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Aliases for PCDHGB3 Gene

Aliases for PCDHGB3 Gene

  • Protocadherin Gamma Subfamily B, 3 2 3 5
  • PCDH-GAMMA-B3 3 4
  • Protocadherin Gamma-B3 3

External Ids for PCDHGB3 Gene

Previous GeneCards Identifiers for PCDHGB3 Gene

  • GC05P140566
  • GC05P141307
  • GC05P140711
  • GC05P140778
  • GC05P140730
  • GC05P141050
  • GC05P141079
  • GC05P135895
  • GC05P141117
  • GC05P141132
  • GC05P141178
  • GC05P141209
  • GC05P141248
  • GC05P141296
  • GC05P141373
  • GC05P141443
  • GC05P141519
  • GC05P141625
  • GC05P141727

Summaries for PCDHGB3 Gene

Entrez Gene Summary for PCDHGB3 Gene

  • This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell 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 gamma cluster genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHGB3 Gene

PCDHGB3 (Protocadherin Gamma Subfamily B, 3) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB2.

UniProtKB/Swiss-Prot for PCDHGB3 Gene

  • Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGB3 Gene

Genomics for PCDHGB3 Gene

Regulatory Elements for PCDHGB3 Gene

Enhancers for PCDHGB3 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 0.5 ENCODE 17 +599.3 599303 3.0 HDGF PKNOX1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 PCDHB5 KIAA0141 HDAC3 PCDHGA5 PCDHB12 RNF14 PCDHB11 PCDHB4 PCDHB19P PCDHB18P
GH05F141319 0.4 ENCODE 11.5 -49.6 -49615 1.9 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 PCDHB15 FCHSD1 MRPL11P2 VTRNA1-1 PCDHGB4 PCDHB11 PCDHB13 HDAC3 PCDHGB3 PCDHB12
GH05F141563 1.2 Ensembl ENCODE 11.4 +194.1 194149 1.4 PKNOX1 ATF1 ARNT SIN3A DMAP1 BRCA1 ZNF2 YY1 CBX5 ZNF143 PCDHGB4 PCDHB11 PCDHB13 PCDHGB3 PCDHB12 PCDHB7 PCDHGB6 PCDHGA7 PCDHB18P PCDHGA8
GH05F141922 0.8 ENCODE 11.3 +553.5 553505 2.1 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 PCDHGB4 PCDHB11 PCDHB13 PCDHGB3 PCDHB12 PCDHB7 PCDHGB6 PCDHGA7 PCDHB18P PCDHGA8
GH05F141940 0.8 Ensembl ENCODE 11.3 +572.0 572006 2.9 PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 CBX5 PCDH1 PCDHGB4 PCDHB17P PCDHB11 PCDHB13 PCDH12 PCDHGB3 PCDHB12 PCDHB7 PCDHGB6
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PCDHGB3 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHGB3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001874447 37 999 CTCF SMC3 ZSCAN29 RAD21

Genomic Location for PCDHGB3 Gene

Chromosome:
5
Start:
141,370,264 bp from pter
End:
141,512,979 bp from pter
Size:
142,716 bases
Orientation:
Plus strand

Genomic View for PCDHGB3 Gene

Genes around PCDHGB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGB3 Gene

Proteins for PCDHGB3 Gene

  • Protein details for PCDHGB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5G1-PCDGF_HUMAN
    Recommended name:
    Protocadherin gamma-B3
    Protein Accession:
    Q9Y5G1
    Secondary Accessions:
    • A7E229
    • Q9Y5C7

    Protein attributes for PCDHGB3 Gene

    Size:
    929 amino acids
    Molecular mass:
    101232 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PCDHGB3 Gene

    Alternative splice isoforms for PCDHGB3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB3 Gene

Post-translational modifications for PCDHGB3 Gene

  • Glycosylation at Asn 136, Asn 419, and Asn 545
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGB3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB3 Gene

Domains & Families for PCDHGB3 Gene

Gene Families for PCDHGB3 Gene

Protein Domains for PCDHGB3 Gene

Suggested Antigen Peptide Sequences for PCDHGB3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y5G1

UniProtKB/Swiss-Prot:

PCDGF_HUMAN :
  • Contains 6 cadherin domains.
Domain:
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHGB3: view

