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PCDHA@ Cluster

gene cluster   GIFtS: 33
GCID: GC05P140147

Protocadherin Alpha Cluster, Complex Locus

(Previous name: protocadherin alpha cluster)
(Previous symbol: CNRS1)
  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)
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Aliases
Protocadherin Alpha Cluster, Complex Locus1 2
CNRS11 2
Protocadherin Alpha Cluster1 2
CNR12
PCDH-alpha-13

External Ids:    HGNC: 86621   Entrez Gene: 561172   Ensembl: ENSG000002049707   OMIM: 6049665   UniProtKB: Q9Y5I33   

Export aliases for PCDHA@ gene to outside databases

Previous GC identifer: GC05U990123


(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 PCDHA@ Gene:
The protocadherin alpha gene cluster is one of three related clusters tandemly linked on chromosome five. The
clusters have a genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene
cluster is composed of 15 genes and 1 pseudogene, which are members of the cadherin superfamily and related to
the mouse CNR genes. The sequence of the 13 upstream genes and the pseudogene are highly similar to one another,
while a subfamily (C) contains two more distantly related coding sequences. The alpha cluster genes are organized
in a tandem array of 15 large, variable region exons followed by a constant region, which contains 3 exons shared
by all genes in the cluster. Each variable region exon encodes an extracellular domain comprised of 6 cadherin
ectodomains and a transmembrane region. The constant region exons encode a common cytoplasmic tail. These neural
adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell
connections in the brain. Alternative splicing has been described for the alpha cluster genes. (provided by
RefSeq, Jul 2008)

GeneCards Summary for PCDHA@ Gene:
PCDHA@ (protocadherin alpha cluster, complex locus) is a gene cluster. Diseases associated with PCDHA@ include wilms tumor, and neuronitis. An important paralog of this gene is PCDHAC1.

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

summary for PCDHA@ 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.




(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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RefSeq DNA sequence:
NC_000005.10  NC_018916.2  NT_029289.12  
Regulatory elements:
   Search for regulatory transcription factor binding sites for PCDHA@
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPCDHA@ promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PCDHA@


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

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

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P140147:  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 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.,
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UniProtKB/Swiss-Prot: PCDA1_HUMAN, Q9Y5I3 (See protein sequence)
Recommended Name: Protocadherin alpha-1 precursor  
Size: 950 amino acids; 102952 Da
Secondary accessions: O75288 Q9NRT7
Alternative splicing: 3 isoforms:  Q9Y5I3-1   Q9Y5I3-2   Q9Y5I3-3   

Explore the universe of human proteins at neXtProt for PCDHA@: NX_Q9Y5I3

Explore proteomics data for PCDHA@ at MOPED


See PCDHA@ Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


ENSEMBL proteins: 
 ENSP00000420840   ENSP00000378129   ENSP00000367373  

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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 Q9Y5I3

ProtoNet protein and cluster: Q9Y5I3

1 Blocks protein domain: IPB002126 Cadherin

UniProtKB/Swiss-Prot: PCDA1_HUMAN, Q9Y5I3
Similarity: Contains 6 cadherin domains


PCDHA@ 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: 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:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005509calcium ion binding ----
     
PCDHA@ for ontologies           About GeneDecksing


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
PCDA1_HUMAN, Q9Y5I3: Isoform 1: Cell membrane; Single-pass type I membrane protein (By similarity)
PCDA1_HUMAN, Q9Y5I3: Isoform 2: Secreted (Potential)

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

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region ----
GO:0005887integral component of plasma membrane ----
GO:0016020membrane ----

PCDHA@ 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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2 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for PCDHA@
    Reelin Pathway (Cajal-Retzius cells)
CRHR Pathway


    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PCDHA@
Interactions:

    Search GeneGlobe Interaction Network for PCDHA@

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

1 Interacting protein for PCDHA@ (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:    About this table

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

PCDHA@ 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 

Compounds for PCDHA@ 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]



(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, Primers from OriGene, and/or QIAGEN )
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Unigene Clusters for PCDHA@:

Protocadherin alpha cluster, complex locus
Hs.199343  [show with all ESTs], Hs.570901  [show with all ESTs], Hs.599714  [show with all ESTs]
Unigene Representative Sequences: NM_014005, BC043441, BC042887
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000504120(uc003lhb.2) ENST00000394633(uc003lha.2) ENST00000378133(uc003lgz.3)

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Additional mRNA sequence: BC042887.1 

Selected DOTS entries (see all 43):

DT.100796094  DT.91759865  DT.70103864  DT.409021  DT.91759859  DT.120835552  DT.91726025  DT.100796093 
DT.65286649  DT.91759861  DT.216532  DT.95296330  DT.95296331  DT.95349167  DT.87046613  DT.91759860 
DT.91759862  DT.91906247  DT.95296340  DT.120835478  DT.91759863  DT.207484  DT.100796091  DT.75106614 

