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PCDHA12 Gene

protein-coding   GIFtS: 42
GCID: GC05P140451

Protocadherin Alpha 12

  Search for PCDHA12
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 121 2
KIAA0345-Like 21 2
PCDH-alpha-122 3
PCDH-ALPHA122
Protocadherin Alpha-122

External Ids:    HGNC: 86661   Entrez Gene: 561372   Ensembl: ENSG000002516647   OMIM: 6063185   UniProtKB: Q9UN753   

Export aliases for PCDHA12 gene to outside databases

Previous GC identifers: GC05P140071 GC05P140759 GC05P140204 GC05P140197 GC05P140168 GC05P140240 GC05P140249 GC05P140258 GC05P140267 GC05P140277 GC05P140287 GC05P140298 GC05P140307 GC05P140319 GC05P140328 GC05P140340 GC05P135399 GC05P140360 GC05P140380 GC05P140390 GC05P140403 GC05P140420 GC05P140437


(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 PCDHA12 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 PCDHA12 Gene:
PCDHA12 (protocadherin alpha 12) is a protein-coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHAC1.

UniProtKB/Swiss-Prot: PCDAC_HUMAN, Q9UN75
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 PCDHA12 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 PCDHA12 gene promoter:
         p300   FOXD3   AP-4   C/EBPalpha   CHOP-10   FOXO4   HFH-1   Sox9   FOXO1a   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHA12 promoter sequence
   Search Chromatin IP Primers for PCDHA12

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHA12


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

PCDHA12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHA12 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140451:  view genomic region     (about GC identifiers)

Start:
140,254,931 bp from pter      End:
140,391,929 bp from pter
Size:
136,999 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PCDAC_HUMAN, Q9UN75 (See protein sequence)
Recommended Name: Protocadherin alpha-12 precursor  
Size: 941 amino acids; 101652 Da
Secondary accessions: O75278 Q2M1N8
Alternative splicing: 2 isoforms:  Q9UN75-1   Q9UN75-2   

Explore the universe of human proteins at neXtProt for PCDHA12: NX_Q9UN75

Post-translational modifications: 

  • Glycosylation2 at Asn257, Asn265, Asn548
  • Modification sites at PhosphoSitePlus
  • REFSEQ proteins (2 alternative transcripts): 
    NP_061726.1  NP_114070.1  

    ENSEMBL proteins: 
     ENSP00000381628  

    PCDHA12 Human Recombinant Protein Products:

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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 Q9UN75

    ProtoNet protein and cluster: Q9UN75

    1 Blocks protein domain: IPB002126 Cadherin

    UniProtKB/Swiss-Prot: PCDAC_HUMAN, Q9UN75
    Similarity: Contains 6 cadherin domains


    Find genes that share domains with PCDHA12           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PCDAC_HUMAN, Q9UN75
    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--
         
    Find genes that share ontologies with PCDHA12           About GenesLikeMe


    Animal Models:
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    (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
    PCDAC_HUMAN, Q9UN75: Cell membrane; Single-pass type I membrane protein (By similarity)

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with PCDHA12           About GenesLikeMe


    (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 PCDHA12
    Interactions:

        Search GeneGlobe Interaction Network for PCDHA12

    1 Interacting protein for PCDHA12 (Q9UN753) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CRKP461083I2D: score=1 
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007156homophilic cell adhesion IEA--

    Find genes that share ontologies with PCDHA12           About GenesLikeMe



    (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 PCDHA12 (PCDAC)

    1 HMDB Compound for PCDHA12    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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for PCDHA12 gene (2 alternative transcripts): 
    NM_018903.3  NM_031864.2  

    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000398631(uc003lic.2)
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate PCDHA12 (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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      QuantiFast Probe-based Assays in human, mouse, rat PCDHA12

    Selected AceView cDNA sequences (see all 261):

    AF152317 AA757839 NM_018898 NM_031856 AA889198 NM_031501 AF152485 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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    PCDHA12 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    PCDHA12 Expression
    About this image

