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Aliases for PCDHB6 Gene

Aliases for PCDHB6 Gene

  • Protocadherin Beta 6 2 3 5
  • Protocadherin Beta-6 3
  • PCDH-Beta-6 4
  • PCDH-BETA6 3

External Ids for PCDHB6 Gene

Previous GeneCards Identifiers for PCDHB6 Gene

  • GC05P140346
  • GC05P141112
  • GC05P140512
  • GC05P140558
  • GC05P140510
  • GC05P135674
  • GC05P140529
  • GC05P141350
  • GC05P141500
  • GC05P141607
  • GC05P141710
  • GC05P141809

Summaries for PCDHB6 Gene

Entrez Gene Summary for PCDHB6 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. Unlike the alpha and gamma clusters, the transcripts from these genes do not share common 3' exons. 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 neural connections. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

GeneCards Summary for PCDHB6 Gene

PCDHB6 (Protocadherin Beta 6) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB5.

UniProtKB/Swiss-Prot for PCDHB6 Gene

  • Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB6 Gene

Genomics for PCDHB6 Gene

Regulatory Elements for PCDHB6 Gene

Enhancers for PCDHB6 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
GH05G141968 1.2 ENCODE 16.1 +819.5 819545 3.0 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC TBX21 ZNF610 KIAA0141 PCDHGA5 PCDHB12 RNF14 PCDHB11 PCDHB4 PCDHB18P PCDHB15 PCDHB9 PCDHGA6
GH05G141563 1.6 Ensembl ENCODE dbSUPER 10.8 +414.4 414391 1.4 PKNOX1 ARNT SIN3A DMAP1 ZNF2 YY1 CBX5 ZNF143 ZNF207 FOS PCDHA3 PCDHB8 PCDHB3 PCDHB9 PCDHB7 PCDHB15 PCDHGC3 PCDHGB2 ENSG00000272108 PCDHB4
GH05G140717 1.2 ENCODE 10.8 -430.9 -430886 2.7 MLX CREB3L1 ZNF416 ZNF263 SP3 PPARGC1A MEF2D GLIS1 RCOR2 NBN HDAC3 TMCO6 PURA LOC102723915 PCDHA3 IGIP PCDHB3 PCDHB9 PCDHB7 PCDHB15
GH05G140317 1.1 dbSUPER 10.8 -831.9 -831899 1.5 FOXA2 AGO1 ARID4B DMAP1 ZNF2 FOS ZNF548 SP5 JUNB REST PFDN1 PURA PCDHB18P PCDHB3 PCDHB9 PCDHB7 PCDHB15 ENSG00000272108 PCDHB4 HBEGF
GH05G141084 1.3 FANTOM5 Ensembl ENCODE 1.7 -65.3 -65278 1.4 CTCF PKNOX1 SAP130 RAD21 YY1 E2F1 ZNF23 GATA3 POLR2A SMC3 PCDHB1 IGIP PCDHGC4 PCDHB3 PCDHB10 PCDHB17P PCDHAC2 PCDHB9 PCDHB2 ENSG00000272070
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDHB6 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHB6 Gene

Chromosome:
5
Start:
141,150,022 bp from pter
End:
141,153,287 bp from pter
Size:
3,266 bases
Orientation:
Plus strand

Genomic View for PCDHB6 Gene

Genes around PCDHB6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB6 Gene

Proteins for PCDHB6 Gene

  • Protein details for PCDHB6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5E3-PCDB6_HUMAN
    Recommended name:
    Protocadherin beta-6
    Protein Accession:
    Q9Y5E3
    Secondary Accessions:
    • B2R8R9

    Protein attributes for PCDHB6 Gene

    Size:
    794 amino acids
    Molecular mass:
    87350 Da
    Quaternary structure:
    • Forms homodimers in trans (molecules expressed by two different cells). Forms promiscuous heterodimers in cis (at the plasma membrane of the same cell) with other protocadherins.

neXtProt entry for PCDHB6 Gene

Post-translational modifications for PCDHB6 Gene

  • Glycosylation at posLast=4646, Asn183, Asn416, and posLast=565565
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB6 Gene

Domains & Families for PCDHB6 Gene

Gene Families for PCDHB6 Gene

Protein Domains for PCDHB6 Gene

Suggested Antigen Peptide Sequences for PCDHB6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y5E3

UniProtKB/Swiss-Prot:

PCDB6_HUMAN :
  • Cadherin 1 to cadherin 4 domains mediate homophilic trans-interaction, the interaction with an identical protocadherin expressed by a neighboring cell. This is a head-to-tail interaction, the cadherin 1 domain interacting with the cadherin 4 domain and the cadherin 2 domain interacting the cadherin 3 domain of the other protocadherin. The cadherin 6 domain mediates promiscuous interactions with protocadherins on the same cell membrane. Each cadherin domain binds three calcium ions.
Domain:
  • Cadherin 1 to cadherin 4 domains mediate homophilic trans-interaction, the interaction with an identical protocadherin expressed by a neighboring cell. This is a head-to-tail interaction, the cadherin 1 domain interacting with the cadherin 4 domain and the cadherin 2 domain interacting the cadherin 3 domain of the other protocadherin. The cadherin 6 domain mediates promiscuous interactions with protocadherins on the same cell membrane. Each cadherin domain binds three calcium ions.
genes like me logo Genes that share domains with PCDHB6: view

Function for PCDHB6 Gene

Molecular function for PCDHB6 Gene

UniProtKB/Swiss-Prot Function:
Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain.

