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PCDH20 Gene

protein-coding   GIFtS: 50
GCID: GC13M061983

Protocadherin 20

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Protocadherin 201 2
PCDH132 3 5
Protocadherin 132
protocadherin-132
protocadherin-202
Protocadherin-133

External Ids:    HGNC: 142571   Entrez Gene: 648812   Ensembl: ENSG000001979917   OMIM: 6144495   UniProtKB: Q8N6Y13   

Export aliases for PCDH20 gene to outside databases

Previous GC identifers: GC13M059951 GC13M055978 GC13M060920 GC13M059781 GC13M060881 GC13M042676


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. An important paralog of this gene is PCDHAC1.

UniProtKB/Swiss-Prot: PCD20_HUMAN, Q8N6Y1
Function: Potential calcium-dependent cell-adhesion protein

Gene Wiki entry for PCDH20 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000013.10  NC_018924.2  NT_024524.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the PCDH20 gene promoter:
         AML1a   GATA-3   CUTL1   GATA-2   GATA-1   MEF-2A   FOXO4   HSF2   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDH20 promoter sequence
   Search Chromatin IP Primers for PCDH20

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDH20


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q21   Ensembl cytogenetic band:  13q21.2   HGNC cytogenetic band: 13q21

PCDH20 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDH20 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13M061983:  view genomic region     (about GC identifiers)

Start:
61,983,818 bp from pter      End:
62,002,220 bp from pter
Size:
18,403 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PCD20_HUMAN, Q8N6Y1 (See protein sequence)
Recommended Name: Protocadherin-20 precursor  
Size: 951 amino acids; 104919 Da
Sequence caution: Sequence=AAH27907.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: A8K1K9 B1AQU2 Q8NDN4 Q9NRT9

Explore the universe of human proteins at neXtProt for PCDH20: NX_Q8N6Y1

Explore proteomics data for PCDH20 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn135, Asn326, Asn332, Asn680, Asn748, Asn803, Asn844, Asn849
  • Modification sites at PhosphoSitePlus

  • See PCDH20 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_073754.2  
    ENSEMBL proteins: 
     ENSP00000387250   ENSP00000386653  

    PCDH20 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    PCDHN: Cadherins / Protocadherins : Non-clustered

    3 InterPro protein domains:
     IPR015919 Cadherin-like
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q8N6Y1

    ProtoNet protein and cluster: Q8N6Y1

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCD20_HUMAN, Q8N6Y1
    Similarity: Contains 6 cadherin domains


    Find genes that share domains with PCDH20           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCD20_HUMAN, Q8N6Y1
    Function: Potential calcium-dependent cell-adhesion protein

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
    GO:0044822poly(A) RNA binding IDA--
         
    Find genes that share ontologies with PCDH20           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PCDH20
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    Block miRNA regulation of human, mouse, rat PCDH20 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PCDH20 (see all 17):
    hsa-miR-30c hsa-miR-3607-3p hsa-miR-30d hsa-miR-340 hsa-miR-4267 hsa-miR-649 hsa-miR-30a hsa-miR-4325
    SwitchGear 3'UTR luciferase reporter plasmidPCDH20 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PCD20_HUMAN, Q8N6Y1: Cell membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    mitochondrion1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with PCDH20           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PCDH20
    Interactions:

        Search GeneGlobe Interaction Network for PCDH20

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for PCDH20 (Q8N6Y13 ENSP000003866534) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RYKP349253, ENSP000002960844I2D: score=1 STRING: ENSP00000296084
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--

    Find genes that share ontologies with PCDH20           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PCDH20 (PCD20)

    1 HMDB Compound for PCDH20    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PCDH20 gene: 
    NM_022843.3  

    Unigene Cluster for PCDH20:

    Protocadherin 20
    Hs.391781  [show with all ESTs]
    Unigene Representative Sequence: AL833830
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000409204(uc001vid.4) ENST00000409186(uc010thj.2) ENST00000472649

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate PCDH20 (see all 17):
    hsa-miR-30c hsa-miR-3607-3p hsa-miR-30d hsa-miR-340 hsa-miR-4267 hsa-miR-649 hsa-miR-30a hsa-miR-4325
    SwitchGear 3'UTR luciferase reporter plasmidPCDH20 3' UTR sequence
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      QuantiTect SYBR Green Assays in human, mouse, rat PCDH20
      QuantiFast Probe-based Assays in human, mouse, rat PCDH20

    Additional mRNA sequence: 

    AF169693.1 AK025871.1 AK094680.1 AK289924.1 AK314607.1 AL833830.1 BC027907.1 

    3 DOTS entries:

    DT.97768248  DT.99933397  DT.120763635 

    Selected AceView cDNA sequences (see all 36):

    T04933 BU070294 AK094680 C16499 BI546525 BC027907 AF169693 AL833830 
    BI766301 AA040057 AA453141 BU608937 AA625076 BX106673 NM_022843 N34280 
    AA040043 BP379279 CK902366 AI375140 BC038756 Z43057 AK025871 BI462451 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PCDH20 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDH20 Expression
    About this image


