP_047295768.1  cadherin-4 isoform X1

      UniProtKB/TrEMBL
      A0A087WX99
    2. XM_047439813.1XP_047295769.1  cadherin-4 isoform X1

      UniProtKB/TrEMBL
      A0A087WX99

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187623.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      8603..54269
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      63037438..63731679
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322812.1XP_054178787.1  cadherin-4 isoform X1

      UniProtKB/TrEMBL
      A0A087WX99
    2. XM_054322813.1XP_054178788.1  cadherin-4 isoform X1

      UniProtKB/TrEMBL
      A0A087WX99