Human Gene CDH13 (ENST00000431540.7) Description and Page Index
  Description: Homo sapiens cadherin 13 (CDH13), transcript variant 5, mRNA. (from RefSeq NM_001220491)
RefSeq Summary (NM_001220491): This gene encodes a member of the cadherin superfamily. The encoded protein is localized to the surface of the cell membrane and is anchored by a GPI moiety, rather than by a transmembrane domain. The protein lacks the cytoplasmic domain characteristic of other cadherins, and so is not thought to be a cell-cell adhesion glycoprotein. This protein acts as a negative regulator of axon growth during neural differentiation. It also protects vascular endothelial cells from apoptosis due to oxidative stress, and is associated with resistance to atherosclerosis. The gene is hypermethylated in many types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2011].
Gencode Transcript: ENST00000431540.7
Gencode Gene: ENSG00000140945.17
Transcript (Including UTRs)
   Position: hg38 chr16:82,626,970-83,181,094 Size: 554,125 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg38 chr16:82,627,093-83,180,959 Size: 553,867 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr16:82,626,970-83,181,094)mRNA (may differ from genome)Protein (190 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cadherin-13; AltName: Full=Heart cadherin; Short=H-cadherin; AltName: Full=P105; AltName: Full=Truncated cadherin; Short=T-cad; Short=T-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. May act as a negative regulator of neural cell growth.
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor, GPI-anchor.
TISSUE SPECIFICITY: Highly expressed in heart. In the CNS, expressed in cerebral cortex, medulla, hippocampus, amygdala, thalamus and substantia nigra. No expression detected in cerebellum or spinal cord.
DEVELOPMENTAL STAGE: Expressed at higher levels in adult brain than in developing brain.
SIMILARITY: Contains 5 cadherin domains.

-  MalaCards Disease Associations
  MalaCards Gene Search: CDH13
Diseases sorted by gene-association score: lung cancer (4), attention deficit-hyperactivity disorder (2), colorectal cancer (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 66.84 RPKM in Artery - Aorta
Total median expression: 330.85 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 -40.40123-0.328 Picture PostScript Text
3' UTR -16.70135-0.124 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
IPR014868 - Cadherin_pro_dom

Pfam Domains:
PF00028 - Cadherin domain
PF08758 - Cadherin prodomain like

Protein Data Bank (PDB) 3-D Structure
MuPIT help


ModBase Predicted Comparative 3D Structure on P55290
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0030169 low-density lipoprotein particle binding
GO:0042803 protein homodimerization activity
GO:0045296 cadherin binding
GO:0046872 metal ion binding
GO:0055100 adiponectin binding
GO:0071813 lipoprotein particle binding

Biological Process:
GO:0000278 mitotic cell cycle
GO:0001938 positive regulation of endothelial cell proliferation
GO:0001954 positive regulation of cell-matrix adhesion
GO:0002040 sprouting angiogenesis
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007162 negative regulation of cell adhesion
GO:0007266 Rho protein signal transduction
GO:0008285 negative regulation of cell proliferation
GO:0010033 response to organic substance
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0016601 Rac protein signal transduction
GO:0030032 lamellipodium assembly
GO:0030100 regulation of endocytosis
GO:0030335 positive regulation of cell migration
GO:0034332 adherens junction organization
GO:0042058 regulation of epidermal growth factor receptor signaling pathway
GO:0043542 endothelial cell migration
GO:0043616 keratinocyte proliferation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0050850 positive regulation of calcium-mediated signaling
GO:0050927 positive regulation of positive chemotaxis
GO:0051668 localization within membrane
GO:0055096 low-density lipoprotein particle mediated signaling

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005901 caveola
GO:0005925 focal adhesion
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0031012 extracellular matrix
GO:0031225 anchored component of membrane
GO:0043005 neuron projection
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome

-  Descriptions from all associated GenBank mRNAs
  AK304592 - Homo sapiens cDNA FLJ54302 complete cds, highly similar to Cadherin-13 precursor.
EU190357 - Homo sapiens cadherin 13 soluble isoform 2 (CDH13) mRNA, complete cds, alternatively spliced.
EU190358 - Homo sapiens cadherin 13 soluble isoform 1 (CDH13) mRNA, complete cds, alternatively spliced.
AK307862 - Homo sapiens cDNA, FLJ97810.
AK298612 - Homo sapiens cDNA FLJ50610 complete cds, highly similar to Cadherin-13 precursor.
AK295886 - Homo sapiens cDNA FLJ50547 complete cds, highly similar to Cadherin-13 precursor.
BC028624 - Homo sapiens cadherin 13, H-cadherin (heart), mRNA (cDNA clone MGC:33612 IMAGE:4825734), complete cds.
BC030653 - Homo sapiens cadherin 13, H-cadherin (heart), mRNA (cDNA clone MGC:33162 IMAGE:4811561), complete cds.
L34058 - Homo sapiens cadherin-13 mRNA, complete cds.
U59288 - Human H-cadherin mRNA, complete cds.
U59289 - Human H-cadherin mRNA, complete cds.
BC012615 - Homo sapiens, clone IMAGE:4042282, mRNA.
AK304733 - Homo sapiens cDNA FLJ52398 complete cds, highly similar to Cadherin-13 precursor.
CU688968 - Synthetic construct Homo sapiens gateway clone IMAGE:100020037 5' read CDH13 mRNA.
KJ896582 - Synthetic construct Homo sapiens clone ccsbBroadEn_05976 CDH13 gene, encodes complete protein.
AB384879 - Synthetic construct DNA, clone: pF1KB3963, Homo sapiens CDH13 gene for cadherin-13 precursor, complete cds, without stop codon, in Flexi system.
DQ891713 - Synthetic construct clone IMAGE:100004343; FLH179340.01X; RZPDo839F05130D cadherin 13, H-cadherin (heart) (CDH13) gene, encodes complete protein.
DQ894890 - Synthetic construct Homo sapiens clone IMAGE:100009350; FLH179336.01L; RZPDo839F05129D cadherin 13, H-cadherin (heart) (CDH13) gene, encodes complete protein.

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

Protein P55290 (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-418990 Adherens junctions interactions
R-HSA-421270 Cell-cell junction organization
R-HSA-446728 Cell junction organization
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: A8W476, A8W477, CAD13_HUMAN, CDHH, NM_001220491, P55290, Q6GTW4, Q8TBX3, uc010chh.1, uc010chh.2, uc010chh.3, uc010chh.4
UCSC ID: uc010chh.4
RefSeq Accession: NM_001220491
Protein: P55290 (aka CAD13_HUMAN or CADD_HUMAN)
CCDS: CCDS56010.1

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