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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

PCDHA4 Gene

protein-coding GIFtS: 48
GCID: GC05P140186

Protocadherin Alpha 4

See related disease
at

MalaCards

(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 4¹ ²		CNRN1²
KIAA0345-Like 10¹ ²		CRNR1²
Ortholog Of Mouse CNR1¹ ²		PCDH-ALPHA4²
PCDH-alpha-4² ³		Protocadherin Alpha-4²
CNR1²

External Ids:	HGNC: 8670¹	Entrez Gene: 56144²	Ensembl: ENSG00000204967⁷	OMIM: 606310⁵	UniProtKB: Q9UN74³

Export aliases for PCDHA4 gene to outside databases

Previous GC identifers: GC05P140004 GC05P140751 GC05P140153 GC05P140208 GC05P140201 GC05P140170 GC05P140180 GC05P140182 GC05P140183 GC05P140184 GC05P140185 GC05P140188 GC05P140189 GC05P140190 GC05P135331

(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 PCDHA4 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 PCDHA4 Gene:

PCDHA4 (protocadherin alpha 4) is a protein-coding gene. Diseases associated with PCDHA4 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot: PCDA4_HUMAN, Q9UN74

Function: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance

of specific neuronal connections in the brain

summary for PCDHA4 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.

Gene Wiki entry for PCDHA4 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 PCDHA4 gene promoter:
CUTL1 NF-AT Gfi-1 NF-AT4 NF-AT2 COMP1 NF-AT3 c-Myb NF-kappaB1 NF-AT1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: PCDHA4 promoter sequence

Search SABiosciences Chromatin IP Primers for PCDHA4

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHA4

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

PCDHA4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHA4 gene location

GeneLoc information about chromosome 5 GeneLoc Exon Structure

GeneLoc location for GC05P140186: view genomic region (about GC identifiers)

Start:	140,186,659 bp from pter	End:	140,391,929 bp from pter
Size:	205,271 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: PCDA4_HUMAN, Q9UN74 (See protein sequence)

Recommended Name: Protocadherin alpha-4 precursor

Size: 947 amino acids; 102293 Da

Subunit: Interacts with FYN (By similarity)

Subcellular location: Cell membrane; Single-pass type I membrane protein (By similarity)

Secondary accessions: O75285 Q2M253

Alternative splicing: 2 isoforms: Q9UN74-1 Q9UN74-2

Explore the universe of human proteins at neXtProt for PCDHA4: NX_Q9UN74

Explore proteomics data for PCDHA4 at MOPED

Post-translational modifications:

View modification sites using PhosphoSitePlus

View neXtProt modification sites for NX_Q9UN74

PCDHA4 Protein expression data from MOPED¹, PaxDb² and MAXQB³ : About this image

REFSEQ proteins (2 alternative transcripts):

NP_061730.1 NP_113688.1

ENSEMBL proteins:

ENSP00000423470 ENSP00000435300 ENSP00000349344

Human Recombinant Protein Products for PCDHA4:

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Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005886	plasma membrane	--	--
GO:0005887	integral to plasma membrane	TAS	10380929
GO:0016020	membrane	--	--
GO:0016021	integral to membrane	--	--

PCDHA4 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 Q9UN74

ProtoNet protein and cluster: Q9UN74

1 Blocks protein domain: IPB002126 Cadherin

UniProtKB/Swiss-Prot: PCDA4_HUMAN, Q9UN74

Similarity: Contains 6 cadherin domains

PCDHA4 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: PCDA4_HUMAN, Q9UN74

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 ID	Qualified GO term	Evidence	PubMed IDs
GO:0005509	calcium ion binding	IEA	--

PCDHA4 for ontologies About GeneDecksing

Animal Models:

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In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PCDHA4

(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

SuperPaths for PCDHA4 About

See pathways by source

SuperPath

Contained pathways About

Reelin Pathway (Cajal-Retzius cells)

Reelin Pathway (Cajal-Retzius cells)

1 Downloadable PowerPoint Slide of QIAGEN Pathway Central Maps for PCDHA4

Reelin Pathway (Cajal-Retzius cells)

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for PCDHA4

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

5/19 Interacting proteins for PCDHA4 (Q9UN74^{2, 3} ENSP00000349344⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 19)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
APLP1	P51693²^,³	MINT-65771 I2D: score=4
C14orf1	Q9UKR5²^,³	MINT-65780 I2D: score=4
CCDC90B	Q9GZT6²^,³	MINT-65777 I2D: score=4
GAPDH	P04406²^,³	MINT-65769 I2D: score=4
GDF9	O60383²^,³	MINT-65768 I2D: score=4

About this table

Gene Ontology (GO): 3 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007155	cell adhesion	TAS	10380929
GO:0007156	homophilic cell adhesion	IEA	--
GO:0007399	nervous system development	TAS	10380929

PCDHA4 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

Compounds for PCDHA4 available from Tocris Bioscience About this table

Compound	Action	CAS #
ACEA	Potent, highly selective CB1 agonist	[220556-69-4]
AM 251	Potent CB1 antagonist. Also GPR55 agonist	[183232-66-8]
SR 141716A	Selective CB1 receptor antagonist	[158681-13-1]
Tocrifluor T1117	Novel 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]

1 HMDB Compound for PCDHA4 About this table

Compound	Synonyms	CAS #	PubMed Ids
Calcium	Ca (see all 2)	7440-70-2	--

Search CenterWatch for drugs/clinical trials and news about PCDHA4 / PCDA4

(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,
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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 PCDHA4 gene (2 alternative transcripts):

