Human Gene PCDH12 (ENST00000231484.4_6) from GENCODE V47lift37
  Description: protocadherin 12 (from RefSeq NM_016580.4)
Gencode Transcript: ENST00000231484.4_6
Gencode Gene: ENSG00000113555.6_10
Transcript (Including UTRs)
   Position: hg19 chr5:141,323,146-141,337,767 Size: 14,622 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr5:141,324,946-141,337,416 Size: 12,471 Coding Exon Count: 4 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:141,323,146-141,337,767)mRNA (may differ from genome)Protein (1184 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCD12_HUMAN
DESCRIPTION: RecName: Full=Protocadherin-12; AltName: Full=Vascular cadherin-2; AltName: Full=Vascular endothelial cadherin-2; Short=VE-cad-2; Short=VE-cadherin-2; Flags: Precursor;
FUNCTION: Cellular adhesion molecule that may play an important role in cell-cell interactions at interendothelial junctions. Promotes homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions. Unable to bind to catenins, weakly associates with the cytoskeleton (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein. Cell junction.
TISSUE SPECIFICITY: Expressed in highly vascularized tissues including the heart and placenta, but most tissues contain a low level of expression. Prominent expression in the spleen.
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: PCDH12
Diseases sorted by gene-association score: aicardi-goutieres syndrome (4)

-  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: 18.19 RPKM in Spleen
Total median expression: 140.82 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 -122.00351-0.348 Picture PostScript Text
3' UTR -611.501800-0.340 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
IPR013164 - Cadherin_N

Pfam Domains:
PF00028 - Cadherin domain
PF08266 - Cadherin-like

SCOP Domains:
49313 - Cadherin-like
53098 - Ribonuclease H-like

ModBase Predicted Comparative 3D Structure on Q9NPG4
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

Biological Process:
GO:0005977 glycogen metabolic process
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007267 cell-cell signaling
GO:0008038 neuron recognition
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0060711 labyrinthine layer development

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005911 cell-cell junction
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC042634 - Homo sapiens protocadherin 12, mRNA (cDNA clone MGC:34069 IMAGE:5177606), complete cds.
AK024140 - Homo sapiens cDNA FLJ14078 fis, clone HEMBB1002044, moderately similar to Mus musculus mRNA for vascular cadherin-2.
AB026893 - Homo sapiens mRNA for vascular cadherin-2, complete cds.
BC052973 - Homo sapiens protocadherin 12, mRNA (cDNA clone MGC:57546 IMAGE:5174442), complete cds.
AF231025 - Homo sapiens protocadherin 12 (PCDH12) mRNA, complete cds.
AK023785 - Homo sapiens cDNA FLJ13723 fis, clone PLACE2000458, weakly similar to CADHERIN-RELATED TUMOR SUPPRESSOR PRECURSOR.
AK027282 - Homo sapiens cDNA FLJ14376 fis, clone HEMBA1001661, weakly similar to CADHERIN-RELATED TUMOR SUPPRESSOR PRECURSOR.
AK226049 - Homo sapiens mRNA for protocadherin 12 precursor variant, clone: hk07106.
AY358428 - Homo sapiens clone DNA48331 PCDH12 (UNQ395) mRNA, complete cds.
AF240635 - Homo sapiens vascular endothelial cadherin 2 mRNA, complete cds.
JD068466 - Sequence 49490 from Patent EP1572962.
JD339278 - Sequence 320302 from Patent EP1572962.
JD282518 - Sequence 263542 from Patent EP1572962.
JD263989 - Sequence 245013 from Patent EP1572962.
JD186904 - Sequence 167928 from Patent EP1572962.
JD186814 - Sequence 167838 from Patent EP1572962.
AK315029 - Homo sapiens cDNA, FLJ95971, highly similar to Homo sapiens protocadherin 12 (PCDH12), mRNA.
AB384728 - Synthetic construct DNA, clone: pF1KB3028, Homo sapiens PCDH12 gene for protocadherin-12 precursor, complete cds, without stop codon, in Flexi system.
KJ901064 - Synthetic construct Homo sapiens clone ccsbBroadEn_10458 PCDH12 gene, encodes complete protein.
JD303444 - Sequence 284468 from Patent EP1572962.
JD214626 - Sequence 195650 from Patent EP1572962.
JD483675 - Sequence 464699 from Patent EP1572962.
JD436560 - Sequence 417584 from Patent EP1572962.
JD225663 - Sequence 206687 from Patent EP1572962.
JD374017 - Sequence 355041 from Patent EP1572962.
JD459525 - Sequence 440549 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000231484.1, ENST00000231484.2, ENST00000231484.3, NM_016580, PCD12_HUMAN, PCDH12 , Q6UXB6, Q96KB8, Q9H7Y6, Q9H8E0, Q9NPG4, uc317dun.1, uc317dun.2, UNQ395/PRO731
UCSC ID: ENST00000231484.4_6
RefSeq Accession: NM_016580.4
Protein: Q9NPG4 (aka PCD12_HUMAN or PC12_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PCDH12:
ataxias (Hereditary Ataxia Overview)

-  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.