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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

PCDHB3 Gene

protein-coding GIFtS: 47
GCID: GC05P140480

Protocadherin Beta 3

1 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 Beta 3¹ ²
PCDH-BETA3²
Protocadherin Beta-3²
PCDH-beta-3³

External Ids:	HGNC: 8688¹	Entrez Gene: 56132²	Ensembl: ENSG00000113205⁷	OMIM: 606329⁵	UniProtKB: Q9Y5E6³

Export aliases for PCDHB3 gene to outside databases

Previous GC identifers: GC05P140296 GC05P141063 GC05P140463 GC05P140508 GC05P140460 GC05P135624

(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 PCDHB3 Gene:

This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on

chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell

receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin

domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains

interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters,

the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These

neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are

unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural

connections. (provided by RefSeq, Jul 2008)

GeneCards Summary for PCDHB3 Gene:

PCDHB3 (protocadherin beta 3) is a protein-coding gene. Diseases associated with PCDHB3 include neuronitis. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHAC1.

UniProtKB/Swiss-Prot: PCDB3_HUMAN, Q9Y5E6

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 PCDHB3 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

RefSeq DNA sequence:

NC_000005.9 NC_018916.2 NT_029289.11

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the PCDHB3 gene promoter:
Pax-3 AML1a ATF-2 Sox9 CUTL1 c-Jun Tal-1beta C/EBPalpha
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: PCDHB3 promoter sequence

Search SABiosciences Chromatin IP Primers for PCDHB3

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PCDHB3

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

PCDHB3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PCDHB3 gene location

GeneLoc information about chromosome 5 GeneLoc Exon Structure

GeneLoc location for GC05P140480: view genomic region (about GC identifiers)

Start:	140,480,234 bp from pter	End:	140,483,406 bp from pter
Size:	3,173 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: PCDB3_HUMAN, Q9Y5E6 (See protein sequence)

Recommended Name: Protocadherin beta-3 precursor

Size: 796 amino acids; 86773 Da

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

Secondary accessions: B2R8P2

Explore the universe of human proteins at neXtProt for PCDHB3: NX_Q9Y5E6

Explore proteomics data for PCDHB3 at MOPED

Post-translational modifications:

View modification sites using PhosphoSitePlus

View neXtProt modification sites for NX_Q9Y5E6

PCDHB3 Protein expression data from MOPED¹, PaxDb² and MAXQB³ : About this image

REFSEQ proteins: NP_061760.1

ENSEMBL proteins:

ENSP00000231130

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005887	integral to plasma membrane	TAS	10380929
GO:0016020	membrane	--	--
GO:0016021	integral to membrane	NAS	11322959

PCDHB3 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 Q9Y5E6

ProtoNet protein and cluster: Q9Y5E6

1 Blocks protein domain: IPB002126 Cadherin

UniProtKB/Swiss-Prot: PCDB3_HUMAN, Q9Y5E6

Similarity: Contains 6 cadherin domains

PCDHB3 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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, 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, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, 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: PCDB3_HUMAN, Q9Y5E6

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	--

PCDHB3 for ontologies About GeneDecksing

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In Situ Assay
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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 Central^TM Interacting Genes and Proteins Networks for PCDHB3

Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007155	cell adhesion	TAS	10380929
GO:0007156	homophilic cell adhesion	IEA	--
GO:0007268	synaptic transmission	TAS	12231349
GO:0007399	nervous system development	TAS	10380929
GO:0007416	synapse assembly	TAS	12231349

PCDHB3 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, IUPHAR, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

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Browse Tocris compounds for PCDHB3 (PCDB3)

1 HMDB Compound for PCDHB3 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 PCDHB3 / PCDB3

(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,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for PCDHB3 gene:

NM_018937.3

Unigene Cluster for PCDHB3:

Protocadherin beta 3

Hs.674730 [show with all ESTs]

Unigene Representative Sequence: NM_018937

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000231130(uc003lio.3)

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Additional mRNA sequence:

AF152496.1 AF217755.1 AK313451.1 BC104817.1

1 DOTS entry:

DT.86852486

10 AceView cDNA sequences:

AF217755 NM_018937 AF152496 BF477839 BF477537 AW452497 AW302546 BV198750

BQ306284 AI905980

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

PCDHB3 expression in normal human tissues (normalized intensities) PCDHB3 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>^2/3
CGAP TAG: ATGACTGAGG

About this image

PCDHB3 expression in embryonic tissues and stem cells About this table

Data from LifeMap, the Embryonic Development and Stem Cells Database

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


Brain (Nervous System) fully expand to see all 5 entries
ganglion/cranial/facial VII

Eye (Sensory Organs) fully expand to see all 2 entries
Retina
Human corneal endothelial cells

Peripheral Nervous System (Nervous System)
spinal/ganglion/dorsal root ganglion

Endothelium (Cardiovascular System)
Human corneal endothelial cells

Spinal Cord (Nervous System)
spinal/ganglion/dorsal root ganglion

See PCDHB3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for PCDHB3

SOURCE GeneReport for Unigene cluster: Hs.674730

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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 human and mouse.

