Human Gene CDH24 (uc001wil.3)
  Description: Homo sapiens cadherin 24, type 2 (CDH24), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr14:23,516,270-23,526,747 Size: 10,478 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr14:23,517,189-23,524,942 Size: 7,754 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:23,516,270-23,526,747)mRNA (may differ from genome)Protein (819 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDHuman Cortex Gene ExpressionLynx
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAD24_HUMAN
DESCRIPTION: RecName: Full=Cadherin-24; 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. Cadherin-24 mediate strong cell-cell adhesion.
SUBUNIT: Associates with alpha-, beta- and delta-catenins.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (Potential).
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


-  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: 10.91 RPKM in Brain - Cerebellum
Total median expression: 180.75 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 -136.50260-0.525 Picture PostScript Text
3' UTR -338.16833-0.406 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 Q86UP0
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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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0008013 beta-catenin binding
GO:0045294 alpha-catenin binding
GO:0046872 metal ion binding
GO:0070097 delta-catenin binding

Biological Process:
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0034332 adherens junction organization
GO:0098609 cell-cell adhesion

Cellular Component:
GO:0005886 plasma membrane
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AY358199 - Homo sapiens clone DNA203532 CDH24 (UNQ2834) mRNA, complete cds.
BC094810 - Homo sapiens cadherin-like 24, mRNA (cDNA clone IMAGE:6212802), partial cds.
BC009332 - Homo sapiens cDNA clone IMAGE:4126701, containing frame-shift errors.
BC019067 - Homo sapiens cDNA clone IMAGE:4896489, containing frame-shift errors.
BC069190 - Homo sapiens cDNA clone IMAGE:4891825, containing frame-shift errors.
AL137477 - Homo sapiens mRNA; cDNA DKFZp434K2323 (from clone DKFZp434K2323); partial cds.
AK025342 - Homo sapiens cDNA: FLJ21689 fis, clone COL09459.
BC110867 - Homo sapiens cadherin-like 24, mRNA (cDNA clone IMAGE:5757286), complete cds.
BC142724 - Homo sapiens cDNA clone IMAGE:40148889, containing frame-shift errors.
JD218772 - Sequence 199796 from Patent EP1572962.
JD214682 - Sequence 195706 from Patent EP1572962.
JD483693 - Sequence 464717 from Patent EP1572962.
JD466498 - Sequence 447522 from Patent EP1572962.
JD073477 - Sequence 54501 from Patent EP1572962.
JD242028 - Sequence 223052 from Patent EP1572962.
JD167908 - Sequence 148932 from Patent EP1572962.
JD533466 - Sequence 514490 from Patent EP1572962.
JD458628 - Sequence 439652 from Patent EP1572962.
JD445348 - Sequence 426372 from Patent EP1572962.
JD132339 - Sequence 113363 from Patent EP1572962.
JD134965 - Sequence 115989 from Patent EP1572962.
JD548455 - Sequence 529479 from Patent EP1572962.
JD260754 - Sequence 241778 from Patent EP1572962.
AY260900 - Homo sapiens cadherin-24 mRNA, complete cds; alternatively spliced.
AY260901 - Homo sapiens cadherin-24 variant mRNA, complete cds; alternatively spliced.
JD448687 - Sequence 429711 from Patent EP1572962.
JD139398 - Sequence 120422 from Patent EP1572962.
JD235614 - Sequence 216638 from Patent EP1572962.
JD372611 - Sequence 353635 from Patent EP1572962.
AK289576 - Homo sapiens cDNA FLJ77485 complete cds, highly similar to Homo sapiens cadherin-like 24 (CDH24), transcript variant 2, mRNA.
JD523581 - Sequence 504605 from Patent EP1572962.
JD123868 - Sequence 104892 from Patent EP1572962.
BC172283 - Synthetic construct Homo sapiens clone IMAGE:100068977, MGC:198988 cadherin-like 24 (CDH24) mRNA, encodes complete protein.
BC172574 - Synthetic construct Homo sapiens clone IMAGE:100069268, MGC:199279 cadherin-like 24 (CDH24) mRNA, encodes complete protein.
JD199814 - Sequence 180838 from Patent EP1572962.
BX248303 - human full-length cDNA clone CS0DK003YO17 of HeLa cells of Homo sapiens (human).
JD197973 - Sequence 178997 from Patent EP1572962.
JD192718 - Sequence 173742 from Patent EP1572962.
JD478890 - Sequence 459914 from Patent EP1572962.
JD056104 - Sequence 37128 from Patent EP1572962.
JD155236 - Sequence 136260 from Patent EP1572962.
JD112733 - Sequence 93757 from Patent EP1572962.
JD318681 - Sequence 299705 from Patent EP1572962.
JD338153 - Sequence 319177 from Patent EP1572962.
JD419257 - Sequence 400281 from Patent EP1572962.
JD495618 - Sequence 476642 from Patent EP1572962.
JD549096 - Sequence 530120 from Patent EP1572962.
JD455945 - Sequence 436969 from Patent EP1572962.
AK057922 - Homo sapiens cDNA FLJ25193 fis, clone JTH00761.
JD328561 - Sequence 309585 from Patent EP1572962.
JD102367 - Sequence 83391 from Patent EP1572962.
JD158069 - Sequence 139093 from Patent EP1572962.
JD288056 - Sequence 269080 from Patent EP1572962.
JD406839 - Sequence 387863 from Patent EP1572962.
AK307746 - Homo sapiens cDNA, FLJ97694.
BX248750 - human full-length cDNA 5-PRIME end of clone CS0DE010YP19 of Placenta of Homo sapiens (human).
JD079312 - Sequence 60336 from Patent EP1572962.
JD401046 - Sequence 382070 from Patent EP1572962.
JD194222 - Sequence 175246 from Patent EP1572962.
JD401045 - Sequence 382069 from Patent EP1572962.
JD157346 - Sequence 138370 from Patent EP1572962.
JD390450 - Sequence 371474 from Patent EP1572962.

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

Protein Q86UP0 (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: CAD24_HUMAN, CDH11L, D3DS44, NM_022478, NP_071923, Q86UP0, Q86UP1, Q9NT84, UNQ2834/PRO34009
UCSC ID: uc001wil.3
RefSeq Accession: NM_022478
Protein: Q86UP0 (aka CAD24_HUMAN or CADO_HUMAN)
CCDS: CCDS9585.1, CCDS9586.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: yes RNA accession: NM_022478.3
exon count: 14CDS single in 3' UTR: no RNA size: 3567
ORF size: 2460CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4666.00frame shift in genome: no % Coverage: 99.61
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.