Human Gene CDH15 (ENST00000289746.3_4) from GENCODE V47lift37
  Description: cadherin 15 (from RefSeq NM_004933.3)
Gencode Transcript: ENST00000289746.3_4
Gencode Gene: ENSG00000129910.8_7
Transcript (Including UTRs)
   Position: hg19 chr16:89,238,156-89,261,900 Size: 23,745 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr16:89,238,240-89,261,563 Size: 23,324 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:89,238,156-89,261,900)mRNA (may differ from genome)Protein (814 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAD15_HUMAN
DESCRIPTION: RecName: Full=Cadherin-15; AltName: Full=Cadherin-14; AltName: Full=Muscle cadherin; Short=M-cadherin; Flags: Precursor;
FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. M-cadherin is part of the myogenic program and may provide a trigger for terminal muscle differentiation.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Expressed in the brain and cerebellum.
DISEASE: Note=A chromosomal aberration involving CDH15 and KIRREL3 is found in a patient with severe mental retardation and dysmorphic facial features. Translocation t(11;16)(q24.2;q24).
DISEASE: Defects in CDH15 are the cause of mental retardation autosomal dominant type 3 (MRD3) [MIM:612580]. Mental retardation is characterized by significantly sub-average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period.
SIMILARITY: Contains 5 cadherin domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CDH15
Diseases sorted by gene-association score: autosomal dominant non-syndromic intellectual disability* (117), hypotrichosis, congenital, with juvenile macular dystrophy (12), 16q24.3 microdeletion syndrome (10), deafness, autosomal recessive 89 (9), telogen effluvium (9), mental retardation, x-linked, syndromic 13 (8), kbg syndrome (5), hair disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 54.64 RPKM in Brain - Cerebellum
Total median expression: 127.63 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -33.6084-0.400 Picture PostScript Text
3' UTR -138.70337-0.412 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002126 - Cadherin
IPR015919 - Cadherin-like
IPR020894 - Cadherin_CS
IPR000233 - Cadherin_cytoplasmic-dom

Pfam Domains:
PF00028 - Cadherin domain
PF01049 - Cadherin cytoplasmic region

SCOP Domains:
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on P55291
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0034332 adherens junction organization
GO:0051149 positive regulation of muscle cell differentiation

Cellular Component:
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005901 caveola
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031594 neuromuscular junction
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  D83542 - Homo sapiens mRNA for cadherin-15, complete cds.
BC008951 - Homo sapiens cadherin 15, type 1, M-cadherin (myotubule), mRNA (cDNA clone MGC:3599 IMAGE:3027886), complete cds.
DQ893277 - Synthetic construct clone IMAGE:100005907; FLH195874.01X; RZPDo839H03152D cadherin 15, M-cadherin (myotubule) (CDH15) gene, encodes complete protein.
DQ896608 - Synthetic construct Homo sapiens clone IMAGE:100011068; FLH195870.01L; RZPDo839H03151D cadherin 15, M-cadherin (myotubule) (CDH15) gene, encodes complete protein.
JD327063 - Sequence 308087 from Patent EP1572962.
AK308596 - Homo sapiens cDNA, FLJ98637.
AK308631 - Homo sapiens cDNA, FLJ98672.
JD257254 - Sequence 238278 from Patent EP1572962.
LF375155 - JP 2014500723-A/182658: Polycomb-Associated Non-Coding RNAs.
MA610732 - JP 2018138019-A/182658: Polycomb-Associated Non-Coding RNAs.
LF375156 - JP 2014500723-A/182659: Polycomb-Associated Non-Coding RNAs.
JD060355 - Sequence 41379 from Patent EP1572962.
LF375157 - JP 2014500723-A/182660: Polycomb-Associated Non-Coding RNAs.
JD216655 - Sequence 197679 from Patent EP1572962.
JD114244 - Sequence 95268 from Patent EP1572962.
JD409092 - Sequence 390116 from Patent EP1572962.
LF375158 - JP 2014500723-A/182661: Polycomb-Associated Non-Coding RNAs.
MA610733 - JP 2018138019-A/182659: Polycomb-Associated Non-Coding RNAs.
MA610734 - JP 2018138019-A/182660: Polycomb-Associated Non-Coding RNAs.
MA610735 - JP 2018138019-A/182661: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P55291 (Reactome details) participates in the following event(s):

R-HSA-419001 Connection of adjacent cells through calcium-dependent trans-dimerization of cadherin
R-HSA-419002 Interaction of cadherin with Beta/gamma catenin, alpha catenin and p120 catenin
R-HSA-375140 CDO binds promyogenic cadherins
R-HSA-376121 Bnip2 interacts with CDO complex
R-HSA-376119 Interaction of Bnip-2 with Cdc42
R-HSA-376117 JLP interacts with CDO complex
R-HSA-449200 Interaction of ABL1 with CDO complex
R-HSA-448957 Interaction of p38 MAPK with JLP
R-HSA-418990 Adherens junctions interactions
R-HSA-421270 Cell-cell junction organization
R-HSA-375170 CDO in myogenesis
R-HSA-446728 Cell junction organization
R-HSA-525793 Myogenesis
R-HSA-1500931 Cell-Cell communication
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: CAD15_HUMAN, CDH14, CDH3, ENST00000289746.1, ENST00000289746.2, NM_004933, P55291, uc317kss.1, uc317kss.2
UCSC ID: ENST00000289746.3_4
RefSeq Accession: NM_004933.3
Protein: P55291 (aka CAD15_HUMAN or CADF_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.