Human Gene PCDH8 (uc001vhj.3) Description and Page Index
  Description: Homo sapiens protocadherin 8 (PCDH8), transcript variant 2, mRNA.
RefSeq Summary (NM_032949): This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The gene encodes an integral membrane protein that is thought to function in cell adhesion in a CNS-specific manner. Unlike classical cadherins, which are generally encoded by 15-17 exons, this gene includes only 3 exons. Notable is the large first exon encoding the extracellular region, including 6 cadherin domains and a transmembrane region. Alternative splicing yields isoforms with unique cytoplasmic tails. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr13:53,418,109-53,422,775 Size: 4,667 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr13:53,418,695-53,422,571 Size: 3,877 Coding Exon Count: 3 

Page IndexSequence and LinksGenetic AssociationsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:53,418,109-53,422,775)mRNA (may differ from genome)Protein (973 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PCDH8
CDC HuGE Published Literature: PCDH8
Positive Disease Associations: Coronary Artery Disease
Related Studies:
  1. Coronary Artery Disease
    , , . [PubMed 0]

-  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: 10.58 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 65.00 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 -76.40204-0.375 Picture PostScript Text
3' UTR -128.50586-0.219 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
  Pfam Domains:
PF00028 - Cadherin domain
PF08266 - Cadherin-like

SCOP Domains:
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on O95206-2
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  LF210179 - JP 2014500723-A/17682: Polycomb-Associated Non-Coding RNAs.
AF061573 - Homo sapiens protocadherin (PCDH8) mRNA, complete cds.
BC036025 - Homo sapiens protocadherin 8, mRNA (cDNA clone MGC:33061 IMAGE:5278690), complete cds.
AK297652 - Homo sapiens cDNA FLJ56819 complete cds, highly similar to Protocadherin-8 precursor.
JD038623 - Sequence 19647 from Patent EP1572962.
JD359705 - Sequence 340729 from Patent EP1572962.
AK293747 - Homo sapiens cDNA FLJ60443 complete cds, moderately similar to Protocadherin-8 precursor.
JD200088 - Sequence 181112 from Patent EP1572962.
AY013873 - Homo sapiens protocadherin ARCADLIN (PCDH8) mRNA, complete cds, alternatively spliced.
DQ893339 - Synthetic construct clone IMAGE:100005969; FLH196374.01X; RZPDo839C07156D protocadherin 8 (PCDH8) gene, encodes complete protein.
LF335441 - JP 2014500723-A/142944: Polycomb-Associated Non-Coding RNAs.
LF335443 - JP 2014500723-A/142946: Polycomb-Associated Non-Coding RNAs.
LF212589 - JP 2014500723-A/20092: Polycomb-Associated Non-Coding RNAs.
LF213355 - JP 2014500723-A/20858: Polycomb-Associated Non-Coding RNAs.
JD448234 - Sequence 429258 from Patent EP1572962.
JD358020 - Sequence 339044 from Patent EP1572962.
JD256364 - Sequence 237388 from Patent EP1572962.
MA445756 - JP 2018138019-A/17682: Polycomb-Associated Non-Coding RNAs.
MA571018 - JP 2018138019-A/142944: Polycomb-Associated Non-Coding RNAs.
MA571020 - JP 2018138019-A/142946: Polycomb-Associated Non-Coding RNAs.
MA448166 - JP 2018138019-A/20092: Polycomb-Associated Non-Coding RNAs.
MA448932 - JP 2018138019-A/20858: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_032949, NP_116567, O95206-2
UCSC ID: uc001vhj.3
RefSeq Accession: NM_032949
Protein: O95206-2, splice isoform of O95206 CCDS: CCDS9439.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_032949.2
exon count: 3CDS single in 3' UTR: no RNA size: 3786
ORF size: 2922CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6044.00frame shift in genome: no % Coverage: 98.05
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.