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PCDHB3 Gene(Protein Coding)

Protocadherin Beta 3

GCID:
GC05P141806
GIFtS:
50
Genes Participants
UDN Logo

Aliases for PCDHB3 Gene

Aliases for PCDHB3 Gene

  • Protocadherin Beta 3 2 3 5
  • Protocadherin Beta-3 3
  • PCDH-Beta-3 4
  • PCDH-BETA3 3

External Ids for PCDHB3 Gene

Previous GeneCards Identifiers for PCDHB3 Gene

  • GC05P140296
  • GC05P141063
  • GC05P140463
  • GC05P140508
  • GC05P140460
  • GC05P135624
  • GC05P140480
  • GC05P141277
  • GC05P141497
  • GC05P141604
  • GC05P141707

Summaries for PCDHB3 Gene

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. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB2.

UniProtKB/Swiss-Prot for PCDHB3 Gene

  • 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB3 Gene

Genomics for PCDHB3 Gene

Products:

  1. Regulatory Element

Regulatory Elements for PCDHB3 Gene

Enhancers for PCDHB3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05F141968 1.2 ENCODE 15.4 +869.3 869325 3.0 HDGF PKNOX1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 PCDHB5 KIAA0141 HDAC3 PCDHGA5 PCDHB12 RNF14 PCDHB11 PCDHB4 PCDHB19P PCDHB18P
GH05F141084 1.3 FANTOM5 Ensembl ENCODE 12 -15.4 -15424 1.6 CTCF PKNOX1 SAP130 RAD21 YY1 E2F1 ZNF23 GATA3 POLR2A ZNF143 PCDHB1 PCDHB3 PCDHB10 PCDHB9 PCDHB2 ENSG00000272154 PCDHB14 PCDHB18P PCDHGB6 PCDHB7
GH05F141940 1.4 Ensembl ENCODE 10 +842.0 842028 2.9 PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 CBX5 PCDH1 PCDHGB4 PCDHB17P PCDHB11 PCDHB13 PCDH12 PCDHGB3 PCDHB12 PCDHB7 PCDHGB6
GH05F141563 1.3 Ensembl ENCODE 10 +464.2 464171 1.4 PKNOX1 ATF1 ARNT SIN3A DMAP1 BRCA1 ZNF2 YY1 CBX5 ZNF143 PCDHGB4 PCDHB11 PCDHB13 PCDHGB3 PCDHB12 PCDHB7 PCDHGB6 PCDHGA7 PCDHB18P PCDHGA8
GH05F141319 1.2 ENCODE 10 +220.4 220408 1.9 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 PCDHB15 FCHSD1 MRPL11P2 VTRNA1-1 PCDHGB4 PCDHB11 PCDHB13 HDAC3 PCDHGB3 PCDHB12
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDHB3 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHB3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001874425 558 800 CTCF ZNF654 MAX RAD21 JUND GATA3 POLR2A SMC3 CUX1

Transcription factor binding sites by QIAGEN in the PCDHB3 gene promoter:

Genomic Location for PCDHB3 Gene

Chromosome:
5
Start:
141,100,242 bp from pter
End:
141,103,827 bp from pter
Size:
3,586 bases
Orientation:
Plus strand

Genomic View for PCDHB3 Gene

Genes around PCDHB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PCDHB3 Gene

Proteins for PCDHB3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for PCDHB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5E6-PCDB3_HUMAN
    Recommended name:
    Protocadherin beta-3
    Protein Accession:
    Q9Y5E6
    Secondary Accessions:
    • B2R8P2

    Protein attributes for PCDHB3 Gene

    Size:
    796 amino acids
    Molecular mass:
    86773 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB3 Gene

Protein Expression for PCDHB3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PCDHB3 Gene

  • Glycosylation at Asn 169, Asn 418, Asn 436, and Asn 567
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB3 Gene

Domains & Families for PCDHB3 Gene

Gene Families for PCDHB3 Gene

HGNC:

Protein Domains for PCDHB3 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PCDHB3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y5E6

UniProtKB/Swiss-Prot:

PCDB3_HUMAN :
  • Contains 6 cadherin domains.
Domain:
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHB3: view

Function for PCDHB3 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for PCDHB3 Gene

UniProtKB/Swiss-Prot 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) - Molecular Function for PCDHB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB3: view
genes like me logo Genes that share phenotypes with PCDHB3: view

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHB3 Gene

Localization for PCDHB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB3 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PCDHB3 gene
Compartment Confidence
plasma membrane 5
extracellular 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PCDHB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS 10380929
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 11322959
genes like me logo Genes that share ontologies with PCDHB3: view

Pathways & Interactions for PCDHB3 Gene

SuperPathways for PCDHB3 Gene

PathCards logo More details on SuperPathways for PCDHB3
No Data Available

Interacting Proteins for PCDHB3 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 6)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000231130%0d%0a9606.ENSP00000344818%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000344456%0d%0a9606.ENSP00000311113%0d%0a
Selected Interacting proteins: ENSP00000231130 Q9Y5E6-PCDB3_HUMAN for PCDHB3 Gene via STRING IID

