U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

CDH4 cadherin 4 [ Homo sapiens (human) ]

Gene ID: 1002, updated on 1-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (61252261..61940617)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (63037438..63731679)
105.20220307 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 cadherin binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
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 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 IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in multicellular organism development IBA
Inferred from Biological aspect of Ancestor
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_2023_10

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