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PCDHAC2 Gene

protein-coding   GIFtS: 42
GCID: GC05P140345

Protocadherin Alpha Subfamily C, 2

  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)
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Aliases
Protocadherin Alpha Subfamily C, 21 2
PCDH-ALPHA-C22
Protocadherin Alpha-C22
PCDH-alpha-C23

External Ids:    HGNC: 86771   Entrez Gene: 561342   Ensembl: ENSG000002432327   OMIM: 6063215   UniProtKB: Q9Y5I43   

Export aliases for PCDHAC2 gene to outside databases

Previous GC identifers: GC05P140079 GC05P140761 GC05P140215 GC05P140222 GC05P140177 GC05P140179 GC05P140326 GC05P135490


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for PCDHAC2 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 PCDHAC2 Gene:
PCDHAC2 (protocadherin alpha subfamily C, 2) is a protein-coding gene. Diseases associated with PCDHAC2 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB16.

UniProtKB/Swiss-Prot: PCDC2_HUMAN, Q9Y5I4
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 PCDHAC2 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the PCDHAC2 gene promoter:
         TBP   AML1a   NCX/Ncx   Cdc5   C/EBPalpha   RORalpha1   PPAR-gamma1   Pax-4a   ATF   RSRFC4   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHAC2 promoter sequence
   Search Chromatin IP Primers for PCDHAC2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHAC2


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

PCDHAC2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHAC2 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140345:  view genomic region     (about GC identifiers)

Start:
140,345,747 bp from pter      End:
140,391,936 bp from pter
Size:
46,190 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PCDC2_HUMAN, Q9Y5I4 (See protein sequence)
Recommended Name: Protocadherin alpha-C2 precursor  
Size: 1007 amino acids; 109450 Da
Secondary accessions: Q2M3V1 Q9Y5F4
Alternative splicing: 2 isoforms:  Q9Y5I4-1   Q9Y5I4-2   

Explore the universe of human proteins at neXtProt for PCDHAC2: NX_Q9Y5I4

Explore proteomics data for PCDHAC2 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn280, Asn436, Asn586, Asn657
  • Modification sites at PhosphoSitePlus

  • See PCDHAC2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_061722.1  NP_114089.1  

    ENSEMBL proteins: 
     ENSP00000289269  

    PCDHAC2 Human Recombinant Protein Products:

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    Novus Biologicals PCDHAC2 Lysates
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    Browse Proteins at Cloud-Clone Corp.

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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 Q9Y5I4

    ProtoNet protein and cluster: Q9Y5I4

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDC2_HUMAN, Q9Y5I4
    Similarity: Contains 6 cadherin domains


    PCDHAC2 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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCDC2_HUMAN, Q9Y5I4
    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:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005509calcium ion binding IEA--
         
    PCDHAC2 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for PCDHAC2:
     Increased gamma-H2AX phosphory 

         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Pcdhac2):
     normal 

    PCDHAC2 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PCDHAC2
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    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate PCDHAC2 (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
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    Browse Sino Biological Human cDNA Clones
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHAC2


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PCDC2_HUMAN, Q9Y5I4: Cell membrane; Single-pass type I membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular2
    endoplasmic reticulum1
    peroxisome1

    Gene Ontology (GO): 2 cellular component terms:    About this table

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

    PCDHAC2 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PCDHAC2
    Interactions:

        Search GeneGlobe Interaction Network for PCDHAC2

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for PCDHAC2 (ENSP000002892694) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HGSENSP000003312014STRING: ENSP00000331201
    PCDHB16ENSP000003542934STRING: ENSP00000354293
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007155cell adhesion TAS10380929
    GO:0007156homophilic cell adhesion IEA--
    GO:0007399nervous system development TAS10380929

    PCDHAC2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PCDHAC2 (PCDC2)

    1 HMDB Compound for PCDHAC2    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--



    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PCDHAC2 gene (2 alternative transcripts): 
    NM_018899.5  NM_031883.2  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000289269(uc003lii.3)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate PCDHAC2 (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
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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    OriGene qPCR primer pairs and template standards for PCDHAC2
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      QuantiTect SYBR Green Assays in human, mouse, rat PCDHAC2
      QuantiFast Probe-based Assays in human, mouse, rat PCDHAC2