Orthologs for PCDHB3 gene from 1/7 species (see all 7) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Pcdhb3^{1 , 5}	protocadherin beta 3^{1, 5}	80.58(n)¹ 79.26(a)¹		18 (19.46 cM)⁵ 93874¹ NM_053128.2¹ NP_444358.2¹ 37300799⁵

ENSEMBL Gene Tree for PCDHB3 (if available)
TreeFam Gene Tree for PCDHB3 (if available)

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

Paralogs for PCDHB3 gene

PCDHAC1² PCDHB16² PCDHB2² PCDHAC2² PCDHB7² PCDHB15² PCDHGA10² PCDHGA12²

PCDHGB2² PCDHGA9² PCDHGA8² PCDHGC3² PCDHGA5² PCDHA8² PCDHB5² PCDHB13²

PCDHGA4² PCDHGA7² PCDHB4² PCDHB11² PCDHA2² ENSG00000255622² PCDHB14² PCDHB12²

PCDHB8² PCDHGB1² PCDHGB4² PCDHA5² PCDHGA2² PCDHGA6² PCDHGA11² PCDHB6²

PCDHGC4² PCDHGC5² PCDHGA1² PCDHB10² PCDHB1² PCDHGB7² PCDHGA3²

18/72 SIMAP similar genes for PCDHB3 using alignment to 2 protein entries: PCDB3_HUMAN (see all proteins) (see all similar genes):

ME1 PCDHB16 PCDHB11 PCDHB13 PCDHB14 PCDHB15

PCDHB2 PCDHB8 PCDHB12 DKFZp586I1919 ME4 PCDHB18

PCDHB4 PCDHB6 PCDHB5 PCDHB10 PCDHB17 PCDHB7

PCDHB3 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
				--	--	--		--	--
rs186686639^1,2		--	140478260(+)	`ATATTG/TAAATA`	1	--	us2k¹		0	--	--	--	--
rs189606584^1,2		--	140478392(+)	`TTGTCA/GCTTTC`	1	--	us2k¹		0	--	--	--	--
rs148190621^1,2	C	--	140478806(+)	`CAAATA/GATAGC`	1	--	us2k¹		0	--	--	--	--
rs183332548^1,2		--	140478981(+)	`AACAAA/CCTTGC`	1	--	us2k¹		0	--	--	--	--
rs187706521^1,2		--	140478991(+)	`CAATGA/GCTTCC`	1	--	us2k¹		0	--	--	--	--
rs144271353^1,2	C	--	140479009(+)	`CTTAG-/AATAATAA`	1	--	us2k¹		0	--	--	--	--
rs36113538^1,2	C	--	140479016(+)	`AATAATAA/-AATCC`	2	--	us2k¹ cds¹		1		NA	2
rs31851^1,2	C,F,A,H	--	140479105(-)	`TGAAGG/TACAGT`	1	--	us2k¹ tfbs³		22		MN NS EA NA WA CSA	2420
rs13183611^1,2	C,F,A,H	--	140479121(+)	`TATCTA/CTTAAT`	1	--	us2k¹ tfbs³		7		NS EA NA	612
rs116021130^1,2	C,F	--	140479219(+)	`TGCACC/GTTGGG`	1	--	us2k¹		1		NA	120

HapMap Linkage Disequilibrium report for PCDHB3 (140480234 - 140483406 bp)

Structural Variations
Database of Genomic Variants (DGV) 6 variations for PCDHB3: About this table

Variant ID	Type	Subtype	PubMed ID
dgv6348n71	CNV	Loss	21882294
nsv522785	CNV	Loss	19592680
nsv428127	CNV	Loss	18775914
nsv882971	CNV	Loss	21882294
nsv516514	CNV	Gain	19592680
dgv1857e1	CNV	Complex	17122850

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

PCDHB3 for disorders           About GeneDecksing

OMIM gene information: 606329    OMIM disorders: --

2 diseases for PCDHB3:    About MalaCards

neuronitis

Genetic Association Database (GAD): PCDHB3

Export disorders for PCDHB3 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 PCDHB3 gene integrated from 9 sources:
(articles sorted by number of sources associating them with PCDHB3)

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 human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PubMed id 11322959)^{1, 2} Vanhalst K.... van Roy F. (2001)
Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)¹ Povlsen L.K....Choudhary C. (2012)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)² Ota T.... Sugano S. (2004)
Protocadherins. (PubMed id 12231349)¹ Frank M. and Kemler R. (2002)
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)
Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PubMed id 10817752)¹ Yagi T. and Takeichi M. (2000)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
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)
About This Section

Entrez Gene: 56132	HGNC: 8688	AceView: PCDHB3	Ensembl:ENSG00000113205	euGenes: HUgn56132
ECgene: PCDHB3	H-InvDB: PCDHB3

(According to HUGE)
About This Section

(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 PCDHB3	Pharmacogenomics, SNPs, Pathways

Intellectual Property for PCDHB3 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 PCDHB3 gene:
Search GeneIP for patents involving PCDHB3

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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, LifeMap BioReagents, and Sirion Biotech, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory)
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013

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PCDHB3 Gene

Protocadherin Beta 3

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PCDHB3 Gene

Protocadherin Beta 3

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