Human Gene CDH26 (ENST00000348616.9_4) from GENCODE V47lift37
  Description: cadherin 26, transcript variant d (from RefSeq NR_145482.2)
Gencode Transcript: ENST00000348616.9_4
Gencode Gene: ENSG00000124215.17_11
Transcript (Including UTRs)
   Position: hg19 chr20:58,533,478-58,589,584 Size: 56,107 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr20:58,533,782-58,587,785 Size: 54,004 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:58,533,478-58,589,584)mRNA (may differ from genome)Protein (832 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAD26_HUMAN
DESCRIPTION: RecName: Full=Cadherin-like protein 26; AltName: Full=Cadherin-like protein VR20; 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 (By similarity).
SIMILARITY: Contains 4 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


-  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: 3.85 RPKM in Prostate
Total median expression: 22.96 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 -86.20304-0.284 Picture PostScript Text
3' UTR -407.101799-0.226 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:
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on Q8IXH8
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    
 RGDEnsembl   
      
      

-  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

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF169690 - Homo sapiens cadherin-like protein VR20 mRNA, partial cds.
AK074477 - Homo sapiens cDNA FLJ23897 fis, clone LNG15183.
AK055202 - Homo sapiens cDNA FLJ30640 fis, clone CTONG2002816, highly similar to Homo sapiens cadherin-like 26 (CDH26), transcript variant a, mRNA.
JD535697 - Sequence 516721 from Patent EP1572962.
JD263314 - Sequence 244338 from Patent EP1572962.
JD433830 - Sequence 414854 from Patent EP1572962.
JD424190 - Sequence 405214 from Patent EP1572962.
BC136306 - Homo sapiens cadherin-like 26, mRNA (cDNA clone MGC:167916 IMAGE:9020293), complete cds.
BC143931 - Homo sapiens cDNA clone IMAGE:9052449.
BC062570 - Homo sapiens cadherin-like 26, mRNA (cDNA clone IMAGE:5176769), complete cds.
KJ903030 - Synthetic construct Homo sapiens clone ccsbBroadEn_12424 CDH26 gene, encodes complete protein.
JD127325 - Sequence 108349 from Patent EP1572962.
JD241373 - Sequence 222397 from Patent EP1572962.
JD327156 - Sequence 308180 from Patent EP1572962.
JD177871 - Sequence 158895 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A2A2M5, B3KNX3, CAD26_HUMAN, ENST00000348616.1, ENST00000348616.2, ENST00000348616.3, ENST00000348616.4, ENST00000348616.5, ENST00000348616.6, ENST00000348616.7, ENST00000348616.8, NR_145482, Q6P5Y6, Q8IXH8, Q8TCH3, Q9BQN4, Q9NRU1, uc317xsb.1, uc317xsb.2
UCSC ID: ENST00000348616.9_4
RefSeq Accession: NM_177980.4
Protein: Q8IXH8 (aka CAD26_HUMAN or CADQ_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.