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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

PCDHA6 Gene

protein-coding   GIFtS: 45
GCID: GC05P140439

Protocadherin Alpha 6


(Previous symbol: CNRS2)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Protocadherin Alpha 61 2     CNRN22
CNRS21 2 3     CRNR22
KIAA0345-Like 81 2     PCDH-ALPHA62
PCDH-alpha-62 3     Protocadherin Alpha-62
CNR22     

External Ids:    HGNC: 86721   Entrez Gene: 561422   Ensembl: ENSG000000818427   OMIM: 6063125   UniProtKB: Q9UN733   

Export aliases for PCDHA6 gene to outside databases

Previous GC identifers: GC05P140024 GC05P140753 GC05P140155 GC05P140210 GC05P140217 GC05P140172 GC05P140187 GC05P140321 GC05P140342 GC05P135352 GC05P140362 GC05P140378 GC05P140392 GC05P140406 GC05P140422


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for PCDHA6 Gene:
This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked
on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor
gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes
and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15
N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are
shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin
ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion
proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and
function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional
variants have been suggested but their full-length nature has yet to be determined. (provided by RefSeq, Jul
2008)

GeneCards Summary for PCDHA6 Gene: 
PCDHA6 (protocadherin alpha 6) is a protein-coding gene. Diseases associated with PCDHA6 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot: PCDA6_HUMAN, Q9UN73
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain

summary for PCDHA6 Gene:
The CB2 receptor, also known as the peripheral cannabinoid receptor, is a member of the cannabinoid receptor
group of G-protein-coupled receptors that also includes CB1 and GPR55. They are located primarily in immune
cells both within & outside the central nervous system. The function of these receptors includes modulation
of cytokine release and immune cell migration. In the brain CB2 receptors are expressed by microglia, blood
vessels & some neurons.

Gene Wiki entry for PCDHA6 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PCDHA6 gene promoter:
         Elk-1   Brachyury   SREBP-1c   SREBP-1b   AREB6   SREBP-1a   E2F-1   E2F   Ik-2   HSF2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHA6 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDHA6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHA6


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

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31

PCDHA6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHA6 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140439:  view genomic region     (about GC identifiers)

Start:
140,207,563 bp from pter      End:
140,391,929 bp from pter
Size:
184,367 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: PCDA6_HUMAN, Q9UN73 (See protein sequence)
Recommended Name: Protocadherin alpha-6 precursor  
Size: 950 amino acids; 102716 Da
Subcellular location: Isoform 1: Cell membrane; Single-pass type I membrane protein (By similarity)
Subcellular location: Isoform 2: Secreted (Potential)
Sequence caution: Sequence=AAF89691.1; Type=Erroneous initiation;
Secondary accessions: O75283 Q9NRT8
Alternative splicing: 3 isoforms:  Q9UN73-1   Q9UN73-2   Q9UN73-3   

Explore the universe of human proteins at neXtProt for PCDHA6: NX_Q9UN73

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9UN73

  • PCDHA6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --
    REFSEQ proteins (3 alternative transcripts): 
    NP_061732.1  NP_114036.1  NP_114037.1  

    ENSEMBL proteins: 
     ENSP00000433378   ENSP00000434113  

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    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005887integral to plasma membrane TAS10380929
    GO:0016020membrane ----

    PCDHA6 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    PCDHC: Cadherins / Protocadherins : Clustered

    4 InterPro protein domains:
     IPR015919 Cadherin-like
     IPR013164 Cadherin_N
     IPR020894 Cadherin_CS
     IPR002126 Cadherin

    Graphical View of Domain Structure for InterPro Entry Q9UN73

    ProtoNet protein and cluster: Q9UN73

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDA6_HUMAN, Q9UN73
    Similarity: Contains 6 cadherin domains


    PCDHA6 for domains           About GeneDecksing


    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCDA6_HUMAN, Q9UN73
    Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
    of specific neuronal connections in the brain

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    PCDHA6 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PCDHA6

    2 Interacting proteins for PCDHA6 (Q9UN733) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CRKP461083I2D: score=2 
    RELNP785093I2D: score=1 
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion TAS10380929
    GO:0007156homophilic cell adhesion IEA--
    GO:0007399nervous system development TAS10380929

    PCDHA6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Compounds for PCDHA6 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    HU 308Potent and selective CB2 agonist[256934-39-1]
    AM 630CB2 selective antagonist/inverse agonist[164178-33-0]
    GP 1aHighly selective CB2 agonist[511532-96-0]
    JWH 133 (in Tocrisolve 100) Potent, selective CB2 agonist (in water-soluble emulsion) [259869-55-1]
    JWH 133 Potent, selective CB2 agonist [259869-55-1]

    1 HMDB Compound for PCDHA6    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHA6 / PCDA6

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PCDHA6 gene (3 alternative transcripts): 
    NM_018909.3  NM_031848.2  NM_031849.2  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000529310(uc003lho.2 uc003lhn.2) ENST00000527624
    miRNA
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    hsa-miR-194* hsa-miR-3130-5p hsa-miR-4272 hsa-miR-106a hsa-miR-15a hsa-miR-485-3p hsa-miR-4305 hsa-miR-3653
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    24/261 AceView cDNA sequences (see all 261):

