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Aliases for PCDHB15 Gene

Aliases for PCDHB15 Gene

  • Protocadherin Beta 15 2 3 5
  • Protocadherin Beta-15 3
  • PCDH-Beta-15 4
  • PCDH-BETA15 3

External Ids for PCDHB15 Gene

Previous GeneCards Identifiers for PCDHB15 Gene

  • GC05P140441
  • GC05P141208
  • GC05P140608
  • GC05P140653
  • GC05P140611
  • GC05P140613
  • GC05P140617
  • GC05P140620
  • GC05P140626
  • GC05P140630
  • GC05P140634
  • GC05P140637
  • GC05P140640
  • GC05P140644
  • GC05P140648
  • GC05P140651
  • GC05P140658
  • GC05P140664
  • GC05P135770
  • GC05P140669
  • GC05P140674
  • GC05P140679
  • GC05P140685
  • GC05P140695
  • GC05P141278
  • GC05P141369
  • GC05P141422
  • GC05P141507
  • GC05P141613
  • GC05P141716
  • GC05P141815
  • GC05P141914
  • GC05P142022
  • GC05P142127

Summaries for PCDHB15 Gene

Entrez Gene Summary for PCDHB15 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 PCDHB15 Gene

PCDHB15 (Protocadherin Beta 15) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA6.

UniProtKB/Swiss-Prot for PCDHB15 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 PCDHB15 Gene

Additional gene information for PCDHB15 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB15 Gene

Genomics for PCDHB15 Gene

GeneHancer (GH) Regulatory Elements for PCDHB15 Gene

Promoters and enhancers for PCDHB15 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J141244 Promoter/Enhancer 1.1 Ensembl ENCODE 650.7 -0.1 -52 1 CTCF ZNF654 REST CEBPG RAD21 ATF2 ATF4 ZBTB17 ENSG00000280029 PCDHB15 PCDHB19P ENSG00000279983 PCDHB@
GH05J142221 Enhancer 1.4 Ensembl ENCODE dbSUPER 28.4 +977.3 977305 3.3 FOXA2 SMAD1 FEZF1 ZNF2 ZNF213 ZNF143 FOS SP3 JUNB REST PCDHB18P PCDHGA7 PCDHGA6 PCDHB15 PCDHGB3 PCDHB19P PCDHGB4 PCDHGA8 PCDHGB8P PCDHGA5
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 18.9 +724.2 724218 3 CLOCK DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC GLIS1 RNF14 PCDH12 LOC102723915 HDAC3 PCDHB18P PCDHGA6 PCDHGA7 DELE1 PCDHGA5 ENSG00000271871
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 21.4 -526.2 -526213 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
GH05J141319 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 15.2 +75.3 75301 1.9 PKNOX1 SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 POLR2B ZNF213 TAF7 ANKHD1 WDR55 LOC102723915 FCHSD1 HDAC3 TMCO6 PCDHB15 VTRNA1-1 MRPL11P2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHB15 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHB15 gene promoter:
  • Ik-2
  • YY1
  • Nkx2-5
  • LUN-1
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • POU3F2
  • PPAR-alpha
  • NRSF form 2
  • NRSF form 1

Genomic Locations for PCDHB15 Gene

Genomic Locations for PCDHB15 Gene
chr5:141,245,349-141,249,365
(GRCh38/hg38)
Size:
4,017 bases
Orientation:
Plus strand
chr5:140,625,147-140,627,802
(GRCh37/hg19)
Size:
2,656 bases
Orientation:
Plus strand

Genomic View for PCDHB15 Gene

Genes around PCDHB15 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB15 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB15 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB15 Gene

Proteins for PCDHB15 Gene

  • Protein details for PCDHB15 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5E8-PCDBF_HUMAN
    Recommended name:
    Protocadherin beta-15
    Protein Accession:
    Q9Y5E8
    Secondary Accessions:
    • Q8IUX5

    Protein attributes for PCDHB15 Gene

    Size:
    787 amino acids
    Molecular mass:
    86329 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB15 Gene

Post-translational modifications for PCDHB15 Gene

  • Glycosylation at isoforms=567 and Asn418
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB15 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB15 Gene

Domains & Families for PCDHB15 Gene

Gene Families for PCDHB15 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PCDHB15 Gene

Suggested Antigen Peptide Sequences for PCDHB15 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHB15: view

No data available for UniProtKB/Swiss-Prot for PCDHB15 Gene

Function for PCDHB15 Gene

Molecular function for PCDHB15 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.