    PCDH20 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Zeugopod Epiphyseal End
             HyStem+BMP4-induced MEL2 cells
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Oligodendrocyte Precursor Cells Forebrain White Matter
             Cerebellum
     
     Dermis (Integumentary System)    fully expand to see all 2 entries
             Zigzag Dermal Papilla Cells Dermal Papilla
     
     NULL (Uncategorized)
             Vascular endothelial growth factor-induced cells
     
     Neurons
             GABAergic Amacrine Cells Inner Nuclear Layer
    PCDH20 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDH20 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.391781
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PCDH20 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdh201 , 5 protocadherin 201, 5 87.21(n)1
    92.43(a)1
      14 (44.43 cM)5
    2192571  NM_178685.51  NP_848800.31 
     884647475 
    chicken
    (Gallus gallus)
    Aves PCDH201 protocadherin 20 76.32(n)
    82.54(a)
      428063  XM_004938656.1  XP_004938713.1 
    lizard
    (Anolis carolinensis)
    Reptilia PCDH206
    protocadherin 20
    76(a)
    1 ↔ 1
    3(76240477-76250370)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia pcdh201 protocadherin 20 70.52(n)
    74.02(a)
      100101710  NM_001100230.1  NP_001093700.1 
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh201 protocadherin 20 60.72(n)
    59.5(a)
      100007362  XM_001345807.3  XP_001345843.3 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDH20 gene
    PCDHAC12  PCDHA22  PCDH72  PCDH12  PCDHA122  PCDH11Y2  PCDHA52  PCDH122  
    PCDHA112  PCDHA12  PCDH182  PCDH92  PCDH192  PCDH82  PCDH172  PCDHGC32  
    PCDHA72  PCDH11X2  PCDHA62  PCDHA82  PCDH102  PCDHA102  PCDHA132  PCDHA92  
    PCDHA32  PCDHA42  
    5 SIMAP similar genes for PCDH20 using alignment to 1 protein entry:     PCD20_HUMAN:
    PCDH9    PCDH11X    PCDH11Y    PCDH1    PCDH7

    Find genes that share paralogs with PCDH20           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PCDH20 (see all 225)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0361114
    A breast cancer sample4--see VAR_0361112 V M mis40--------
    rs1831546401,2
    --61983477(+) CATTGC/TTGCCT 1 -- int10--------
    rs79905361,2
    C,F,A,H--61983572(+) CTTGGT/CTGTTT 1 -- int18Minor allele frequency- C:0.35NA WA EA 504
    rs1878038161,2
    --61983649(+) TAACAA/GAGGAT 1 -- int10--------
    rs1388719131,2
    --61984000(+) GAAAAC/TATATA 1 -- ut310--------
    rs1179045451,2
    C,F--61984060(+) ATGCCA/GAAAAG 1 -- ut311Minor allele frequency- G:0.02NA 120
    rs1924268091,2
    C--61984098(+) TTCCTG/TGTTTA 1 -- ut310--------
    rs1427384431,2
    --61984130(+) TCTCAC/TATAAA 1 -- ut310--------
    rs412934381,2
    C,F--61984275(+) TTTAAT/CCCAAA 1 -- ut311Minor allele frequency- C:0.02NA 120
    rs1849555901,2
    --61984320(+) AACCTA/GAACAA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for PCDH20 (61983818 - 62002220 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for PCDH20:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv900245CNV Loss21882294
    nsv832628CNV Loss17160897
    nsv510587CNV Loss20534489

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 614449    OMIM disorders: --


    Find genes that share disorders with PCDH20           About GenesLikeMe

    Genetic Association Database (GAD): PCDH20

    Export disorders for PCDH20 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PCDH20 gene, integrated from 10 sources (see all 21):
    (articles sorted by number of sources associating them with PCDH20)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. (PubMed id 22359512)1 Demirkan A....Schmitz G. (PLoS Genet. 2012)
    4. Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms. (PubMed id 23212062)1 Fanous A.H....Levinson D.F. (Am J Psychiatry 2012)
    5. Identification of IL6R and chromosome 11q13.5 as risk loci for asthma. (PubMed id 21907864)1 Ferreira M.A....Thompson P.J. (Lancet 2011)
    6. Mindbomb 1, an E3 ubiquitin ligase, forms a complex with RYK to activate Wnt/I^-catenin signaling. (PubMed id 21875946)1 Berndt J.D....Moon R.T. (J. Cell Biol. 2011)
    7. Joint influence of small-effect genetic variants on human longevity. (PubMed id 20834067)1 Yashin A.I....Ukraintseva S.V. (Aging (Albany NY) 2010)
    8. Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study. (PubMed id 17903306)4 Newton-Cheh C....Larson M.G. (BMC Med. Genet. 2007)
    9. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (BMC Med. Genet. 2007)
    10. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 64881 HGNC: 14257 AceView: PCDH20 Ensembl:ENSG00000197991 euGenes: HUgn64881
    ECgene: PCDH20 H-InvDB: PCDH20

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PCDH20 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PCDH20 gene:
    Search GeneIP for patents involving PCDH20

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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