Gene Ontology (GO) - Biological Process for PCDHB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 10380929
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007268 chemical synaptic transmission TAS 12231349
GO:0007399 nervous system development TAS 10380929
GO:0007416 synapse assembly TAS 12231349
genes like me logo Genes that share ontologies with PCDHB3: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB3 Gene

Drugs & Compounds for PCDHB3 Gene

Products:

  1. Drug

(1) Drugs for PCDHB3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with PCDHB3: view

Transcripts for PCDHB3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for PCDHB3 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(10) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCDHB3 Gene

Protocadherin beta 3:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB3 Gene

No ASD Table

Relevant External Links for PCDHB3 Gene

GeneLoc Exon Structure for
PCDHB3
ECgene alternative splicing isoforms for
PCDHB3

Expression for PCDHB3 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHB3 Gene

mRNA expression in normal human tissues for PCDHB3 Gene
mRNA expression by BioGPS for PCDHB3 GenemRNA expression by GTEx for PCDHB3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDHB3 Gene

This gene is overexpressed in Blymphocyte (26.9), Frontal cortex (14.0), Fetal gut (11.1), and Retina (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHB3 Gene



NURSA nuclear receptor signaling pathways regulating expression of PCDHB3 Gene:

PCDHB3

SOURCE GeneReport for Unigene cluster for PCDHB3 Gene:

Hs.674730
genes like me logo Genes that share expression patterns with PCDHB3: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for PCDHB3 Gene

Orthologs for PCDHB3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHB3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PCDHB3 34 35
  • 98.79 (n)
dog
(Canis familiaris)
 Mammalia LOC487168 34
  • 86.15 (n)
rat
(Rattus norvegicus)
 Mammalia Pcdhb3 34
  • 80.54 (n)
mouse
(Mus musculus)
 Mammalia Pcdhb3 34 16 35
  • 80.28 (n)
cow
(Bos Taurus)
 Mammalia LOC786512 34
  • 75.04 (n)
oppossum
(Monodelphis domestica)
 Mammalia -- 35
  • 66 (a)
 ManyToMany
-- 35
  • 66 (a)
 ManyToMany
-- 35
  • 66 (a)
 ManyToMany
-- 35
  • 66 (a)
 ManyToMany
-- 35
  • 65 (a)
 ManyToMany
-- 35
  • 65 (a)
 ManyToMany
-- 35
  • 64 (a)
 ManyToMany
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 35
  • 64 (a)
 ManyToMany
-- 35
  • 63 (a)
 ManyToMany
-- 35
  • 63 (a)
 ManyToMany
chicken
(Gallus gallus)
 Aves LOC100857544 34
  • 58.8 (n)
zebrafish
(Danio rerio)
 Actinopterygii pcdh2g17 34
  • 52.45 (n)
Species where no ortholog for PCDHB3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDHB3 Gene

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

Paralogs for PCDHB3 Gene

Paralogs for PCDHB3 Gene

(72) SIMAP similar genes for PCDHB3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with PCDHB3: view

Variants for PCDHB3 Gene

Sequence variations from dbSNP and Humsavar for PCDHB3 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs10463345 -- 141,103,456(+) CATTA(C/T)AAAGC utr-variant-3-prime
rs1055410 -- 141,100,595(-) GACAG(A/C)GCTGG utr-variant-5-prime
rs1055411 -- 141,100,523(-) TCAGA(C/G)TTGCT utr-variant-5-prime
rs111229803 -- 141,101,074(+) GAAAA(C/T)CCTAG reference, missense
rs111445581 -- 141,099,737(+) ACTGT(G/T)TAAAC upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for PCDHB3 Gene

Variant ID Type Subtype PubMed ID
esv2759382 CNV gain 17122850
esv3606961 CNV loss 21293372
nsv428127 CNV loss 18775914
nsv516514 CNV gain 19592680
nsv522785 CNV loss 19592680
nsv599905 CNV gain 21841781
nsv599906 CNV loss 21841781
nsv599907 CNV loss 21841781
nsv968254 CNV duplication 23825009

Variation tolerance for PCDHB3 Gene

Residual Variation Intolerance Score: 79.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.47; 82.07% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHB3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB3 Gene

Disorders for PCDHB3 Gene

Relevant External Links for PCDHB3

Genetic Association Database (GAD)
PCDHB3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHB3

No disorders were found for PCDHB3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB3 Gene

Publications for PCDHB3 Gene

  1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PMID: 10380929) Wu Q. … Maniatis T. (Cell 1999) 2 3 4 64
  2. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PMID: 11322959) Vanhalst K. … van Roy F. (FEBS Lett. 2001) 3 4 64
  3. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 4 64
  5. Protocadherins. (PMID: 12231349) Frank M. … Kemler R. (Curr. Opin. Cell Biol. 2002) 3 64

Products for PCDHB3 Gene

Sources for PCDHB3 Gene

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