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

PCDHA4 Gene

protein-coding   GIFtS: 48
GCID: GC05P140186

Protocadherin Alpha 4

  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 41 2     CNRN12
KIAA0345-Like 101 2     CRNR12
Ortholog Of Mouse CNR11 2     PCDH-ALPHA42
PCDH-alpha-42 3     Protocadherin Alpha-42
CNR12     

External Ids:    HGNC: 86701   Entrez Gene: 561442   Ensembl: ENSG000002049677   OMIM: 6063105   UniProtKB: Q9UN743   

Export aliases for PCDHA4 gene to outside databases

Previous GC identifers: GC05P140004 GC05P140751 GC05P140153 GC05P140208 GC05P140201 GC05P140170 GC05P140180 GC05P140182 GC05P140183 GC05P140184 GC05P140185 GC05P140188 GC05P140189 GC05P140190 GC05P135331


(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 PCDHA4 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 PCDHA4 Gene: 
PCDHA4 (protocadherin alpha 4) is a protein-coding gene. Diseases associated with PCDHA4 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot: PCDA4_HUMAN, Q9UN74
Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance
of specific neuronal connections in the brain

summary for PCDHA4 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.

Gene Wiki entry for PCDHA4 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 PCDHA4 gene promoter:
         CUTL1   NF-AT   Gfi-1   NF-AT4   NF-AT2   COMP1   NF-AT3   c-Myb   NF-kappaB1   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHA4 promoter sequence
   Search SABiosciences Chromatin IP Primers for PCDHA4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHA4


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

PCDHA4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHA4 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140186:  view genomic region     (about GC identifiers)

Start:
140,186,659 bp from pter      End:
140,391,929 bp from pter
Size:
205,271 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: PCDA4_HUMAN, Q9UN74 (See protein sequence)
Recommended Name: Protocadherin alpha-4 precursor  
Size: 947 amino acids; 102293 Da
Subunit: Interacts with FYN (By similarity)
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: O75285 Q2M253
Alternative splicing: 2 isoforms:  Q9UN74-1   Q9UN74-2   

Explore the universe of human proteins at neXtProt for PCDHA4: NX_Q9UN74

Explore proteomics data for PCDHA4 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9UN74

  • PCDHA4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDHA4 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_061730.1  NP_113688.1  

    ENSEMBL proteins: 
     ENSP00000423470   ENSP00000435300   ENSP00000349344  

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    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane ----
    GO:0005887integral to plasma membrane TAS10380929
    GO:0016020membrane ----
    GO:0016021integral to membrane ----

    PCDHA4 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 Q9UN74

    ProtoNet protein and cluster: Q9UN74

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDA4_HUMAN, Q9UN74
    Similarity: Contains 6 cadherin domains


    PCDHA4 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: PCDA4_HUMAN, Q9UN74
    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--
         
    PCDHA4 for ontologies           About GeneDecksing


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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

    SuperPaths for PCDHA4 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Reelin Pathway (Cajal-Retzius cells)
    Reelin Pathway (Cajal-Retzius cells)

    1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for PCDHA4
        Reelin Pathway (Cajal-Retzius cells)


    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PCDHA4

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

    5/19 Interacting proteins for PCDHA4 (Q9UN742, 3 ENSP000003493444) via UniProtKB, MINT, STRING, and/or I2D (see all 19)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    APLP1P516932, 3MINT-65771 I2D: score=4 
    C14orf1Q9UKR52, 3MINT-65780 I2D: score=4 
    CCDC90BQ9GZT62, 3MINT-65777 I2D: score=4 
    GAPDHP044062, 3MINT-65769 I2D: score=4 
    GDF9O603832, 3MINT-65768 I2D: score=4 
    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

    PCDHA4 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 PCDHA4 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]

    1 HMDB Compound for PCDHA4    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHA4 / PCDA4

    (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 PCDHA4 gene (2 alternative transcripts): 
    NM_018907.3  NM_031500.2  

    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000512229 ENST00000530339(uc003lhh.1 uc003lhi.2) ENST00000356878(uc011daa.2)

    miRNA
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    24/261 AceView cDNA sequences (see all 261):

    AF152310 BM129562 AI268404 AF152305 F06310 AF152313 AF152477 AI419005 
    NM_031861 NM_031496 NM_018911 NM_018902 AF152304 BC003126 NM_031865 BI753524 
    AA552914 NM_018910 BM684041 AF152475 CB218096 AW470523 AF152478 BC033735 

