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

PCDHGA6 Gene

protein-coding   GIFtS: 38
GCID: GC05P141299

Protocadherin Gamma Subfamily A, 6

  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 Gamma Subfamily A, 61 2
PCDH-GAMMA-A62
Protocadherin Gamma-A62
PCDH-gamma-A63

External Ids:    HGNC: 87041   Entrez Gene: 561092   Ensembl: ENSG000002537317   OMIM: 6062935   UniProtKB: Q9Y5G73   

Export aliases for PCDHGA6 gene to outside databases

Previous GC identifers: GC05P140570 GC05P141308 GC05P140705 GC05P140764 GC05P140784 GC05P140723 GC05P140817 GC05P140825 GC05P140841 GC05P140866 GC05P140892 GC05P140914 GC05P140926 GC05P140948 GC05P140969 GC05P140991 GC05P141010 GC05P141039 GC05P141067 GC05P135898 GC05P141105 GC05P141146 GC05P141184 GC05P141215 GC05P141255


(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 PCDHGA6 Gene:
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on
chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism
may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3
subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more
distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed
by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes
the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region
exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a
critical role in the establishment and function of specific cell-cell connections in the brain. Alternative
splicing has been described for the gamma cluster genes. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHGA6 Gene: 
PCDHGA6 (protocadherin gamma subfamily A, 6) is a protein-coding gene. Diseases associated with PCDHGA6 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHAC1.

UniProtKB/Swiss-Prot: PCDG6_HUMAN, Q9Y5G7
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain




(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 PCDHGA6 gene promoter:
         Lmo2   LCR-F1   E47   FOXL1   MZF-1   AREB6   Hand1   STAT3   ZID   Ik-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for PCDHGA6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHGA6


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

PCDHGA6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHGA6 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P141299:  view genomic region     (about GC identifiers)

Start:
140,753,651 bp from pter      End:
140,892,546 bp from pter
Size:
138,896 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: PCDG6_HUMAN, Q9Y5G7 (See protein sequence)
Recommended Name: Protocadherin gamma-A6 precursor  
Size: 932 amino acids; 100871 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: A6H8K7 B2RN55 Q9Y5D1
Alternative splicing: 2 isoforms:  Q9Y5G7-1   Q9Y5G7-2   

Explore the universe of human proteins at neXtProt for PCDHGA6: NX_Q9Y5G7

Explore proteomics data for PCDHGA6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y5G7

  • PCDHGA6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDHGA6 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_061742.1  NP_114475.1  

    ENSEMBL proteins: 
     ENSP00000429601  

    Human Recombinant Protein Products for PCDHGA6: 
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    Browse Sino Biological Cell Lysates 
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    Browse Proteins at Cloud-Clone Corp. 

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

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

    PCDHGA6 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 Q9Y5G7

    ProtoNet protein and cluster: Q9Y5G7

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDG6_HUMAN, Q9Y5G7
    Similarity: Contains 6 cadherin domains


    PCDHGA6 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: PCDG6_HUMAN, Q9Y5G7
    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--
         
    PCDHGA6 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 PCDHGA6

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

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

    PCDHGA6 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

    Browse Tocris compounds for PCDHGA6 (PCDG6)

    1 HMDB Compound for PCDHGA6    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHGA6 / PCDG6

    (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 PCDHGA6 gene (2 alternative transcripts): 
    NM_018919.2  NM_032086.1  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000517434(uc003ljy.2)
    miRNA
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    hsa-miR-1226 hsa-miR-448 hsa-miR-4272 hsa-miR-765 hsa-miR-624* hsa-miR-650 hsa-miR-3150a-3p hsa-miR-548a-3p
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    Inhib. RNA
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    24/737 AceView cDNA sequences (see all 737):

    BM742071 NM_032092 NM_014004 BU162901 CR614433 AA338834 NM_003735 NM_032011 
    NM_032053 NM_032088 AI933744 NM_018916 BU196681 NM_018913 AW517238 AF152339 
    AF152337 AF152334 CA443219 CR612895 AB011160 BU731047 BE019025 BQ680433 