Gene Ontology (GO) - Molecular Function for PCDHB6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding ISS --
GO:0042802 identical protein binding ISS --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB6: view

Phenotypes for PCDHB6 Gene

genes like me logo Genes that share phenotypes with PCDHB6: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDHB6

CRISPR Products

miRNA for PCDHB6 Gene

miRTarBase miRNAs that target PCDHB6

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHB6 Gene

Localization for PCDHB6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB6 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 PCDHB6 gene
Compartment Confidence
plasma membrane 5
extracellular 2
nucleus 2
cytosol 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for PCDHB6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane ISS,TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,NAS 11322959
genes like me logo Genes that share ontologies with PCDHB6: view

Pathways & Interactions for PCDHB6 Gene

SuperPathways for PCDHB6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHB6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,TAS 10380929
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules ISS,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 PCDHB6: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB6 Gene

Drugs & Compounds for PCDHB6 Gene

(1) Drugs for PCDHB6 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 PCDHB6: view

Transcripts for PCDHB6 Gene

mRNA/cDNA for PCDHB6 Gene

Unigene Clusters for PCDHB6 Gene

Protocadherin beta 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB6 Gene

No ASD Table

Relevant External Links for PCDHB6 Gene

GeneLoc Exon Structure for
PCDHB6
ECgene alternative splicing isoforms for
PCDHB6

Expression for PCDHB6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHB6 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHB6 Gene:

PCDHB6

SOURCE GeneReport for Unigene cluster for PCDHB6 Gene:

Hs.283085

Evidence on tissue expression from TISSUES for PCDHB6 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with PCDHB6: 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 , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHB6 Gene

Orthologs for PCDHB6 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHB6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHB6 34 35
  • 98.15 (n)
dog
(Canis familiaris)
Mammalia PCDHB6 34
  • 85.68 (n)
cow
(Bos Taurus)
Mammalia PCDHB6 35
  • 83 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdhb13 34 16 35
  • 79.91 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 64 (a)
ManyToMany
-- 35
  • 64 (a)
ManyToMany
-- 35
  • 63 (a)
ManyToMany
-- 35
  • 63 (a)
ManyToMany
-- 35
  • 62 (a)
ManyToMany
-- 35
  • 62 (a)
ManyToMany
-- 35
  • 61 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 62 (a)
ManyToMany
-- 35
  • 60 (a)
ManyToMany
-- 35
  • 60 (a)
ManyToMany
Species where no ortholog for PCDHB6 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)
  • rat (Rattus norvegicus)
  • 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 PCDHB6 Gene

ENSEMBL:
Gene Tree for PCDHB6 (if available)
TreeFam:
Gene Tree for PCDHB6 (if available)

Paralogs for PCDHB6 Gene

genes like me logo Genes that share paralogs with PCDHB6: view

Variants for PCDHB6 Gene

Sequence variations from dbSNP and Humsavar for PCDHB6 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000162805 -- 141,153,116(+) ACTTA(C/T)GCATA utr-variant-3-prime
rs1000901518 -- 141,150,578(+) CAAGT(A/G)TTACT reference, synonymous-codon, utr-variant-5-prime
rs1002964750 -- 141,150,418(+) ACTGA(G/T)GGTGG intron-variant, reference, missense
rs1003376146 -- 141,148,800(+) TCAGA(C/G)TTTAG upstream-variant-2KB
rs1004214676 -- 141,149,800(+) GTTCT(A/G)GAGGG upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for PCDHB6 Gene

Variant ID Type Subtype PubMed ID
dgv1045e199 CNV deletion 23128226
esv25821 CNV loss 19812545
esv2759382 CNV gain 17122850
esv3606963 CNV loss 21293372
nsv10755 CNV loss 18304495
nsv428127 CNV loss 18775914
nsv471634 CNV gain+loss 15918152
nsv5029 CNV insertion 18451855
nsv522785 CNV loss 19592680
nsv599907 CNV loss 21841781
nsv599908 CNV loss 21841781
nsv968995 CNV duplication 23825009

Variation tolerance for PCDHB6 Gene

Residual Variation Intolerance Score: 98.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 15.18; 96.96% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHB6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHB6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB6 Gene

Disorders for PCDHB6 Gene

Relevant External Links for PCDHB6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHB6

No disorders were found for PCDHB6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB6 Gene

Publications for PCDHB6 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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 4 64
  4. Protocadherins. (PMID: 12231349) Frank M. … Kemler R. (Curr. Opin. Cell Biol. 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 PCDHB6 Gene

Sources for PCDHB6 Gene

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