Human Gene PCDH8 (ENST00000377942.7_7) from GENCODE V47lift37
  Description: protocadherin 8, transcript variant 1 (from RefSeq NM_002590.4)
Gencode Transcript: ENST00000377942.7_7
Gencode Gene: ENSG00000136099.13_9
Transcript (Including UTRs)
   Position: hg19 chr13:53,417,024-53,422,775 Size: 5,752 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 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 (chr13:53,417,024-53,422,775)mRNA (may differ from genome)Protein (1070 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCDH8_HUMAN
DESCRIPTION: RecName: Full=Protocadherin-8; AltName: Full=Arcadlin; Flags: Precursor;
FUNCTION: Calcium-dependent cell-adhesion protein (By similarity). May play a role in activity-induced synaptic reorganization underlying long term memory (By similarity). Could be involved in CDH2 internalization through TAOK2/p38 MAPK pathway. In hippocampal neurons, may play a role in the down-regulation of dendritic spines, maybe through its action on CDH2 endocytosis (By similarity).
SUBUNIT: The N-terminal extracellular domain forms homophilic interactions; these interactions activate p38 MAPK via TAOK2 and trigger endocytosis (By similarity). Interacts with CDH2; this interaction may lead to CDH2 cointernalization (By similarity). Interacts with CDH11 (By similarity). Interacts with TAOK2 (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (By similarity). Cell projection, dendrite (By similarity). Cell junction, synapse, presynaptic cell membrane. Cell junction, synapse, postsynaptic cell membrane. Note=Also expressed in neuronal cell bodies (By similarity). Localized to excitatory, but not with inhibitory, synapses (By similarity).
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


-  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: 10.58 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
  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 -77.20204-0.378 Picture PostScript Text
3' UTR -371.601671-0.222 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

ModBase Predicted Comparative 3D Structure on O95206
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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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding

Biological Process:
GO:0001756 somitogenesis
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007267 cell-cell signaling
GO:0007268 chemical synaptic transmission
GO:0007399 nervous system development
GO:0016331 morphogenesis of embryonic epithelium

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030425 dendrite
GO:0042734 presynaptic membrane
GO:0042995 cell projection
GO:0045202 synapse
GO:0045211 postsynaptic membrane


-  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: B4DMV7, ENST00000377942.1, ENST00000377942.2, ENST00000377942.3, ENST00000377942.4, ENST00000377942.5, ENST00000377942.6, NM_002590, O95206, PCDH8_HUMAN, Q5TAN1, Q5TAN2, Q8IYE9, Q96SF1, uc318nys.1, uc318nys.2
UCSC ID: ENST00000377942.7_7
RefSeq Accession: NM_002590.4
Protein: O95206 (aka PCDH8_HUMAN or PCH8_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.