    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™, 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

    PCDHGA6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHGA6 Expression
    About this image


    See PCDHGA6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHGA6
        SABiosciences Custom PCR Arrays for PCDHGA6
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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 PCDHGA6 gene from 3/6 species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhga61 , 5 protocadherin gamma subfamily A, 61, 5 81.33(n)1
    80.26(a)1
      18 (19.57 cM)5
    937141  NM_033589.11  NP_291067.11 
     377072295 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 10)
    Uncharacterized protein
    (see all 10)
    57(a)
    56(a)
    (see all 10)
    many ↔ many
    many ↔ many
    (see all 10)
    4(76897250-76899667)
    4(76884496-76886922)
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh1g96
    BX119910.156
    (see all 24)
    Uncharacterized protein
    (see all 24)
    47(a)
    46(a)
    (see all 24)
    many ↔ many
    many ↔ many
    (see all 24)
    10(21767295-21770275)
    10(21770733-21773977)


    ENSEMBL Gene Tree for PCDHGA6 (if available)
    TreeFam Gene Tree for PCDHGA6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHGA6 gene
    PCDHAC12  PCDHB162  PCDHB22  PCDHAC22  PCDHB72  PCDHB152  PCDHGA102  PCDHGB22  
    PCDHGA122  PCDHGA92  PCDHGA82  PCDHGC32  PCDHGA52  PCDHA82  PCDHB52  PCDHB132  
    PCDHGA42  PCDHGA72  PCDHB42  PCDHB112  PCDHA22  ENSG000002556222  PCDHB142  PCDHB122  
    PCDHB82  PCDHGB12  PCDHGB42  PCDHA52  PCDHGA22  PCDHB32  PCDHGA112  PCDHB62  
    PCDHGC42  PCDHGC52  PCDHGA12  PCDHB102  PCDHB12  PCDHGB72  PCDHGA32  
    18/78 SIMAP similar genes for PCDHGA6 using alignment to 2 protein entries:     PCDG6_HUMAN (see all proteins) (see all similar genes):
    PCDHGA4    PCDHGA2    PCDHGA5    PCDHGA8    PCDHGA11    PCDHGA12
    PCDHGA7    PCDHGA1    PCDHGA10    PCDHGA9    PCDHGC3    PCDHGA3
    ME3    ME6    PCDHGB2    PCDHGB7    PCDHGB3    PCDHGB4

    PCDHGA6 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 PCDHGA6 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_0485604
    ----see VAR_0485602 R S mis40--------

    HapMap Linkage Disequilibrium report for PCDHGA6 (140753651 - 140892546 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/15 variations for PCDHGA6 (see all 15):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2730847CNV Deletion23290073
    esv267823CNV Insertion20981092
    nsv823280CNV Loss20364138
    nsv462470CNV Loss19166990
    nsv327707CNV Loss16902084
    dgv6351n71CNV Loss21882294
    nsv882990CNV Loss21882294
    dgv6352n71CNV Loss21882294
    nsv518799CNV Loss19592680
    dgv6353n71CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
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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: 606293    OMIM disorders: --

    2 diseases for PCDHGA6:    About MalaCards
    neuronitis    


    PCDHGA6 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHGA6

    Export disorders for PCDHGA6 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 PCDHGA6 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PCDHGA6)
        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. A catalogue of putative HIV-1 protease host cell subst rates. (PubMed id 22944692)1 Impens F....Gevaert K. (2012)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    4. 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)
    5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)
    6. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PubMed id 10835267)1 Nollet F....van Roy F. (2000)
    7. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)
    8. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)1 Yagi T. and Takeichi M. (2000)

    (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: 56109 HGNC: 8704 AceView: PCDHGC3 Ensembl:ENSG00000253731 euGenes: HUgn56109
    ECgene: PCDHGA6 H-InvDB: PCDHGA6

    (According to HUGE)
    About This Section
      --

    (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 PCDHGA6 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 PCDHGA6 gene:
    Search GeneIP for patents involving PCDHGA6

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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