    PCDHA12 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for PCDHA12 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pcdha95
    Pcdha101
    protocadherin alpha 95
    protocadherin alpha 101
    77.97(n)1
    78.99(a)1
      18 (19.46 cM)5
    129431  NM_009961.11  NP_034091.11 
     369978805 
    chicken
    (Gallus gallus)
    Aves PCDHA116
    --
    Uncharacterized protein
    52(a)
    46(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 11 unspliced isoform; Uncharac...
    (see all 16)
    55(a)
    55(a)
    (see all 16)
    many ↔ many
    many ↔ many
    (see all 16)
    4(77317799-77320222)
    4(77309198-77311624)
    zebrafish
    (Danio rerio)
    Actinopterygii pcdh2ab16
    pcdh2ab36
    (see all 16)
    protocadherin 2 alpha b 3
    (see all 16)
    43(a)
    42(a)
    (see all 16)
    many ↔ many
    many ↔ many
    (see all 16)
    14(2495124-2497505) ENSDARG00000071904
    14(2503338-2505713) ENSDARG00000071905


    ENSEMBL Gene Tree for PCDHA12 (if available)
    TreeFam Gene Tree for PCDHA12 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PCDHA12 gene
    PCDHAC12  PCDHA22  PCDH72  PCDH202  PCDH12  PCDH11Y2  PCDHA52  PCDH122  
    PCDHA112  PCDHA12  PCDH182  PCDH92  PCDH192  PCDH82  PCDH172  PCDHGC32  
    PCDHA72  PCDH11X2  PCDHA62  PCDHA82  PCDH102  PCDHA102  PCDHA132  PCDHA92  
    PCDHA32  PCDHA42  
    Selected SIMAP similar genes for PCDHA12 using alignment to 1 protein entry:     PCDAC_HUMAN(see all similar genes):
    PCDHA10    PCDHA6    PCDHA7    PCDHA8    PCDHA13    PCDHA1
    PCDHA11    PCDHA2    PCDHA3    PCDHA5    PCDHA9    PCDHA4
    PCDHB17    PCDHB3    PCDHAC2    PCDHGA3    DKFZp586I1919    PCDHB10

    Find genes that share paralogs with PCDHA12           About GenesLikeMe



    (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) 10 variations for PCDHA12:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2505753CNV Deletion19546169
    nsv882956CNV Loss21882294
    dgv6344n71CNV Loss21882294
    dgv6343n71CNV Loss21882294
    nsv882970CNV Loss21882294
    nsv882957CNV Loss21882294
    nsv10754CNV Gain18304495
    nsv823264CNV Gain20364138
    dgv1857e1CNV Complex17122850
    dgv1856e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 606318    OMIM disorders: --


    Find genes that share disorders with PCDHA12           About GenesLikeMe

    Genetic Association Database (GAD): PCDHA12

    Export disorders for PCDHA12 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 PCDHA12 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with PCDHA12)
        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. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)1, 2 Schmutz J.... Rubin E.M. (Nature 2004)
    3. 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)
    4. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. (PubMed id 17474147)1 Wu C....Li S.S. (Proteomics 2007)
    5. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1 Otsuki T....Isogai T. (DNA Res. 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. (Genome Res. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    8. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1 Wu Q.... Maniatis T. (Genome Res. 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. (J. Mol. Biol. 2000)
    10. Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)1 Sugino H....Yagi T. (Genomics 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: 56137 HGNC: 8666 AceView: PCDHA9 Ensembl:ENSG00000251664 euGenes: HUgn56137
    ECgene: PCDHA12 H-InvDB: PCDHA12

    (According to HUGE)
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    HUGE: KIAA0345-like 2

    (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 PCDHA12 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for PCDHA12 gene:
    Search GeneIP for patents involving PCDHA12

    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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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)
    About This Section

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     QuantiFast Probe-based Assays in human, mouse, rat PCDHA12 QuantiTect SYBR Green Assays in human, mouse, rat PCDHA12
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     Browse ESI BIO Cell Lines and PureStem Progenitors for PCDHA12
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     Search Addgene for plasmids for PCDHA12
      Search eBioscience for proteins for PCDHA12
      Search eBioscience for elisas for PCDHA12
      eBioscience FlowRNA Probe Sets
           
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