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

PCDHA5 Gene

protein-coding   GIFtS: 42
GCID: GC05P140438

Protocadherin Alpha 5


(Previous symbol: CNRS6)
  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 51 2     CNR62
CNRS61 2 3     CNRN62
KIAA0345-Like 91 2     CRNR62
Ortholog Of Mouse CNR61 2     PCDH-ALPHA52
PCDH-alpha-52 3     Protocadherin Alpha-52

External Ids:    HGNC: 86711   Entrez Gene: 561432   Ensembl: ENSG000002049657   OMIM: 6063115   UniProtKB: Q9Y5H73   

Export aliases for PCDHA5 gene to outside databases

Previous GC identifers: GC05P140017 GC05P140752 GC05P140154 GC05P140209 GC05P140216 GC05P140171 GC05P140181 GC05P140325 GC05P140341 GC05P135346 GC05P140361 GC05P140376 GC05P140391 GC05P140405 GC05P140421


(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 PCDHA5 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 PCDHA5 Gene: 
PCDHA5 (protocadherin alpha 5) is a protein-coding gene. Diseases associated with PCDHA5 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHAC1.

UniProtKB/Swiss-Prot: PCDA5_HUMAN, Q9Y5H7
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 PCDHA5 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 PCDHA5 gene promoter:
         USF1   Elk-1   SREBP-1c   SREBP-1b   Gfi-1   Ik-2   SREBP-1a   HSF2   USF-1   c-Myb   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for PCDHA5

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHA5


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

PCDHA5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHA5 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140438:  view genomic region     (about GC identifiers)

Start:
140,201,222 bp from pter      End:
140,391,929 bp from pter
Size:
190,708 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: PCDA5_HUMAN, Q9Y5H7 (See protein sequence)
Recommended Name: Protocadherin alpha-5 precursor  
Size: 936 amino acids; 102048 Da
Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)
Secondary accessions: O75284 Q8N4R3
Alternative splicing: 3 isoforms:  Q9Y5H7-1   Q9Y5H7-2   Q9Y5H7-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for PCDHA5: NX_Q9Y5H7

Explore proteomics data for PCDHA5 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9Y5H7

  • PCDHA5 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PCDHA5 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_061731.1  NP_113689.1  

    ENSEMBL proteins: 
     ENSP00000433416   ENSP00000436557   ENSP00000367366  

    Human Recombinant Protein Products for PCDHA5: 
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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

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

    PCDHA5 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 Q9Y5H7

    ProtoNet protein and cluster: Q9Y5H7

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDA5_HUMAN, Q9Y5H7
    Similarity: Contains 6 cadherin domains


    PCDHA5 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: PCDA5_HUMAN, Q9Y5H7
    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--
         
    PCDHA5 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 PCDHA5

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

    1 Interacting protein for PCDHA5 (Q9Y5H73 ENSP000003673664) 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

    PCDHA5 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 PCDHA5 (PCDA5)

    1 HMDB Compound for PCDHA5    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--

    Search CenterWatch for drugs/clinical trials and news about PCDHA5 / PCDA5

    (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 PCDHA5 gene (2 alternative transcripts): 
    NM_018908.2  NM_031501.1  

    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000529619 ENST00000529859(uc003lhl.2 uc003lhk.1) ENST00000378126(uc003lhj.1)

    miRNA
    Products:
         
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    8/93 QIAGEN miScript miRNA Assays for microRNAs that regulate PCDHA5 (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
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    24/261 AceView cDNA sequences (see all 261):

    NM_031411 NM_031500 AW572498 AF152305 NM_018907 AI370466 AF152483 AI419005 
    NM_031882 AF152311 NM_031856 CB218096 AF152313 AA973493 AF152487 NM_031883 
    NM_031861 AF152306 BC003126 NM_018910 NM_031864 BI753524 NM_018900 NM_031860 

    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

    PCDHA5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHA5 Expression
    About this image


    See PCDHA5 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PCDHA5
        SABiosciences Custom PCR Arrays for PCDHA5
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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 PCDHA5 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 Pcdha51 , 5 protocadherin alpha 51, 5 85.07(n)1
    87.03(a)1
      18 (19.46 cM)5
    129411  NM_009959.11  NP_034089.11 
     369604405 
    chicken
    (Gallus gallus)
    Aves PCDHA116
    --
    --
    53(a)
    48(a)
    many ↔ many
    many ↔ many
    13(185486-285392)
    13(292413-317534)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    (see all 16)
    Protocadherin alpha 5 unspliced isoform; Uncharact...
    Protocadherin alpha 10 unspliced isoform; Uncharac...
    (see all 16)
    58(a)
    57(a)
    (see all 16)
    many ↔ many
    many ↔ many
    (see all 16)
    4(77380556-77382976)
    4(77317799-77320222)
    zebrafish
    (Danio rerio)
    Actinopterygii CR847851.26
    pcdh2ab56
    (see all 35)
    protocadherin 2 alpha b 5
    (see all 35)
    43(a)
    42(a)
    (see all 35)
    many ↔ many
    many ↔ many
    (see all 35)
    14(2425668-2426945)
    14(2507189-2509570)


    ENSEMBL Gene Tree for PCDHA5 (if available)
    TreeFam Gene Tree for PCDHA5 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PCDHA5 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  PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  PCDHB62  
    PCDHGC42  PCDHGC52  PCDHGA12  PCDHB102  PCDHB12  PCDHGB72  PCDHGA32  
    18/61 SIMAP similar genes for PCDHA5 using alignment to 1 protein entry:     PCDA5_HUMAN(see all similar genes):
    PCDHA1    PCDHA2    PCDHA7    PCDHA4    PCDHA11    PCDHA13
    PCDHA6    PCDHA8    PCDHA3    PCDHA10    PCDHA12    PCDHA9
    PCDHB17    PCDHAC2    PCDHB13    PCDHGA3    PCDH10    PCDHB11

    PCDHA5 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 PCDHA5 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_0485264
    ----see VAR_0485262 A V mis40--------

    HapMap Linkage Disequilibrium report for PCDHA5 (140201222 - 140391929 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/47 variations for PCDHA5 (see all 47):    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: 606311    OMIM disorders: --

    2 diseases for PCDHA5:    About MalaCards
    neuronitis    


    PCDHA5 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHA5

    Export disorders for PCDHA5 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 PCDHA5 gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with PCDHA5)
        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. 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. 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: 56143 HGNC: 8671 AceView: PCDHA9 Ensembl:ENSG00000204965 euGenes: HUgn56143
    ECgene: PCDHA5 H-InvDB: PCDHA5

    (According to HUGE)
    About This Section
    HUGE: KIAA0345-like 9

    (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 PCDHA5 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 PCDHA5 gene:
    Search GeneIP for patents involving PCDHA5

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



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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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