    Selected AceView cDNA sequences (see all 261):

    AA757839 AF152317 NM_031856 AF152485 NM_018898 NM_031501 AA889198 NM_031496 
    NM_018905 NM_031848 BM682903 BM719606 BC033735 AF152309 AF152305 NM_031852 
    F05011 AF169695 NM_031865 AF152314 NM_018909 NM_014005 NM_018901 AW470523 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PCDHAC2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHAC2 Expression
    About this image

    PCDHAC2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PCDHAC2 Protein Expression
        Custom PCR Arrays for PCDHAC2
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHAC2

    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHAC2 gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdhac21 , 5 protocadherin alpha subfamily C, 21, 5 89.3(n)1
    93.14(a)1
      18 (19.46 cM)5
    3532371  NM_001003672.11  NP_001003672.11 
     371439695 
    chicken
    (Gallus gallus)
    Aves PCDHAC21 protocadherin alpha subfamily C, 2 70.98(n)
    71.92(a)
      497224  NM_001111131.1  NP_001104601.1 
    lizard
    (Anolis carolinensis)
    Reptilia PCDHAC26
    protocadherin alpha subfamily C, 2
    42(a)
    1 ↔ 1
    4(76528115-76585021)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia pcdhac21 protocadherin alpha subfamily C, 2 63.96(n)
    63.96(a)
      100125023  XM_004912782.1  XP_004912839.1 
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh2ac1 protocadherin 2 alpha c 57.5(n)
    53.53(a)
      493587  NM_001007762.1  NP_001007763.1 


    ENSEMBL Gene Tree for PCDHAC2 (if available)
    TreeFam Gene Tree for PCDHAC2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHAC2 gene
    PCDHB162  PCDHB22  PCDHB72  PCDHB152  PCDHGA102  PCDHGA122  PCDHGB22  PCDHGA92  
    PCDHGA82  PCDHGB32  PCDHGB62  PCDHGA52  PCDHB52  PCDHB132  PCDHGA42  PCDHGA72  
    PCDHB42  PCDHB112  ENSG000002556222  PCDHB142  PCDHB122  PCDHB82  PCDHGB12  PCDHGB42  
    PCDHGA22  PCDHGA62  PCDHB32  PCDHGA112  PCDHB62  PCDHGC42  PCDHGC52  PCDHGA12  
    PCDHB102  PCDHB12  PCDHGA32  PCDHGB72  
    Selected SIMAP similar genes for PCDHAC2 using alignment to 2 protein entries:     PCDC2_HUMAN (see all proteins) (see all similar genes):
    ME1    PCDHGA3    PCDHA3    PCDHA8    ME2    ME6
    PCDHA1    ME4    PCDHA10    PCDHA2    PCDHA5    PCDHA6
    PCDHA9    PCDHA12    PCDHAC1    PCDHGC5    DKFZp586I1919    PCDH19

    PCDHAC2 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for PCDHAC2:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv1857e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PCDHAC2
    DNA2.0 Custom Variant and Variant Library Synthesis for PCDHAC2

    (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.)
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    OMIM gene information: 606321    OMIM disorders: --

    1 disease for PCDHAC2:    
    About MalaCards
    neuronitis


    PCDHAC2 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PCDHAC2

    Export disorders for PCDHAC2 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)
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    PubMed articles for PCDHAC2 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with PCDHAC2)
        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. (Cell 1999)
    2. 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. (PLoS Genet. 2012)
    3. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    4. 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. (Genome Res. 2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    7. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 2001)
    8. 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. (J. Mol. Biol. 2000)
    9. Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)1 Sugino H....Yagi T. (Genomics 2000)
    10. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)1 Wu Q. and Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 56134 HGNC: 8677 AceView: PCDHA9 Ensembl:ENSG00000243232 euGenes: HUgn56134
    ECgene: PCDHAC2 H-InvDB: PCDHAC2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PCDHAC2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PCDHAC2 gene:
    Search GeneIP for patents involving PCDHAC2

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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