Human Gene CDH5 (ENST00000341529.8_4) from GENCODE V47lift37
  Description: cadherin 5 (from RefSeq NM_001795.5)
Gencode Transcript: ENST00000341529.8_4
Gencode Gene: ENSG00000179776.20_11
Transcript (Including UTRs)
   Position: hg19 chr16:66,400,594-66,438,687 Size: 38,094 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr16:66,413,241-66,437,072 Size: 23,832 Coding Exon Count: 11 

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 (chr16:66,400,594-66,438,687)mRNA (may differ from genome)Protein (784 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CADH5_HUMAN
DESCRIPTION: RecName: Full=Cadherin-5; AltName: Full=7B4 antigen; AltName: Full=Vascular endothelial cadherin; Short=VE-cadherin; AltName: CD_antigen=CD144; 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. This cadherin may play a important role in endothelial cell biology through control of the cohesion and organization of the intercellular junctions. It associates with alpha-catenin forming a link to the cytoskeleton. Acts in concert with KRIT1 to establish and maintain correct endothelial cell polarity and vascular lumen. These effects are mediated by recruitment and activation of the Par polarity complex and RAP1B. Required for activation of PRKCZ and for the localization of phosphorylated PRKCZ, PARD3, TIAM1 and RAP1B to the cell junction.
SUBUNIT: Interacts via cadherin 5 domain with PTPRB (By similarity). Interacts with TRPC4. Interacts with KRIT1.
SUBCELLULAR LOCATION: Cell junction. Cell membrane; Single-pass type I membrane protein (Probable). Note=Found at cell-cell boundaries and probably at cell-matrix boundaries. KRIT1 and CDH5 reciprocally regulate their localization to endothelial cell-cell junctions.
TISSUE SPECIFICITY: Endothelial tissues and brain.
PTM: Phosphorylated on tyrosine residues by KDR/VEGFR-2. Dephosphorylated by PTPRB (By similarity).
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: CDH5
Diseases sorted by gene-association score: periapical granuloma (12), epithelioid sarcoma (11), uveal melanoma (10), ovarian hyperstimulation syndrome (7), hereditary spastic paraplegia 3a (5), acute myocardial infarction (3), myocardial infarction (1)

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

+  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: 47.31 RPKM in Lung
Total median expression: 482.17 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 -25.3087-0.291 Picture PostScript Text
3' UTR -546.001615-0.338 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 P33151
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:0005102 receptor binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0019903 protein phosphatase binding
GO:0044325 ion channel binding
GO:0046872 metal ion binding

Biological Process:
GO:0001955 blood vessel maturation
GO:0007043 cell-cell junction assembly
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007179 transforming growth factor beta receptor signaling pathway
GO:0008285 negative regulation of cell proliferation
GO:0034332 adherens junction organization
GO:0045766 positive regulation of angiogenesis
GO:0050728 negative regulation of inflammatory response
GO:0098609 cell-cell adhesion
GO:1903142 positive regulation of establishment of endothelial barrier
GO:2000114 regulation of establishment of cell polarity

Cellular Component:
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0005912 adherens junction
GO:0005913 cell-cell adherens junction
GO:0005923 bicellular tight junction
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0071944 cell periphery


