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Aliases for PCDHGB6 Gene

Aliases for PCDHGB6 Gene

  • Protocadherin Gamma Subfamily B, 6 2 3 5
  • PCDH-GAMMA-B6 3 4

External Ids for PCDHGB6 Gene

Previous GeneCards Identifiers for PCDHGB6 Gene

  • GC05P140589
  • GC05P141314
  • GC05P140714
  • GC05P140772
  • GC05P140793
  • GC05P140732
  • GC05P140809
  • GC05P140830
  • GC05P140847
  • GC05P140872
  • GC05P140879
  • GC05P140899
  • GC05P140933
  • GC05P140955
  • GC05P140976
  • GC05P141000
  • GC05P141027
  • GC05P141046
  • GC05P141073
  • GC05P135932
  • GC05P141111
  • GC05P141153
  • GC05P141170
  • GC05P141206
  • GC05P141246
  • GC05P141333
  • GC05P141389
  • GC05P141456
  • GC05P141534

Summaries for PCDHGB6 Gene

Entrez Gene Summary for PCDHGB6 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 PCDHGB6 Gene

PCDHGB6 (Protocadherin Gamma Subfamily B, 6) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA5.

UniProtKB/Swiss-Prot for PCDHGB6 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 PCDHGB6 Gene

Genomics for PCDHGB6 Gene

Regulatory Elements for PCDHGB6 Gene

Promoters for PCDHGB6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PCDHGB6 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHGB6 Gene

Chromosome:
5
Start:
141,408,021 bp from pter
End:
141,512,979 bp from pter
Size:
104,959 bases
Orientation:
Plus strand

Genomic View for PCDHGB6 Gene

Genes around PCDHGB6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGB6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGB6 Gene

Proteins for PCDHGB6 Gene

  • Protein details for PCDHGB6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5F9-PCDGI_HUMAN
    Recommended name:
    Protocadherin gamma-B6
    Protein Accession:
    Q9Y5F9
    Secondary Accessions:
    • Q9Y5C5

    Protein attributes for PCDHGB6 Gene

    Size:
    930 amino acids
    Molecular mass:
    101043 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGB6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB6 Gene

Proteomics data for PCDHGB6 Gene at MOPED

Post-translational modifications for PCDHGB6 Gene

  • Glycosylation at Asn 304, Asn 419, and Asn 545
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGB6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB6 Gene

Domains & Families for PCDHGB6 Gene

Gene Families for PCDHGB6 Gene

Protein Domains for PCDHGB6 Gene

Suggested Antigen Peptide Sequences for PCDHGB6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y5F9

UniProtKB/Swiss-Prot:

PCDGI_HUMAN :
  • Contains 6 cadherin domains.
Domain:
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHGB6: view

Function for PCDHGB6 Gene

Molecular function for PCDHGB6 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 for PCDHGB6 Gene

GenomeRNAi human phenotypes for PCDHGB6:
genes like me logo Genes that share phenotypes with PCDHGB6: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGB6 Gene

Localization for PCDHGB6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB6 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDHGB6 Gene COMPARTMENTS Subcellular localization image for PCDHGB6 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PCDHGB6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHGB6: view

Pathways & Interactions for PCDHGB6 Gene

SuperPathways for PCDHGB6 Gene

No Data Available

Interacting Proteins for PCDHGB6 Gene

Gene Ontology (GO) - Biological Process for PCDHGB6 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB6 Gene

Drugs & Compounds for PCDHGB6 Gene

(1) Drugs for PCDHGB6 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 PCDHGB6: view

Transcripts for PCDHGB6 Gene

mRNA/cDNA for PCDHGB6 Gene

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB6 Gene

No ASD Table

Relevant External Links for PCDHGB6 Gene

GeneLoc Exon Structure for
PCDHGB6
ECgene alternative splicing isoforms for
PCDHGB6

Expression for PCDHGB6 Gene

mRNA expression in normal human tissues for PCDHGB6 Gene

Protein differential expression in normal tissues from HIPED for PCDHGB6 Gene

This gene is overexpressed in Islet of Langerhans (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PCDHGB6 Gene



genes like me logo Genes that share expression patterns with PCDHGB6: view

Protein tissue co-expression partners for PCDHGB6 Gene

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PCDHGB6 Gene

Orthologs for PCDHGB6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGB6 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PCDHGB6 35
  • 86.21 (n)
  • 86.71 (a)
dog
(Canis familiaris)
Mammalia PCDHGB6 35
  • 84.39 (n)
  • 84.6 (a)
mouse
(Mus musculus)
Mammalia Pcdhgb6 35
  • 82.19 (n)
  • 82.95 (a)
Pcdhgb6 16
chimpanzee
(Pan troglodytes)
Mammalia PCDHGB6 35
  • 99.53 (n)
  • 99.57 (a)
rat
(Rattus norvegicus)
Mammalia LOC102552497 35
  • 80.5 (n)
  • 81.61 (a)
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 58 (a)
ManyToMany
-- 36
  • 59 (a)
ManyToMany
-- 36
  • 56 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 59 (a)
ManyToMany
-- 36
  • 59 (a)
ManyToMany
-- 36
  • 58 (a)
ManyToMany
-- 36
  • 56 (a)
ManyToMany
-- 36
  • 60 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 50 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 53 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
Species with no ortholog for PCDHGB6:
  • 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)
  • 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 PCDHGB6 Gene

ENSEMBL:
Gene Tree for PCDHGB6 (if available)
TreeFam:
Gene Tree for PCDHGB6 (if available)

Paralogs for PCDHGB6 Gene

genes like me logo Genes that share paralogs with PCDHGB6: view

Variants for PCDHGB6 Gene

Sequence variations from dbSNP and Humsavar for PCDHGB6 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
VAR_021883 -
VAR_021884 -
VAR_048572 -

Structural Variations from Database of Genomic Variants (DGV) for PCDHGB6 Gene

Variant ID Type Subtype PubMed ID
dgv1857e1 CNV Complex 17122850
dgv6351n71 CNV Loss 21882294
dgv6352n71 CNV Loss 21882294
nsv882987 CNV Gain 21882294
nsv882990 CNV Loss 21882294
nsv519627 CNV Loss 19592680
nsv518799 CNV Loss 19592680
nsv327707 CNV Loss 16902084
esv2730847 CNV Deletion 23290073
nsv462470 CNV Loss 19166990
esv25744 CNV Gain 19812545

Variation tolerance for PCDHGB6 Gene

Residual Variation Intolerance Score: 55.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.75; 66.47% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHGB6 Gene

HapMap Linkage Disequilibrium report
PCDHGB6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGB6 Gene

Disorders for PCDHGB6 Gene

Relevant External Links for PCDHGB6

Genetic Association Database (GAD)
PCDHGB6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHGB6

No disorders were found for PCDHGB6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGB6 Gene

Publications for PCDHGB6 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 67
  2. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. (PMID: 24081945) Sandoval J. … Esteller M. (J. Clin. Oncol. 2013) 3
  3. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 3
  4. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PMID: 10716726) Wu Q. … Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000) 3
  5. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PMID: 10817752) Yagi T. … Takeichi M. (Genes Dev. 2000) 3

Products for PCDHGB6 Gene

Sources for PCDHGB6 Gene

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