NM_018907.3 NM_031500.2

3 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000512229 ENST00000530339(uc003lhh.1 uc003lhi.2) ENST00000356878(uc011daa.2)

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24/261 AceView cDNA sequences (see all 261):

AF152310 BM129562 AI268404 AF152305 F06310 AF152313 AF152477 AI419005

NM_031861 NM_031496 NM_018911 NM_018902 AF152304 BC003126 NM_031865 BI753524

AA552914 NM_018910 BM684041 AF152475 CB218096 AW470523 AF152478 BC033735

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

PCDHA4 expression in normal human tissues (normalized intensities) PCDHA4 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: --

About this image

PCDHA4 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database

5/1 selected tissues (see all 1) fully expand


Adipose (Muscoskeletal System)
Mesenchymal Stem Cells Subcutaneous White Adipose

See PCDHA4 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PCDHA4

SABiosciences Custom PCR Arrays for PCDHA4

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In Situ
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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 PCDHA4 gene from 4/10 species (see all 10) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Pcdha4^{1 , 5}	protocadherin alpha 4^{1, 5}	83.95(n)¹ 86.38(a)¹		18 (19.46 cM)⁵ 12936¹ NM_007766.2¹ NP_031792.1¹ 36952689⁵
chicken (Gallus gallus)	Aves	PCDHA11⁶ --	--	54(a) 47(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 5 unspliced isoform; Uncharact... (see all 16)	57(a) 57(a) (see all 16)	many ↔ many many ↔ many (see all 16)	4(77317799-77320222) 4(77380556-77382976)
zebrafish (Danio rerio)	Actinopterygii	CR847851.2⁶ pcdh2ab5⁶ (see all 35)	protocadherin 2 alpha b 5 (see all 35)	44(a) 42(a) (see all 35)	many ↔ many many ↔ many (see all 35)	14(2425668-2426945) 14(2507189-2509570)

ENSEMBL Gene Tree for PCDHA4 (if available)
TreeFam Gene Tree for PCDHA4 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for PCDHA4 gene

PCDH7² PCDH20² PCDH1² PCDHA12² PCDH11Y² PCDH12² PCDHA11² PCDHA1²

PCDH18² PCDH9² PCDH19² PCDH8² PCDH17² PCDHGB3² PCDHA7² PCDHGB6²

PCDH11X² PCDHA6² PCDH10² PCDHA10² PCDHA13² PCDHA9² PCDHA3²

18/70 SIMAP similar genes for PCDHA4 using alignment to 2 protein entries: PCDA4_HUMAN (see all proteins) (see all similar genes):

PCDHA2 PCDHA7 PCDHA9 PCDHA3 PCDHA1 PCDHA6

PCDHA11 PCDHA5 PCDHA13 PCDHA8 PCDHA10 PCDHA12

ME6 ME1 ME4 PCDHAC2 PCDHB13 PCDHB17

PCDHA4 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

SNP ID	Valid	Clinical significance	Chr 5 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
VAR_024390⁴		--	--	see VAR_024390	2	P S	mis⁴		0	--	--	--	--
VAR_059180⁴		--	--	see VAR_059180	2	E D	mis⁴		0	--	--	--	--
rs11459112^1,2	C	--	140186225(+)	`GGGTGA/-AAGAG`	1	--	us2k¹		1		NA	2

HapMap Linkage Disequilibrium report for PCDHA4 (140186659 - 140391929 bp)

Structural Variations
Database of Genomic Variants (DGV) 10/48 variations for PCDHA4 (see all 48): About this table

Variant ID	Type	Subtype	PubMed ID
esv2657537	CNV	Deletion	23128226
nsv820841	CNV	Deletion	20802225
esv2659321	CNV	Deletion	23128226
dgv1044e199	CNV	Deletion	23128226
esv2505753	CNV	Deletion	19546169
esv2730838	CNV	Deletion	23290073
esv2730839	CNV	Deletion	23290073
esv2421858	CNV	Deletion	20811451
dgv1043e199	CNV	Deletion	23128226
nsv436885	CNV	Insertion	17901297

SABiosciences Cancer Mutation PCR Assays

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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: 606310 OMIM disorders: --

2 diseases for PCDHA4: About MalaCards

neuronitis

PCDHA4 for disorders About GeneDecksing

Genetic Association Database (GAD): PCDHA4

Export disorders for PCDHA4 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 PCDHA4 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with PCDHA4)

Utopia: connect your pdf to the dynamic
world of online information

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)
The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)^{1, 2} Schmutz J.... Rubin E.M. (2004)
Genomic organization of the family of CNR cadherin genes in mice and humans. (PubMed id 10662547)^{1, 3} Sugino H....Yagi T. (2000)
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)
A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)¹ Stelzl U.... Wanker E.E. (2005)
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. (2004)
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)
Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PubMed id 11230163)¹ Wu Q.... Maniatis T. (2001)
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)
Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PubMed id 10716726)¹ Wu Q. and Maniatis T. (2000)

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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 56144	HGNC: 8670	AceView: PCDHA9	Ensembl:ENSG00000204967	euGenes: HUgn56144
ECgene: PCDHA4	H-InvDB: PCDHA4

(According to HUGE)
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HUGE: KIAA0345-like 10" KIAA0345-like 10

(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

Name	Description
PharmGKB entry for PCDHA4	Pharmacogenomics, SNPs, Pathways

Intellectual Property for PCDHA4 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for PCDHA4 gene:
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GeneCards and IP:
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Protocadherin Alpha 4

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