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

PCDHA@ Cluster

gene cluster   GIFtS: 36
GCID: GC05P140147

Protocadherin Alpha Cluster, Complex Locus

(Previous name: protocadherin alpha cluster)
(Previous symbol: CNRS1)
  See related diseases
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 Cluster, Complex Locus1 2
CNRS11 2
Protocadherin Alpha Cluster1 2
CNR12
PCDH-alpha-13

External Ids:    HGNC: 86621   Entrez Gene: 561172   Ensembl: ENSG000002049707   OMIM: 6049665   UniProtKB: Q9Y5I33   

Export aliases for PCDHA@ gene to outside databases

Previous GC identifer: GC05U990123


(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 PCDHA@ Gene:
The protocadherin alpha gene cluster is one of three related clusters tandemly linked on chromosome five. The
clusters have a genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene
cluster is composed of 15 genes and 1 pseudogene, which are members of the cadherin superfamily and related to
the mouse CNR genes. The sequence of the 13 upstream genes and the pseudogene are highly similar to one another,
while a subfamily (C) contains two more distantly related coding sequences. The alpha cluster genes are organized
in a tandem array of 15 large, variable region exons followed by a constant region, which contains 3 exons shared
by all genes in the cluster. Each variable region exon encodes an extracellular domain comprised of 6 cadherin
ectodomains and a transmembrane region. The constant region exons encode a common cytoplasmic tail. These neural
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 alpha cluster genes. (provided by
RefSeq, Jul 2008)

GeneCards Summary for PCDHA@ Gene: 
PCDHA@ (protocadherin alpha cluster, complex locus) is a gene cluster. Diseases associated with PCDHA@ include wilms tumor, and neuronitis. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot: PCDA1_HUMAN, Q9Y5I3
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain

summary for PCDHA@ Gene:
The CB1 receptor, also known as the central cannabinoid receptor, is a member of the cannabinoid receptor
group of G-protein-coupled receptors that also includes CB2 and GPR55. They are found mainly in the
terminals of central and peripheral neurons where they usually mediate inhibition of neurotransmitter
release. They can also be present on some non-neuronal cells, including immune cells.




(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
RefSeq DNA sequence:
NC_000005.9  NC_018916.2  NT_029289.11  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for PCDHA@
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHA@ promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDHA@

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


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

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

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140147:  view genomic region     (about GC identifiers)

Start:
140,165,876 bp from pter      End:
140,391,929 bp from pter
Size:
226,054 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: PCDA1_HUMAN, Q9Y5I3 (See protein sequence)
Recommended Name: Protocadherin alpha-1 precursor  
Size: 950 amino acids; 102952 Da
Subcellular location: Isoform 1: Cell membrane; Single-pass type I membrane protein (By similarity)
Subcellular location: Isoform 2: Secreted (Potential)
Secondary accessions: O75288 Q9NRT7
Alternative splicing: 3 isoforms:  Q9Y5I3-1   Q9Y5I3-2   Q9Y5I3-3   

Explore the universe of human proteins at neXtProt for PCDHA@: NX_Q9Y5I3

Explore proteomics data for PCDHA@ at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y5I3

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

    PCDHA@ Protein Expression

    ENSEMBL proteins: 
     ENSP00000420840   ENSP00000378129   ENSP00000367373  

    Human Recombinant Protein Products for PCDHA@: 
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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 ----
    GO:0005887integral to plasma membrane ----
    GO:0016020membrane ----

    PCDHA@ 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 Q9Y5I3

    ProtoNet protein and cluster: Q9Y5I3

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDA1_HUMAN, Q9Y5I3
    Similarity: Contains 6 cadherin domains


    PCDHA@ 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: PCDA1_HUMAN, Q9Y5I3
    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 ----
         
    PCDHA@ for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for PCDHA@ 
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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 PCDHA@

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

    1 Interacting protein for PCDHA@ (Q9Y5I33 ENSP000003673734) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CRKP461083, ENSP000003005744I2D: score=2 STRING: ENSP00000300574
    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 ----
    GO:0007156homophilic cell adhesion ----
    GO:0007399nervous system development ----

    PCDHA@ 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 PCDHA@ available from Tocris Bioscience    About this table
    CompoundAction CAS #
    ACEA Potent, highly selective CB1 agonist [220556-69-4]
    AM 251Potent CB1 antagonist. Also GPR55 agonist[183232-66-8]
    SR 141716ASelective CB1 receptor antagonist[158681-13-1]
    Tocrifluor T1117Novel fluorescent cannabinoid ligand. Fluorescent form of AM 251 (Cat. No. 1117)[1186195-59-4]
    AM 281 Potent, selective CB1 antagonist/inverse agonist [202463-68-1]

