Human Gene CDH16 (ENST00000299752.9_10) from GENCODE V47lift37
  Description: cadherin 16, transcript variant 1 (from RefSeq NM_004062.4)
Gencode Transcript: ENST00000299752.9_10
Gencode Gene: ENSG00000166589.13_17
Transcript (Including UTRs)
   Position: hg19 chr16:66,942,025-66,952,788 Size: 10,764 Total Exon Count: 18 Strand: -
Coding Region
   Position: hg19 chr16:66,942,295-66,951,968 Size: 9,674 Coding Exon Count: 17 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:66,942,025-66,952,788)mRNA (may differ from genome)Protein (829 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAD16_HUMAN
DESCRIPTION: RecName: Full=Cadherin-16; AltName: Full=Kidney-specific cadherin; Short=Ksp-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.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (Probable).
TISSUE SPECIFICITY: Kidney specific.
SIMILARITY: Contains 6 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: CDH16
Diseases sorted by gene-association score: oxyphilic adenoma (15), renal oncocytoma (14), chromophobe renal cell carcinoma (13), spindle cell carcinoma (7), kidney benign neoplasm (7), renal cell carcinoma, papillary (4), renal cell carcinoma (3)

-  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: 264.03 RPKM in Kidney - Cortex
Total median expression: 289.97 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -39.0095-0.411 Picture PostScript Text
3' UTR -104.30270-0.386 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

Pfam Domains:
PF00028 - Cadherin domain

SCOP Domains:
49265 - Fibronectin type III
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on O75309
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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0046872 metal ion binding

Biological Process:
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007267 cell-cell signaling
GO:0007399 nervous system development
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016323 basolateral plasma membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC027912 - Homo sapiens cadherin 16, KSP-cadherin, mRNA (cDNA clone MGC:34498 IMAGE:5206766), complete cds.
AK225544 - Homo sapiens mRNA for cadherin 16 precursor variant, clone: KDN02470.
AY358911 - Homo sapiens clone DNA66663 Ksp-cadherin (UNQ695) mRNA, complete cds.
AK298255 - Homo sapiens cDNA FLJ57831 complete cds, highly similar to Cadherin-16 precursor.
AK075243 - Homo sapiens cDNA FLJ90762 fis, clone THYRO1000196, highly similar to Homo sapiens Ksp-cadherin (CDH16) mRNA.
AK225552 - Homo sapiens mRNA for cadherin 16 precursor variant, clone: KDN03622.
AF016272 - Homo sapiens Ksp-cadherin (CDH16) mRNA, complete cds.
JD436892 - Sequence 417916 from Patent EP1572962.
JD320602 - Sequence 301626 from Patent EP1572962.
JD064178 - Sequence 45202 from Patent EP1572962.
JD201718 - Sequence 182742 from Patent EP1572962.
JD417882 - Sequence 398906 from Patent EP1572962.
JD425030 - Sequence 406054 from Patent EP1572962.
AK298334 - Homo sapiens cDNA FLJ53455 complete cds, highly similar to Cadherin-16 precursor.
AK313101 - Homo sapiens cDNA, FLJ93586, highly similar to Homo sapiens cadherin 16, KSP-cadherin (CDH16), mRNA.
KJ890881 - Synthetic construct Homo sapiens clone ccsbBroadEn_00275 CDH16 gene, encodes complete protein.
DQ893807 - Synthetic construct Homo sapiens clone IMAGE:100008267; FLH164574.01L; RZPDo839H09161D cadherin 16, KSP-cadherin (CDH16) gene, encodes complete protein.
EU176180 - Synthetic construct Homo sapiens clone IMAGE:100006335; FLH164581.01X; RZPDo839H02250D cadherin 16, KSP-cadherin (CDH16) gene, encodes complete protein.
AB528546 - Synthetic construct DNA, clone: pF1KB5789, Homo sapiens CDH16 gene for Cadherin-16 Precursor, without stop codon, in Flexi system.
JD227159 - Sequence 208183 from Patent EP1572962.
JD539767 - Sequence 520791 from Patent EP1572962.
JD201700 - Sequence 182724 from Patent EP1572962.
JD418996 - Sequence 400020 from Patent EP1572962.
JD437396 - Sequence 418420 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DPA8, CAD16_HUMAN, ENST00000299752.1, ENST00000299752.2, ENST00000299752.3, ENST00000299752.4, ENST00000299752.5, ENST00000299752.6, ENST00000299752.7, ENST00000299752.8, H3BPD3, NM_004062, O75309, Q6UW93, uc317mlt.1, uc317mlt.2, UNQ695/PRO1340
UCSC ID: ENST00000299752.9_10
RefSeq Accession: NM_004062.4
Protein: O75309 (aka CAD16_HUMAN or CADG_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.