Function for PCDHGB3 Gene

Molecular function for PCDHGB3 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 PCDHGB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGB3: view
genes like me logo Genes that share phenotypes with PCDHGB3: 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 PCDHGB3 Gene

Localization for PCDHGB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB3 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDHGB3 Gene COMPARTMENTS Subcellular localization image for PCDHGB3 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PCDHGB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHGB3: view

Pathways & Interactions for PCDHGB3 Gene

SuperPathways for PCDHGB3 Gene

No Data Available

Interacting Proteins for PCDHGB3 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 7)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000461862%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000344456%0d%0a9606.ENSP00000311113%0d%0a9606.ENSP00000362481%0d%0a
Selected Interacting proteins: ENSP00000461862 Q9Y5G1-PCDGF_HUMAN for PCDHGB3 Gene via STRING IID

Gene Ontology (GO) - Biological Process for PCDHGB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,IBA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development IBA --
genes like me logo Genes that share ontologies with PCDHGB3: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB3 Gene

Drugs & Compounds for PCDHGB3 Gene

(1) Drugs for PCDHGB3 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 PCDHGB3: view

Transcripts for PCDHGB3 Gene

mRNA/cDNA for PCDHGB3 Gene

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB3 Gene

No ASD Table

Relevant External Links for PCDHGB3 Gene

GeneLoc Exon Structure for
PCDHGB3
ECgene alternative splicing isoforms for
PCDHGB3

Expression for PCDHGB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHGB3 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHGB3 Gene



Protein tissue co-expression partners for PCDHGB3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGB3 Gene:

PCDHGB3
genes like me logo Genes that share expression patterns with PCDHGB3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PCDHGB3 Gene

Orthologs for PCDHGB3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGB3 Gene

Organism Taxonomy Gene Similarity Type Details
rat
(Rattus norvegicus)
Mammalia Pcdhgb8 34
  • 71.76 (n)
mouse
(Mus musculus)
Mammalia Pcdhgb8 34 16
  • 71.37 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 63 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 54 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 57 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 54 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 35
  • 35 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 52 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 48 (a)
ManyToMany
-- 35
  • 48 (a)
ManyToMany
Species where no ortholog for PCDHGB3 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)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • 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)
  • 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)
  • zebrafish (Danio rerio)

Evolution for PCDHGB3 Gene

ENSEMBL:
Gene Tree for PCDHGB3 (if available)
TreeFam:
Gene Tree for PCDHGB3 (if available)

Paralogs for PCDHGB3 Gene

Variants for PCDHGB3 Gene

Sequence variations from dbSNP and Humsavar for PCDHGB3 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs386352347 Uncertain significance 141,485,635(+) CCGTT(A/G)GAAAA intron-variant, reference, synonymous-codon
rs1002519 -- 141,489,436(-) GCCCA(A/G)TTGCA intron-variant, reference, synonymous-codon
rs10035418 -- 141,437,664(+) CGAAG(A/G)GATGT intron-variant
rs10038103 -- 141,414,849(+) CTGGA(C/T)CAGAA intron-variant, reference, synonymous-codon
rs10040701 -- 141,508,490(+) TTTCC(A/G)TATCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGB3 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv3422812 CNV insertion 20981092
esv3606984 CNV loss 21293372
esv3606985 CNV gain 21293372
esv3606987 CNV gain 21293372
nsv1123990 CNV deletion 24896259
nsv1125852 CNV tandem duplication 24896259
nsv327707 CNV deletion 16902084
nsv462470 CNV loss 19166990
nsv518799 CNV loss 19592680
nsv519627 CNV loss 19592680
nsv599922 CNV loss 21841781
nsv599923 CNV loss 21841781
nsv823279 CNV gain 20364138
nsv823280 CNV loss 20364138
nsv968259 CNV duplication 23825009
nsv980740 CNV duplication 23825009

Variation tolerance for PCDHGB3 Gene

Residual Variation Intolerance Score: 82.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.71; 66.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHGB3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGB3 Gene

Disorders for PCDHGB3 Gene

Relevant External Links for PCDHGB3

Genetic Association Database (GAD)
PCDHGB3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHGB3

No disorders were found for PCDHGB3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGB3 Gene

Publications for PCDHGB3 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 DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J. … Rubin E.M. (Nature 2004) 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 4 64
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3 64
  5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 3 64

Products for PCDHGB3 Gene

Sources for PCDHGB3 Gene

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