    Search CenterWatch for drugs/clinical trials and news about PCDHA@

    (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,
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    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

    Unigene Clusters for PCDHA@:

    Protocadherin alpha cluster, complex locus
    Hs.199343  [show with all ESTs], Hs.570901  [show with all ESTs], Hs.599714  [show with all ESTs]
    Unigene Representative Sequences: NM_014005, BC043441, BC042887
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000504120(uc003lhb.2) ENST00000394633(uc003lha.2) ENST00000378133(uc003lgz.3)

    miRNA
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    Inhib. RNA
    Products:
         
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      Search QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PCDHA@

    Additional mRNA sequence: BC042887.1 

    24/43 DOTS entries (see all 43):

    DT.100796094  DT.91759865  DT.70103864  DT.409021  DT.91759859  DT.120835552  DT.91726025  DT.100796093 
    DT.65286649  DT.91759861  DT.216532  DT.95296330  DT.95296331  DT.95349167  DT.87046613  DT.91759860 
    DT.91759862  DT.91906247  DT.95296340  DT.120835478  DT.91759863  DT.207484  DT.100796091  DT.75106614 

    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

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


    See PCDHA@ Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHA@

    SOURCE GeneReport for Unigene clusters: Hs.199343 Hs.570901 Hs.599714
        SABiosciences Custom PCR Arrays for PCDHA@
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHA@

    (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 PCDHA@ gene from 4/7 species (see all 7)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    oppossum
    (Monodelphis domestica)
    Mammalia --
    --
    63(a)
    1 → many
    1(332637457-332900773)
    chicken
    (Gallus gallus)
    Aves PCDHA116
    --
    --
    53(a)
    47(a)
    many ↔ many
    many ↔ many
    13(185486-285392)
    13(292413-317534)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 16)
    Uncharacterized protein
    (see all 16)
    56(a)
    55(a)
    (see all 16)
    many ↔ many
    many ↔ many
    (see all 16)
    4(77380556-77382976)
    4(77393489-77395927)
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh1a66
    pcdh2ab16
    (see all 35)
    protocadherin 2 alpha b 1
    (see all 35)
    42(a)
    42(a)
    (see all 35)
    many ↔ many
    many ↔ many
    (see all 35)
    10(21658144-21660531)
    14(2495124-2497505)


    ENSEMBL Gene Tree for PCDHA@ (if available)
    TreeFam Gene Tree for PCDHA@ (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHA@ gene
    PCDH72  PCDH202  PCDH12  PCDHA122  PCDH11Y2  PCDH122  PCDHA112  PCDH182  
    PCDH92  PCDH192  PCDH82  PCDH172  PCDHGB32  PCDHA72  PCDHGB62  PCDH11X2  
    PCDHA62  PCDH102  PCDHA102  PCDHA132  PCDHA92  PCDHA32  PCDHA42  

    PCDHA@ 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
    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing PCDHA@
    DNA2.0 Custom Variant and Variant Library Synthesis for PCDHA@

    (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: 604966    OMIM disorders: --

    4 diseases for PCDHA@:    About MalaCards
    wilms tumor    neuronitis    hypoxia    schizophrenia


    PCDHA@ for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHA@
    Human Genome Epidemiology (HuGE) Navigator: PCDHA@ (2 documents)

    Export disorders for PCDHA@ 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 PCDHA@ gene, integrated from 9 sources (see all 20):
    (articles sorted by number of sources associating them with PCDHA@)
        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. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PubMed id 19054571)1, 4 GregA^rio S.P....Dias-Neto E. (2009)
    3. Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)1, 3 Sugino H....Yagi T. (2000)
    4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1, 9 Wu Q.... Maniatis T. (2001)
    5. Frequent long-range epigenetic silencing of protocadh erin gene clusters on chromosome 5q31 in Wilms' tumor. (PubMed id 19956686)1 Dallosso A.R....Malik K. (2009)
    6. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (2004)
    7. 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)
    8. A multivariate analysis of 59 candidate genes in personality traits: the temperament and character inventory. (PubMed id 11140838)1 Comings D.E....MacMurray J.P. (2000)
    9. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)
    10. 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: 56117 HGNC: 8662 Ensembl:ENSG00000204970 euGenes: HUgn56117 ECgene: PCDHA@
    H-InvDB: PCDHA@

    (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 PCDHA@ 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 PCDHA@ gene:
    Search GeneIP for patents involving PCDHA@

    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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
     EMD Millipore Custom Antibody & Bulk Services
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     OriGene Custom Antibody Services for PCDHA@   OriGene Custom Protein Services for PCDHA@  

     
     
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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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    (GIFtS: 73)
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