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

PCDHA1 Gene

protein-coding   GIFtS: 47
GCID: GC05P140146

Protocadherin Alpha 1

  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 11 2
KIAA0345-Like 131 2
PCDH-alpha-12 3
PCDH-ALPHA12
Protocadherin Alpha-12

External Ids:    HGNC: 86631   Entrez Gene: 561472   Ensembl: ENSG000002049707   OMIM: 6063075   UniProtKB: Q9Y5I33   

Export aliases for PCDHA1 gene to outside databases

Previous GC identifers: GC05P139982 GC05P140748 GC05P140150 GC05P140194 GC05P135311


(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 PCDHA1 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 PCDHA1 Gene: 
PCDHA1 (protocadherin alpha 1) is a protein-coding gene. Diseases associated with PCDHA1 include thyrotoxicosis, and bipolar disorder. GO annotations related to this gene include calcium ion binding. 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

Gene Wiki entry for PCDHA1 (Protocadherin alpha 1) 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 PCDHA1 gene promoter:
         RelA   CUTL1   NF-AT   NF-AT4   NF-AT2   COMP1   NF-AT3   NF-kappaB1   NF-AT1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for PCDHA1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHA1


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

PCDHA1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHA1 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140146:  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 PCDHA1: NX_Q9Y5I3

Explore proteomics data for PCDHA1 at MOPED 

Post-translational modifications:

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

  • PCDHA1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDHA1 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_061723.1  NP_113598.1  NP_113599.1  

    ENSEMBL proteins: 
     ENSP00000420840   ENSP00000378129   ENSP00000367373  

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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    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:0005576extracellular region IEA--
    GO:0005887integral to plasma membrane TAS10380929
    GO:0016020membrane ----

    PCDHA1 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


    PCDHA1 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 IEA--
         
    PCDHA1 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for PCDHA1:
     Decreased POU5F1-GFP protein e 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Pcdha1):
     normal 

    PCDHA1 for phenotypes           About GeneDecksing

    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidPCDHA1 3' UTR sequence
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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 PCDHA1

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

    1 Interacting protein for PCDHA1 (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 TAS10380929
    GO:0007156homophilic cell adhesion IEA--
    GO:0007399nervous system development TAS10380929

    PCDHA1 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 PCDHA1 (PCDA1)

    1 HMDB Compound for PCDHA1    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHA1 / PCDA1

    (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 PCDHA1 gene (3 alternative transcripts): 
    NM_018900.3  NM_031410.2  NM_031411.2  

    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000504120(uc003lhb.2) ENST00000394633(uc003lha.2) ENST00000378133(uc003lgz.3)

    miRNA
    Products:
         
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    8/93 QIAGEN miScript miRNA Assays for microRNAs that regulate PCDHA1 (see all 93):
    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
    SwitchGear 3'UTR luciferase reporter plasmidPCDHA1 3' UTR sequence
    Inhib. RNA
    Products:
         
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    24/261 AceView cDNA sequences (see all 261):

    NM_031856 NM_031859 AW572498 AF152487 NM_031860 NM_031501 AF152482 AF152315 
    AF169689 NM_031849 BC003126 AF152317 NM_018902 BC033735 NM_018909 AF152306 
    NM_031865 AF152475 AA973493 BM684041 NM_031882 NM_031861 AF152303 AF152305 

    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

    PCDHA1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHA1 Expression
    About this image


    See PCDHA1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHA1
        SABiosciences Custom PCR Arrays for PCDHA1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHA1

    (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 PCDHA1 gene from 4/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdha11 , 5 protocadherin alpha 11, 5 84.3(n)1
    85.11(a)1
      18 (19.46 cM)5
    1167311  NM_054072.11  NP_473413.11 
     369302855 
    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 Dr.198662 Transcribed sequence with weak similarity to protein more 74.8(n)    AL927959.1 