Phenotypes From GWAS Catalog for PCDHB15 Gene

Gene Ontology (GO) - Molecular Function for PCDHB15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB15: view
genes like me logo Genes that share phenotypes with PCDHB15: view

Animal Model Products

miRNA for PCDHB15 Gene

miRTarBase miRNAs that target PCDHB15

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHB15 Gene

Localization for PCDHB15 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB15 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 PCDHB15 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PCDHB15 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 IEA --
genes like me logo Genes that share ontologies with PCDHB15: view

Pathways & Interactions for PCDHB15 Gene

SuperPathways for PCDHB15 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHB15 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS,IEA 10380929
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007268 chemical synaptic transmission IBA --
GO:0007399 nervous system development TAS 10380929
genes like me logo Genes that share ontologies with PCDHB15: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB15 Gene

Drugs & Compounds for PCDHB15 Gene

(1) Drugs for PCDHB15 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with PCDHB15: view

Transcripts for PCDHB15 Gene

mRNA/cDNA for PCDHB15 Gene

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

Unigene Clusters for PCDHB15 Gene

Protocadherin beta 15:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB15 Gene

No ASD Table

Relevant External Links for PCDHB15 Gene

GeneLoc Exon Structure for
PCDHB15
ECgene alternative splicing isoforms for
PCDHB15

Expression for PCDHB15 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHB15 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDHB15 Gene

This gene is overexpressed in Plasma (66.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHB15 Gene



Protein tissue co-expression partners for PCDHB15 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHB15 Gene:

PCDHB15

SOURCE GeneReport for Unigene cluster for PCDHB15 Gene:

Hs.130757

Evidence on tissue expression from TISSUES for PCDHB15 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with PCDHB15: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHB15 Gene

Orthologs for PCDHB15 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHB15 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHB15 34 33
  • 98.48 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PCDHB15 34 33
  • 85.97 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PCDHB15 34 33
  • 85.84 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdhb22 16 34 33
  • 80.54 (n)
rat
(Rattus norvegicus)
Mammalia Pcdhb22 33
  • 80.24 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 66 (a)
ManyToMany
-- 34
  • 65 (a)
ManyToMany
-- 34
  • 64 (a)
ManyToMany
-- 34
  • 64 (a)
ManyToMany
-- 34
  • 64 (a)
ManyToMany
-- 34
  • 63 (a)
ManyToMany
-- 34
  • 63 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 62 (a)
ManyToMany
-- 34
  • 61 (a)
ManyToMany
-- 34
  • 60 (a)
ManyToMany
Species where no ortholog for PCDHB15 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)
  • chicken (Gallus gallus)
  • 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)
  • zebrafish (Danio rerio)

Evolution for PCDHB15 Gene

ENSEMBL:
Gene Tree for PCDHB15 (if available)
TreeFam:
Gene Tree for PCDHB15 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHB15: view image

Paralogs for PCDHB15 Gene

genes like me logo Genes that share paralogs with PCDHB15: view

Variants for PCDHB15 Gene

Sequence variations from dbSNP and Humsavar for PCDHB15 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
VAR_036106 A breast cancer sample p.Ala719Val
VAR_036107 A breast cancer sample p.Gly758Val
rs1001559801 -- 141,244,317(+) T/C upstream_transcript_variant
rs1002336027 -- 141,243,652(+) T/C upstream_transcript_variant
rs1002732743 -- 141,243,935(+) C/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHB15 Gene

Variant ID Type Subtype PubMed ID
esv2759382 CNV gain 17122850
nsv428127 CNV loss 18775914
nsv471634 CNV gain+loss 15918152
nsv599908 CNV loss 21841781
nsv964961 CNV duplication 23825009

Variation tolerance for PCDHB15 Gene

Residual Variation Intolerance Score: 95.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.47; 91.03% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHB15 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHB15

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB15 Gene

Disorders for PCDHB15 Gene

Additional Disease Information for PCDHB15

No disorders were found for PCDHB15 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB15 Gene

Publications for PCDHB15 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 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. 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 letters 2001) 3 4 58
  4. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3 58
  5. The consensus coding sequences of human breast and colorectal cancers. (PMID: 16959974) Sjöblom T … Velculescu VE (Science (New York, N.Y.) 2006) 4 58

Products for PCDHB15 Gene

Sources for PCDHB15 Gene

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