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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Expression evidence for PCDHA@:none

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

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

PCDHA@ Protein Expression

SOURCE GeneReport for Unigene clusters: Hs.199343 Hs.570901 Hs.599714
    Custom PCR Arrays for PCDHA@
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHA@

(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 PCDHA@ gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
oppossum
(Monodelphis domestica)
Mammalia --
Uncharacterized protein
64(a)
1 → many
1(332637457-332900773)
chicken
(Gallus gallus)
Aves PCDHA116
--
Uncharacterized protein
53(a)
47(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)
56(a)
56(a)
(see all 16)
many ↔ many
many ↔ many
(see all 16)
4(77380556-77382976)
4(77317799-77320222)
zebrafish
(Danio rerio)
Actinopterygii pcdh2ab16
pcdh2ab86
(see all 16)
protocadherin 2 alpha b 8
(see all 16)
42(a)
42(a)
(see all 16)
many ↔ many
many ↔ many
(see all 16)
14(2495124-2497505) ENSDARG00000071904
14(2517358-2519727) ENSDARG00000089874


ENSEMBL Gene Tree for PCDHA@ (if available)
TreeFam Gene Tree for PCDHA@ (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for PCDHA@ gene
PCDHAC12  PCDHA22  PCDH72  PCDH202  PCDH12  PCDHA122  PCDH11Y2  PCDHA52  
PCDH122  PCDHA112  PCDH182  PCDH92  PCDH192  PCDH82  PCDH172  PCDHGC32  
PCDHA72  PCDH11X2  PCDHA62  PCDHA82  PCDH102  PCDHA102  PCDHA132  PCDHA92  
PCDHA32  PCDHA42  

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

(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: 604966    OMIM disorders: --

4 diseases for PCDHA@:    
About MalaCards
wilms tumor    neuronitis    hypoxia    schizophrenia


PCDHA@ for disorders           About GeneDecksing

Genetic Association Database (GAD): PCDHA@
Human Genome Epidemiology (HuGE) Navigator: PCDHA@ (2 documents)

Export disorders for PCDHA@ 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 PCDHA@ gene, integrated from 10 sources (see all 21):
(articles sorted by number of sources associating them with PCDHA@)
    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. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. (PubMed id 19054571)1, 4 GregA^rio S.P....Dias-Neto E. (Psychiatry Res 2009)
  3. Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)1, 3 Sugino H....Yagi T. (Genomics 2000)
  4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)1, 9 Wu Q.... Maniatis T. (Genome Res. 2001)
  5. Protocadherin I+ (PCDHA) as a novel susceptibility gene for autism. (PubMed id 23031252)1 Anitha A....Mori N. (amp 2013)
  6. Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor. (PubMed id 19956686)1 Dallosso A.R....Malik K. (PLoS Genet. 2009)
  7. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)
  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. A multivariate analysis of 59 candidate genes in personality traits: the temperament and character inventory. (PubMed id 11140838)1 Comings D.E....MacMurray J.P. (Clin. Genet. 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: 56117 HGNC: 8662 Ensembl:ENSG00000204970 euGenes: HUgn56117 ECgene: PCDHA@
H-InvDB: PCDHA@

(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 PCDHA@ 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 PCDHA@ gene:
Search GeneIP for patents involving PCDHA@

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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 OriGene Custom Antibody Services for PCDHA@   OriGene Custom Protein Services for PCDHA@  

 
 
 Block miRNA regulation of human, mouse, rat PCDHA@ using miScript Target Protectors SeqTarget long-range PCR primers for resequencing PCDHA@
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 Custom PCR Arrays for PCDHA@ Search Chromatin IP Primers for PCDHA@
 Search Pre-validated RT2 qPCR Primer Assays in human, mouse, rat PCDHA@ Search GeneGlobe Interaction Network for PCDHA@
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 GenScript Custom Purified and Recombinant Proteins Services for PCDHA@ GenScript Custom cDNA clones with any tag delivered in your preferred vector Services for PCDHA@
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 Tocris compounds for PCDHA@
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Biologicals
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 Search for Antibodies for PCDHA@ at Abcam
 See all of Abcam's Antibodies, Kits and Proteins for PCDHA@
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 Browse ESI BIO Cell Lines and PureStem Progenitors for PCDHA@
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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHA@
 Browse SwitchGear 3'UTR luciferase reporter plasmids for PCDHA@
 SwitchGear Promoter luciferase reporter plasmids for PCDHA@
 Search ThermoFisher Antibodies for PCDHA@
 Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat PCDHA@
 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PCDHA@
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 Search LSBio for Antibodies for PCDHA@
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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