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

PCDHA6 Gene

protein-coding   GIFtS: 44
GCID: GC05P140422

protocadherin alpha 6


(Previous symbol: CNRS2)
 Explore 1 disease affiliated with
PCDHA6 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for PCDHA6    

Aliases
for PCDHA6 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Protocadherin Alpha 61 2     PCDH-Alpha-61
CNRS21 2 3     CNRN22
CNR21 2     KIAA0345-Like 82
CRNR21 2     Protocadherin Alpha-62
PCDH-ALPHA61 2     

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


Summaries
for PCDHA6 gene

(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:
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)

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:
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


Genomic Views
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 69), 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 plasmid: PCDHA6 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 GC05P140422:  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

Proteins
for PCDHA6 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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 PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9UN73

    • PCDHA6 Protein expression data from MOPED and PaxDb: --
    REFSEQ proteins (3 alternative transcripts): 
    NP_061732.1  NP_114036.1  NP_114037.1  

    ENSEMBL proteins: 
     ENSP00000433378   ENSP00000434113  

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    Uscn Proteins for PCDHA6

    Gene Ontology (GO): 2 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


    PCDHA6 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for PCDHA6 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    PCDHA6 for domains           About GeneDecksing

    4 InterPro domains/families:
     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 family: IPB002126 Cadherin

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


    Function
    for PCDHA6 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         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

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    Gene Editing
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    Clone
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    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



    Pathways & Interactions
    for PCDHA6 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 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



    Drugs & Compounds
    for PCDHA6 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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]
    JWH 133 Potent, selective CB2 agonist [259869-55-1]
    JTE 907Selective CB2 receptor antagonist/inverse agonist[282089-49-0]
    AM 630CB2 selective antagonist/inverse agonist[164178-33-0]
    GP 1aHighly selective CB2 agonist--

    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 

    Transcripts
    for PCDHA6 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for PCDHA6 gene (3 alternative transcripts): 
    NM_018909.2  NM_031848.1  NM_031849.1  

    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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    Inhib. RNA
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    24/261 AceView cDNA sequences (see all 261):

    AW572498 NM_031501 NM_031865 NM_018898 NM_031852 F05011 NM_031410 AI969295 
    BC033735 AA757839 AF152305 AF152314 BM719606 AA889198 AF152309 NM_031495 
    NM_031857 NM_031864 NM_018909 AF152310 AI452508 NM_031856 NM_031496 NM_031848 

    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

    Expression
    for PCDHA6 gene

    (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
    CGAP TAG: --

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image
    Genevestigator expression for PCDHA6
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    In Situ
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    Orthologs
    for PCDHA6 gene

    (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 animals.

    Orthologs for PCDHA6 gene from 4/14 species (see all 14)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves CNRV116
    PCDHA126
    		 Uncharacterized protein
    		 50(a)
    47(a)
    		 many ↔ many
    many ↔ many
    		 13(736149-775133)
    13(709913-728785)
    lizard
    (Anolis carolinensis)    		 Reptilia D0IQ10_ANOCA6
    D0IQ15_ANOCA6
    (see all 16)    		 Protocadherin alpha 10 unspliced isoform
    (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 pcdh2ab86
    pcdh2ab36
    (see all 35)    		 protocadherin 2 alpha b 3
    (see all 35)    		 43(a)
    43(a)
    (see all 35)    		 many ↔ many
    many ↔ many
    (see all 35)    		 14(2517358-2519727)
    14(2503338-2505713)
    worm
    (Caenorhabditis elegans)    		 Secernentea cdh-106
    		 CaDHerin family member (cdh-10)
    		 7(a)
    		 1 → many
    		 IV(2436514-2463368)


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

    Paralogs
    for PCDHA6 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHA6 gene
    PCDHAC12  PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  
    PCDHGB22  PCDHGA82  PCDHGA92  PCDHGB32  PCDHGC32  PCDHGB62  PCDHGA52  PCDHA82  
    PCDHA132  PCDHB52  PCDHB132  PCDHA32  PCDHGA42  PCDHGA72  PCDHA42  PCDHB42  
    PCDHB112  PCDHA22  ENSG000002556222  PCDHB142  PCDHB122  PCDHA122  PCDHB82  PCDHA52  
    PCDHGB12  PCDHGB42  PCDHA12  PCDHGA22  PCDHA112  PCDHA72  PCDHGA112  PCDHGA62  
    PCDHB32  PCDHB62  PCDHGC52  PCDHGC42  PCDHA102  PCDHA92  PCDHGA12  PCDHB102  
    PCDHB12  PCDHGA32  PCDHGB72  
    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



    Genomic Variants
    for PCDHA6 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 22 variations for PCDHA6
         15/21 CNVs (see all 21): 93255 32748 1701 64320 53833 59240 3578 31248 31250 81058 31249 64319 62437 51579 37968
         1 Indel: 64317
    SABiosciences Cancer Mutation PCR Assays
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    Disorders / Diseases
    for PCDHA6 gene

    (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.)
    About This Section
    PCDHA6 for disorders           About GeneDecksing

    OMIM gene information: 606312    OMIM disorders: --

    1 disease for PCDHA6:    About MalaCards
    neuronitis


    Export disorders for PCDHA6 gene to outside databases

    Publications
    for PCDHA6 gene

    (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 14):
    (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. 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)
    10. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)

    External Searches for PCDHA6 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing PCDHA6 gene

    (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

    Other Databases showing PCDHA6 gene

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

    Specialized Databases showing PCDHA6 gene

    (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

    Intellectual Property
    for PCDHA6 gene

    (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:
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