-  Descriptions from all associated GenBank mRNAs
  AB044114 - Homo sapiens mRNA for T-cell receptor beta chain, partial cds, clone:TCRVB.16.
LP896024 - Sequence 888 from Patent EP3253886.
U84722 - Human vascular endothelial cadherin mRNA, complete cds.
AK300461 - Homo sapiens cDNA FLJ51093 complete cds, highly similar to Cadherin-5 precursor.
X59796 - H.sapiens mRNA for cadherin-5.
AK300299 - Homo sapiens cDNA FLJ51087 complete cds, highly similar to Cadherin-5 precursor.
AB209908 - Homo sapiens mRNA for cadherin 5, type 2 preproprotein variant protein.
AB035304 - Homo sapiens CDH5 mRNA for cadherin-5, complete cds.
BC096365 - Homo sapiens cadherin 5, type 2 (vascular endothelium), mRNA (cDNA clone MGC:117072 IMAGE:40012047), complete cds.
BC096363 - Homo sapiens cadherin 5, type 2 (vascular endothelium), mRNA (cDNA clone MGC:117070 IMAGE:40012042), complete cds.
BC096364 - Homo sapiens cadherin 5, type 2 (vascular endothelium), mRNA (cDNA clone MGC:117071 IMAGE:40012045), complete cds.
BC117520 - Homo sapiens cadherin 5, type 2 (vascular endothelium), mRNA (cDNA clone MGC:117073 IMAGE:40012053), complete cds.
JD102272 - Sequence 83296 from Patent EP1572962.
AK310334 - Homo sapiens cDNA, FLJ17376.
X79981 - H.sapiens VE-cadherin mRNA.
JD555562 - Sequence 536586 from Patent EP1572962.
AB385138 - Synthetic construct DNA, clone: pF1KB5634, Homo sapiens CDH5 gene for cadherin-5 precursor, complete cds, without stop codon, in Flexi system.
KJ901329 - Synthetic construct Homo sapiens clone ccsbBroadEn_10723 CDH5 gene, encodes complete protein.
AK300322 - Homo sapiens cDNA FLJ51088 complete cds, highly similar to Cadherin-5 precursor.
JD120393 - Sequence 101417 from Patent EP1572962.
JD473656 - Sequence 454680 from Patent EP1572962.
JD324953 - Sequence 305977 from Patent EP1572962.
JD231451 - Sequence 212475 from Patent EP1572962.
JD103670 - Sequence 84694 from Patent EP1572962.
JD208190 - Sequence 189214 from Patent EP1572962.
JD108125 - Sequence 89149 from Patent EP1572962.
JD360784 - Sequence 341808 from Patent EP1572962.
JD263185 - Sequence 244209 from Patent EP1572962.
JD427198 - Sequence 408222 from Patent EP1572962.
JD178858 - Sequence 159882 from Patent EP1572962.
JD074344 - Sequence 55368 from Patent EP1572962.
JD259324 - Sequence 240348 from Patent EP1572962.
JD256958 - Sequence 237982 from Patent EP1572962.
JD251119 - Sequence 232143 from Patent EP1572962.
JD118993 - Sequence 100017 from Patent EP1572962.
JD216590 - Sequence 197614 from Patent EP1572962.
HZ468426 - JP 2015533085-A/2: Modulation of miRNA activity.
JD541005 - Sequence 522029 from Patent EP1572962.
JD515005 - Sequence 496029 from Patent EP1572962.
JD373753 - Sequence 354777 from Patent EP1572962.
JD220124 - Sequence 201148 from Patent EP1572962.
JD564553 - Sequence 545577 from Patent EP1572962.
JD062214 - Sequence 43238 from Patent EP1572962.
JD436165 - Sequence 417189 from Patent EP1572962.
JD188972 - Sequence 169996 from Patent EP1572962.
JD378388 - Sequence 359412 from Patent EP1572962.
JD151338 - Sequence 132362 from Patent EP1572962.
JD367919 - Sequence 348943 from Patent EP1572962.
JD164420 - Sequence 145444 from Patent EP1572962.
JD152711 - Sequence 133735 from Patent EP1572962.
JD526979 - Sequence 508003 from Patent EP1572962.
JD145977 - Sequence 127001 from Patent EP1572962.
JD402642 - Sequence 383666 from Patent EP1572962.

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

Protein P33151 (Reactome details) participates in the following event(s):

R-HSA-5357477 PAK1-3 phosphorylates VE-cadherin
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-5218920 VEGFR2 mediated vascular permeability
R-HSA-418990 Adherens junctions interactions
R-HSA-4420097 VEGFA-VEGFR2 Pathway
R-HSA-421270 Cell-cell junction organization
R-HSA-194138 Signaling by VEGF
R-HSA-446728 Cell junction organization
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-1500931 Cell-Cell communication
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CADH5_HUMAN, ENST00000341529.1, ENST00000341529.2, ENST00000341529.3, ENST00000341529.4, ENST00000341529.5, ENST00000341529.6, ENST00000341529.7, NM_001795, P33151, Q4VAI5, Q4VAI6, uc317wbi.1, uc317wbi.2
UCSC ID: ENST00000341529.8_4
RefSeq Accession: NM_001795.5
Protein: P33151 (aka CADH5_HUMAN or CAD5_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.