    ENSEMBL Gene Tree for PCDHA1 (if available)
    TreeFam Gene Tree for PCDHA1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHA1 gene
    PCDH72  PCDH202  PCDH12  PCDHA122  PCDH11Y2  PCDH122  PCDHA112  PCDH182  
    PCDH92  PCDH192  PCDH82  PCDH172  PCDHGB32  PCDHA72  PCDHGB62  PCDH11X2  
    PCDHA62  PCDH102  PCDHA102  PCDHA132  PCDHA92  PCDHA32  PCDHA42  
    18/61 SIMAP similar genes for PCDHA1 using alignment to 1 protein entry:     PCDA1_HUMAN(see all similar genes):
    PCDHA11    PCDHA2    PCDHA3    PCDHA4    PCDHA5    PCDHA6
    PCDHA9    PCDHA8    PCDHA7    PCDHA13    PCDHA10    PCDHA12
    PCDHB17    PCDHAC2    PCDHB15    PCDHB16    PCDHGA3    PCDHB10

    PCDHA1 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

    10/272 SNPs in PCDHA1 are shown (see all 272)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1424189411,2
    C--135313854(+) ATTTGC/TTTAAT 1 -- int10--------
    rs796933091,2
    F--135314032(+) ACTCAC/TAAATG 1 -- int11Minor allele frequency- T:0.01WA 118
    rs1877676361,2
    --135314041(+) TGTTCC/TAAAAC 1 -- int10--------
    rs68989061,2
    C,F,A,H--135314047(+) AAAACC/GCTTTA 1 -- int117Minor allele frequency- G:0.50NS EA NA WA CSA 906
    rs68989391,2
    C,F--135314103(+) ACTTTA/CGTCAC 1 -- int112Minor allele frequency- C:0.42NA WA CSA EA 376
    rs1513249601,2
    --135314192(+) ATATCC/GAAAAA 1 -- int10--------
    rs1474150411,2
    --140163933(+) AGGGGA/GAGGTG 3 -- us2k10--------
    rs1148387221,2
    C,F--140164117(+) TCTAGA/GTTCCC 3 -- us2k11Minor allele frequency- G:0.02NA 120
    rs1931391211,2
    --140164177(+) CCTGGA/CGTAAA 3 -- us2k10--------
    rs798388321,2
    F--140164358(+) CACCAC/TTGTGT 3 -- us2k11Minor allele frequency- T:0.03WA 118

    HapMap Linkage Disequilibrium report for PCDHA1 (140165876 - 140391929 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/48 variations for PCDHA1 (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: 606307    OMIM disorders: --

    4 diseases for PCDHA1:    About MalaCards
    thyrotoxicosis    bipolar disorder    schizophrenia    neuronitis

    1 disease from the University of Copenhagen DISEASES database for PCDHA1:
    Thyrotoxicosis

    PCDHA1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHA1
    Human Genome Epidemiology (HuGE) Navigator: PCDHA1 (1 document)

    Export disorders for PCDHA1 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 PCDHA1 gene, integrated from 9 sources (see all 13):
    (articles sorted by number of sources associating them with PCDHA1)
        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. Analysis of protocadherin alpha gene deletion variant in bipolar disorder and schizophrenia. (PubMed id 18496207)1, 4 Lachman H.M....Stopkova P. (2008)
    3. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)1, 2 Schmutz J.... Rubin E.M. (2004)
    4. CTCF/cohesin-mediated DNA looping is required for prot ocadherin a promoter choice. (PubMed id 23204437)1 Guo Y....Wu Q. (2012)
    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. 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)
    7. 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)
    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. Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)1 Sugino H....Yagi T. (2000)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 56147 HGNC: 8663 AceView: PCDHA9 Ensembl:ENSG00000204970 euGenes: HUgn56147
    ECgene: PCDHA1 H-InvDB: PCDHA1

    (According to HUGE)
    About This Section
    HUGE: KIAA0345-like 13

    (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 PCDHA1 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 PCDHA1 gene:
    Search GeneIP for patents involving PCDHA1

    GeneCards and IP:
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