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Aliases for PCDH20 Gene

Aliases for PCDH20 Gene

  • Protocadherin 20 2 3
  • PCDH13 3 4 6
  • Protocadherin-13 3 4
  • Protocadherin 13 3
  • Protocadherin-20 3

External Ids for PCDH20 Gene

Previous GeneCards Identifiers for PCDH20 Gene

  • GC13M059951
  • GC13M055978
  • GC13M060920
  • GC13M059781
  • GC13M060881
  • GC13M061983
  • GC13M042676

Summaries for PCDH20 Gene

Entrez Gene Summary for PCDH20 Gene

  • This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDH20 Gene

PCDH20 (Protocadherin 20) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding.

UniProtKB/Swiss-Prot for PCDH20 Gene

  • Potential calcium-dependent cell-adhesion protein

Gene Wiki entry for PCDH20 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH20 Gene

Genomics for PCDH20 Gene

Regulatory Elements for PCDH20 Gene

Genomic Location for PCDH20 Gene

Start:
61,409,685 bp from pter
End:
61,415,522 bp from pter
Size:
5,838 bases
Orientation:
Minus strand

Genomic View for PCDH20 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PCDH20 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH20 Gene

Proteins for PCDH20 Gene

  • Protein details for PCDH20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N6Y1-PCD20_HUMAN
    Recommended name:
    Protocadherin-20
    Protein Accession:
    Q8N6Y1
    Secondary Accessions:
    • A8K1K9
    • B1AQU2
    • Q8NDN4
    • Q9NRT9

    Protein attributes for PCDH20 Gene

    Size:
    951 amino acids
    Molecular mass:
    104919 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH27907.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for PCDH20 Gene

Proteomics data for PCDH20 Gene at MOPED

Post-translational modifications for PCDH20 Gene

  • Glycosylation at Asn135, Asn326, Asn332, Asn680, Asn748, Asn803, Asn844, and Asn849
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDH20 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDH20 Gene

Domains for PCDH20 Gene

Gene Families for PCDH20 Gene

HGNC:
  • PCDHN :Cadherins / Protocadherins : Non-clustered

Protein Domains for PCDH20 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PCDH20 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8N6Y1

UniProtKB/Swiss-Prot:

PCD20_HUMAN :
  • Q8N6Y1
Domain:
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDH20: view

Function for PCDH20 Gene

Molecular function for PCDH20 Gene

UniProtKB/Swiss-Prot Function: Potential calcium-dependent cell-adhesion protein

Gene Ontology (GO) - Molecular Function for PCDH20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0044822 poly(A) RNA binding IDA 22681889
genes like me logo Genes that share ontologies with PCDH20: view

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for PCDH20 Gene

Localization for PCDH20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH20 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDH20 Gene COMPARTMENTS Subcellular localization image for PCDH20 gene
Compartment Confidence
plasma membrane 5
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PCDH20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDH20: view

Pathways for PCDH20 Gene

SuperPathways for PCDH20 Gene

No Data Available

Interacting Proteins for PCDH20 Gene

Selected Interacting proteins: Q8N6Y1-PCD20_HUMAN for PCDH20 Gene via I2D

Symbol External ID(s) Details
RYK

Gene Ontology (GO) - Biological Process for PCDH20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
genes like me logo Genes that share ontologies with PCDH20: view

No data available for Pathways by source for PCDH20 Gene

Compounds for PCDH20 Gene

(1) HMDB Compounds for PCDH20 Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2
genes like me logo Genes that share compounds with PCDH20: view

Transcripts for PCDH20 Gene

mRNA/cDNA for PCDH20 Gene

(36) Selected AceView cDNA sequences:
(7) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCDH20 Gene

Protocadherin 20:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH20 Gene

No ASD Table

Relevant External Links for PCDH20 Gene

GeneLoc Exon Structure for
PCDH20
ECgene alternative splicing isoforms for
PCDH20

Expression for PCDH20 Gene

mRNA expression in normal human tissues for PCDH20 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCDH20 Gene

This gene is overexpressed in Brain - Hippocampus (5.1) and Brain - Anterior cingulate cortex (BA24) (4.1).

Integrated Proteomics: protein expression from ProteomicsDB and MOPED for PCDH20 Gene

SOURCE GeneReport for Unigene cluster for PCDH20 Gene Hs.391781

genes like me logo Genes that share expressions with PCDH20: view

No data available for mRNA Expression by UniProt/SwissProt for PCDH20 Gene

Orthologs for PCDH20 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH20 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDH20 35
  • 97.52 (n)
  • 97.15 (a)
cow
(Bos Taurus)
Mammalia PCDH20 35
  • 88.42 (n)
  • 90.53 (a)
dog
(Canis familiaris)
Mammalia LOC100686939 35
  • 89.84 (n)
  • 93.21 (a)
mouse
(Mus musculus)
Mammalia Pcdh20 35
  • 87.21 (n)
  • 92.43 (a)
Pcdh20 16
rat
(Rattus norvegicus)
Mammalia Pcdh20 35
  • 86.89 (n)
  • 92.11 (a)
chicken
(Gallus gallus)
Aves PCDH20 35
  • 76.32 (n)
  • 82.54 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh20 35
  • 70.52 (n)
  • 74.02 (a)
zebrafish
(Danio rerio)
Actinopterygii pcdh20 35
  • 60.72 (n)
  • 59.5 (a)
Species with no ortholog for PCDH20:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDH20 Gene

ENSEMBL:
Gene Tree for PCDH20 (if available)
TreeFam:
Gene Tree for PCDH20 (if available)

Paralogs for PCDH20 Gene

Selected SIMAP similar genes for PCDH20 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PCDH20: view

No data available for Paralogs for PCDH20 Gene

Variants for PCDH20 Gene

Sequence variations from dbSNP and Humsavar for PCDH20 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type MAF
rs3812871 -- 61,411,281(+) TCGCA(C/T)ATGCA reference, missense
rs3812872 -- 61,412,785(+) TAAAC(A/C)ACACC reference, synonymous-codon
rs3812873 -- 61,414,020(+) GGGTC(C/G)GAGAG intron-variant
rs3812874 -- 61,415,042(+) CTGTA(G/T)CTGGT missense, reference
rs3812875 -- 61,415,309(+) GCAAG(A/G)GGGCA utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for PCDH20 Gene

Variant ID Type Subtype PubMed ID
nsv900245 CNV Loss 21882294
nsv510587 CNV Loss 20534489
nsv832628 CNV Loss 17160897

Relevant External Links for PCDH20 Gene

HapMap Linkage Disequilibrium report
PCDH20

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH20 Gene

Disorders for PCDH20 Gene

Relevant External Links for PCDH20

Genetic Association Database (GAD)
PCDH20
genes like me logo Genes that share disorders with PCDH20: view

No data available for UniProtKB/Swiss-Prot for PCDH20 Gene

Publications for PCDH20 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  3. Joint influence of small-effect genetic variants on human longevity. (PMID: 20834067) Yashin A.I. … Ukraintseva S.V. (Aging (Albany NY) 2010) 3
  4. Mindbomb 1, an E3 ubiquitin ligase, forms a complex with RYK to activate Wnt/I^-catenin signaling. (PMID: 21875946) Berndt J.D. … Moon R.T. (J. Cell Biol. 2011) 3
  5. Identification of IL6R and chromosome 11q13.5 as risk loci for asthma. (PMID: 21907864) Ferreira M.A. … Thompson P.J. (Lancet 2011) 3

Products for PCDH20 Gene

Sources for PCDH20 Gene

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