    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

    PCDHA4 expression in normal human tissues (normalized intensities)      PCDHA4 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHA4 Expression
    About this image


    PCDHA4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/1 selected tissues (see all 1) fully expand
     
     Adipose (Muscoskeletal System)
             Mesenchymal Stem Cells Subcutaneous White Adipose

    See PCDHA4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHA4
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    In Situ
    Assay Products:
     

     
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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 PCDHA4 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 Pcdha41 , 5 protocadherin alpha 41, 5 83.95(n)1
    86.38(a)1
      18 (19.46 cM)5
    129361  NM_007766.21  NP_031792.11 
     369526895 
    chicken
    (Gallus gallus)
    Aves PCDHA116
    --
    --
    54(a)
    47(a)
    many ↔ many
    many ↔ many
    13(185486-285392)
    13(292413-317534)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 16)
    Protocadherin alpha 10 unspliced isoform; Uncharac...
    Protocadherin alpha 5 unspliced isoform; Uncharact...
    (see all 16)
    57(a)
    57(a)
    (see all 16)
    many ↔ many
    many ↔ many
    (see all 16)
    4(77317799-77320222)
    4(77380556-77382976)
    zebrafish
    (Danio rerio)
    Actinopterygii CR847851.26
    pcdh2ab56
    (see all 35)
    protocadherin 2 alpha b 5
    (see all 35)
    44(a)
    42(a)
    (see all 35)
    many ↔ many
    many ↔ many
    (see all 35)
    14(2425668-2426945)
    14(2507189-2509570)


    ENSEMBL Gene Tree for PCDHA4 (if available)
    TreeFam Gene Tree for PCDHA4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHA4 gene
    PCDH72  PCDH202  PCDH12  PCDHA122  PCDH11Y2  PCDH122  PCDHA112  PCDHA12  
    PCDH182  PCDH92  PCDH192  PCDH82  PCDH172  PCDHGB32  PCDHA72  PCDHGB62  
    PCDH11X2  PCDHA62  PCDH102  PCDHA102  PCDHA132  PCDHA92  PCDHA32  
    18/70 SIMAP similar genes for PCDHA4 using alignment to 2 protein entries:     PCDA4_HUMAN (see all proteins) (see all similar genes):
    PCDHA2    PCDHA7    PCDHA9    PCDHA3    PCDHA1    PCDHA6
    PCDHA11    PCDHA5    PCDHA13    PCDHA8    PCDHA10    PCDHA12
    ME6    ME1    ME4    PCDHAC2    PCDHB13    PCDHB17

    PCDHA4 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

    3 SNPs in PCDHA4 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_0243904
    ----see VAR_0243902 P S mis40--------
    VAR_0591804
    ----see VAR_0591802 E D mis40--------
    rs114591121,2
    C--140186225(+) GGGTGA/-AAGAG 1 -- us2k11Minor allele frequency- -:0.00NA 2

    HapMap Linkage Disequilibrium report for PCDHA4 (140186659 - 140391929 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/48 variations for PCDHA4 (see all 48):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2657537CNV Deletion23128226
    nsv820841CNV Deletion20802225
    esv2659321CNV Deletion23128226
    dgv1044e199CNV Deletion23128226
    esv2505753CNV Deletion19546169
    esv2730838CNV Deletion23290073
    esv2730839CNV Deletion23290073
    esv2421858CNV Deletion20811451
    dgv1043e199CNV Deletion23128226
    nsv436885CNV Insertion17901297

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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: 606310    OMIM disorders: --

    2 diseases for PCDHA4:    About MalaCards
    neuronitis    


    PCDHA4 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHA4

    Export disorders for PCDHA4 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 PCDHA4 gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with PCDHA4)
        Utopia: connect your pdf to the dynamic
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    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 DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)1, 2 Schmutz J.... Rubin E.M. (2004)
    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. 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)
    5. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (2005)
    6. 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)
    7. 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)
    8. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (2001)
    9. 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)
    10. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (2000)

    (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)
    About This Section
    Entrez Gene: 56144 HGNC: 8670 AceView: PCDHA9 Ensembl:ENSG00000204967 euGenes: HUgn56144
    ECgene: PCDHA4 H-InvDB: PCDHA4

    (According to HUGE)
    About This Section
    HUGE: KIAA0345-like 10" KIAA0345-like 10

    (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 PCDHA4 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 PCDHA4 gene:
    Search GeneIP for patents involving PCDHA4

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



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