    AI969295 NM_031865 AF152317 NM_018904 AF152310 NM_031856 NM_031410 NM_014005 
    AF152312 NM_031857 AF152486 F05011 AF169695 BC033735 NM_031495 NM_031848 
    NM_018901 NM_031496 AF152309 BM719606 BM682903 NM_018909 AF152305 AF152314 

    GeneLoc Exon Structure

    5/18 Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA6 (see all 18)    About this scheme

    ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b
    SP1:                          -     -     -     -     -     -     -     -     -     -     -     -     -     -     -                       -               
    SP2:              -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -     -                       -               
    SP3:                                                                                      -     -     -     -     -                       -               
    SP4:                                                                                                        -     -                       -               
    SP5:                                                                                                              -                                       


    ECgene alternative splicing isoforms for PCDHA6

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    PCDHA6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHA6 Expression
    About this image


    Genevestigator expression for PCDHA6
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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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHA6 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdha61 , 5 protocadherin alpha 61, 5 83.65(n)1
    85.52(a)1
      18 (19.46 cM)5
    129371  NM_007767.31  NP_031793.21 
     369677565 
    chicken
    (Gallus gallus)
    Aves PCDHA116
    --
    --
    53(a)
    48(a)
    many ↔ many
    many ↔ many
    13(185486-285392)
    13(292413-317534)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 16)
    Protocadherin alpha 5 unspliced isoform; Uncharact...
    Protocadherin alpha 10 unspliced isoform; Uncharac...
    (see all 16)
    58(a)
    56(a)
    (see all 16)
    many ↔ many
    many ↔ many
    (see all 16)
    4(77380556-77382976)
    4(77317799-77320222)
    zebrafish
    (Danio rerio)
    Actinopterygii CR847851.26
    pcdh2ab36
    (see all 35)
    protocadherin 2 alpha b 3
    (see all 35)
    44(a)
    43(a)
    (see all 35)
    many ↔ many
    many ↔ many
    (see all 35)
    14(2425668-2426945)
    14(2503338-2505713)


    ENSEMBL Gene Tree for PCDHA6 (if available)
    TreeFam Gene Tree for PCDHA6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHA6 gene
    PCDH72  PCDH202  PCDH12  PCDHA122  PCDH11Y2  PCDH122  PCDHA112  PCDHA12  
    PCDH182  PCDH92  PCDH192  PCDH82  PCDH172  PCDHGB32  PCDHA72  PCDHGB62  
    PCDH11X2  PCDH102  PCDHA102  PCDHA132  PCDHA92  PCDHA32  PCDHA42  
    18/61 SIMAP similar genes for PCDHA6 using alignment to 1 protein entry:     PCDA6_HUMAN(see all similar genes):
    PCDHA8    PCDHA13    PCDHA3    PCDHA1    PCDHA11    PCDHA2
    PCDHA4    PCDHA10    PCDHA12    PCDHA5    PCDHA7    PCDHA9
    PCDHB17    PCDHAC2    PCDHB13    PCDHB8    PCDHAC1    PCDHGA3

    PCDHA6 for paralogs           About GeneDecksing



    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    1 SNPs in PCDHA6 are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0610614
    ----see VAR_0610612 L V mis40--------

    HapMap Linkage Disequilibrium report for PCDHA6 (140207563 - 140391929 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/46 variations for PCDHA6 (see all 46):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2657537CNV Deletion23128226
    nsv820841CNV Deletion20802225
    dgv1044e199CNV Deletion23128226
    esv2505753CNV Deletion19546169
    esv2730838CNV Deletion23290073
    esv2730839CNV Deletion23290073
    esv2421858CNV Deletion20811451
    dgv1043e199CNV Deletion23128226
    nsv436885CNV Insertion17901297
    nsv882952CNV Loss21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 606312    OMIM disorders: --

    2 diseases for PCDHA6:    About MalaCards
    neuronitis    


    PCDHA6 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHA6

    Export disorders for PCDHA6 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)
    About This Section

    PubMed articles for PCDHA6 gene, integrated from 9 sources (see all 15):
    (articles sorted by number of sources associating them with PCDHA6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PubMed id 10380929)1, 2, 3 Wu Q. and Maniatis T. (1999)
    2. 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. (2004)
    3. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)1, 2 Schmutz J.... Rubin E.M. (2004)
    4. Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)1, 3 Sugino H....Yagi T. (2000)
    5. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PubMed id 22589738)1 Fox C.S....Borecki I.B. (2012)
    6. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    7. Dynamics of cullin-RING ubiquitin ligase network revea led by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (2010)
    8. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. (PubMed id 17474147)1 Wu C....Li S.S. (2007)
    9. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 56142 HGNC: 8672 AceView: PCDHA9 Ensembl:ENSG00000081842 euGenes: HUgn56142
    ECgene: PCDHA6 H-InvDB: PCDHA6

    (According to HUGE)
    About This Section
    HUGE: KIAA0345-like 8

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for PCDHA6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for PCDHA6 gene:
    Search GeneIP for patents involving PCDHA6

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



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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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