Human Gene CDH12 (uc003jgk.2)
  Description: Homo sapiens cadherin 12, type 2 (N-cadherin 2) (CDH12), mRNA.
RefSeq Summary (NM_004061): This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature cadherin protein. These integral membrane proteins mediate calcium-dependent cell-cell adhesion and are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. This particular cadherin appears to be expressed specifically in the brain and its temporal pattern of expression would be consistent with a role during a critical period of neuronal development, perhaps specifically during synaptogenesis. [provided by RefSeq, Nov 2015].
Transcript (Including UTRs)
   Position: hg19 chr5:21,750,973-22,853,731 Size: 1,102,759 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr5:21,751,846-22,078,785 Size: 326,940 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:21,750,973-22,853,731)mRNA (may differ from genome)Protein (794 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CAD12_HUMAN
DESCRIPTION: RecName: Full=Cadherin-12; AltName: Full=Brain cadherin; Short=BR-cadherin; AltName: Full=Neural type cadherin 2; Short=N-cadherin 2; 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.
TISSUE SPECIFICITY: Brain.
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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CDH12
CDC HuGE Published Literature: CDH12
Positive Disease Associations: Audiometry, Pure-Tone , Body Composition , Depressive Disorder, Major , Hemoglobin A, Glycosylated , Tunica Media , waist circumference
Related Studies:
  1. Audiometry, Pure-Tone
    , , . [PubMed 0]
  2. Body Composition
    , , . [PubMed 0]
  3. Depressive Disorder, Major
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CDH12
Diseases sorted by gene-association score: cri-du-chat syndrome (5)

-  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: 1.05 RPKM in Pituitary
Total median expression: 8.64 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 -348.721087-0.321 Picture PostScript Text
3' UTR -189.68873-0.217 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 P55289
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  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:0034332 adherens junction organization

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


-  Descriptions from all associated GenBank mRNAs
  BC047608 - Homo sapiens cadherin 12, type 2 (N-cadherin 2), mRNA (cDNA clone MGC:50597 IMAGE:5751948), complete cds.
L33477 - Human (clone 8B1) Br-cadherin mRNA, complete cds.
AK295123 - Homo sapiens cDNA FLJ59304 complete cds, highly similar to Cadherin-12 precursor.
L34057 - Homo sapiens cadherin-12 mRNA, complete cds.
AK314800 - Homo sapiens cDNA, FLJ95673, Homo sapiens cadherin 12, type 2 (N-cadherin 2) (CDH12), mRNA.
EU832103 - Synthetic construct Homo sapiens clone HAIB:100067132; DKFZo008B0525 cadherin 12, type 2 (N-cadherin 2) protein (CDH12) gene, encodes complete protein.
EU832197 - Synthetic construct Homo sapiens clone HAIB:100067226; DKFZo004B0526 cadherin 12, type 2 (N-cadherin 2) protein (CDH12) gene, encodes complete protein.
AK092176 - Homo sapiens cDNA FLJ34857 fis, clone NT2NE2012533, highly similar to Cadherin-12 precursor.
JD315125 - Sequence 296149 from Patent EP1572962.
JD303133 - Sequence 284157 from Patent EP1572962.
JD260512 - Sequence 241536 from Patent EP1572962.
JD174295 - Sequence 155319 from Patent EP1572962.
JD116721 - Sequence 97745 from Patent EP1572962.
JD288916 - Sequence 269940 from Patent EP1572962.
JD539301 - Sequence 520325 from Patent EP1572962.
JD111658 - Sequence 92682 from Patent EP1572962.
JD241021 - Sequence 222045 from Patent EP1572962.
JD541736 - Sequence 522760 from Patent EP1572962.
JD423668 - Sequence 404692 from Patent EP1572962.
JD338794 - Sequence 319818 from Patent EP1572962.
JD396597 - Sequence 377621 from Patent EP1572962.
JD045127 - Sequence 26151 from Patent EP1572962.
JD488028 - Sequence 469052 from Patent EP1572962.
JD179022 - Sequence 160046 from Patent EP1572962.
JD540947 - Sequence 521971 from Patent EP1572962.
JD282632 - Sequence 263656 from Patent EP1572962.
JD523196 - Sequence 504220 from Patent EP1572962.

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

Protein P55289 (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: B2RBT1, CAD12_HUMAN, NM_004061, NP_004052, P55289, Q86UD2
UCSC ID: uc003jgk.2
RefSeq Accession: NM_004061
Protein: P55289 (aka CAD12_HUMAN or CADC_HUMAN)
CCDS: CCDS3890.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004061.3
exon count: 15CDS single in 3' UTR: no RNA size: 4345
ORF size: 2385CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 4370.50frame shift in genome: no % Coverage: 100.00
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.