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Aliases for PCDHGB1 Gene

Aliases for PCDHGB1 Gene

  • Protocadherin Gamma Subfamily B, 1 2 3
  • PCDH-GAMMA-B1 3 4
  • Protocadherin Gamma Subfamily B 2
  • Isoform 2 2
  • 1 2

External Ids for PCDHGB1 Gene

Previous GeneCards Identifiers for PCDHGB1 Gene

  • GC05P140546
  • GC05P141303
  • GC05P140709
  • GC05P140768
  • GC05P140788
  • GC05P140727
  • GC05P140813
  • GC05P140824
  • GC05P140853
  • GC05P140859
  • GC05P140885
  • GC05P140907
  • GC05P140922
  • GC05P140944
  • GC05P140965
  • GC05P140987
  • GC05P141014
  • GC05P141037
  • GC05P141081
  • GC05P135874
  • GC05P141102
  • GC05P141141
  • GC05P141180
  • GC05P141211
  • GC05P141250
  • GC05P141279
  • GC05P141377
  • GC05P141446

Summaries for PCDHGB1 Gene

Entrez Gene Summary for PCDHGB1 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 PCDHGB1 Gene

PCDHGB1 (Protocadherin Gamma Subfamily B, 1) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA11.

UniProtKB/Swiss-Prot for PCDHGB1 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 PCDHGB1 Gene

Genomics for PCDHGB1 Gene

Regulatory Elements for PCDHGB1 Gene

Genomic Location for PCDHGB1 Gene

Chromosome:
5
Start:
141,350,102 bp from pter
End:
141,512,979 bp from pter
Size:
162,878 bases
Orientation:
Plus strand

Genomic View for PCDHGB1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PCDHGB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGB1 Gene

Proteins for PCDHGB1 Gene

  • Protein details for PCDHGB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5G3-PCDGD_HUMAN
    Recommended name:
    Protocadherin gamma-B1
    Protein Accession:
    Q9Y5G3
    Secondary Accessions:
    • Q3SY75
    • Q9Y5C8

    Protein attributes for PCDHGB1 Gene

    Size:
    927 amino acids
    Molecular mass:
    100360 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGB1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB1 Gene

Proteomics data for PCDHGB1 Gene at MOPED

Post-translational modifications for PCDHGB1 Gene

  • Glycosylation at Asn 41, Asn 73, Asn 300, Asn 415, and Asn 541
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGB1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB1 Gene

Domains & Families for PCDHGB1 Gene

Gene Families for PCDHGB1 Gene

Protein Domains for PCDHGB1 Gene

Suggested Antigen Peptide Sequences for PCDHGB1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y5G3

UniProtKB/Swiss-Prot:

PCDGD_HUMAN :
  • Contains 6 cadherin domains.
Domain:
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHGB1: view

Function for PCDHGB1 Gene

Molecular function for PCDHGB1 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 PCDHGB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with PCDHGB1: view
genes like me logo Genes that share phenotypes with PCDHGB1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PCDHGB1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGB1 Gene

Localization for PCDHGB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB1 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDHGB1 Gene COMPARTMENTS Subcellular localization image for PCDHGB1 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PCDHGB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
GO:0030426 growth cone IEA --
genes like me logo Genes that share ontologies with PCDHGB1: view

Pathways & Interactions for PCDHGB1 Gene

SuperPathways for PCDHGB1 Gene

No Data Available

Interacting Proteins for PCDHGB1 Gene

Gene Ontology (GO) - Biological Process for PCDHGB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
genes like me logo Genes that share ontologies with PCDHGB1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB1 Gene

Drugs & Compounds for PCDHGB1 Gene

(1) Drugs for PCDHGB1 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 PCDHGB1: view

Transcripts for PCDHGB1 Gene

mRNA/cDNA for PCDHGB1 Gene

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PCDHGB1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB1 Gene

No ASD Table

Relevant External Links for PCDHGB1 Gene

GeneLoc Exon Structure for
PCDHGB1
ECgene alternative splicing isoforms for
PCDHGB1

Expression for PCDHGB1 Gene

mRNA expression in normal human tissues for PCDHGB1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PCDHGB1 Gene



genes like me logo Genes that share expression patterns with PCDHGB1: view

Protein tissue co-expression partners for PCDHGB1 Gene

- Elite partner

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

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 , Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PCDHGB1 Gene

Orthologs for PCDHGB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCDHGB1 Gene

Organism Taxonomy Gene Similarity Type Details
mouse
(Mus musculus)
Mammalia Pcdhgb1 35
  • 83.17 (n)
  • 82.91 (a)
Pcdhgb1 16
chimpanzee
(Pan troglodytes)
Mammalia PCDHGB1 35
  • 99.53 (n)
  • 99.14 (a)
dog
(Canis familiaris)
Mammalia PCDHGB1 36
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 61 (a)
ManyToMany
-- 36
  • 64 (a)
ManyToMany
-- 36
  • 56 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 58 (a)
ManyToMany
-- 36
  • 58 (a)
ManyToMany
-- 36
  • 59 (a)
ManyToMany
-- 36
  • 56 (a)
ManyToMany
-- 36
  • 58 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 36
  • 50 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 52 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
-- 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
  • 49 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 50 (a)
ManyToMany
-- 36
  • 52 (a)
ManyToMany
-- 36
  • 51 (a)
ManyToMany
-- 36
  • 53 (a)
ManyToMany
-- 36
  • 49 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta Cad89D 37
  • 28 (a)
Species with no ortholog for PCDHGB1:
  • 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)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • 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 PCDHGB1 Gene

ENSEMBL:
Gene Tree for PCDHGB1 (if available)
TreeFam:
Gene Tree for PCDHGB1 (if available)

Paralogs for PCDHGB1 Gene

genes like me logo Genes that share paralogs with PCDHGB1: view

Variants for PCDHGB1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCDHGB1 Gene

Variant ID Type Subtype PubMed ID
dgv1857e1 CNV Complex 17122850
dgv6351n71 CNV Loss 21882294
dgv6352n71 CNV Loss 21882294
dgv6353n71 CNV Loss 21882294
nsv882987 CNV Gain 21882294
nsv882990 CNV Loss 21882294
nsv823279 CNV Gain 20364138
nsv823280 CNV Loss 20364138
nsv519627 CNV Loss 19592680
esv267823 CNV Insertion 20981092
nsv518799 CNV Loss 19592680
nsv327707 CNV Loss 16902084
esv2730847 CNV Deletion 23290073
nsv462470 CNV Loss 19166990
esv25744 CNV Gain 19812545

Variation tolerance for PCDHGB1 Gene

Residual Variation Intolerance Score: 33.24% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.09; 60.96% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHGB1 Gene

HapMap Linkage Disequilibrium report
PCDHGB1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations from dbSNP and Humsavar for PCDHGB1 Gene

Disorders for PCDHGB1 Gene

Relevant External Links for PCDHGB1

Genetic Association Database (GAD)
PCDHGB1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHGB1
genes like me logo Genes that share disorders with PCDHGB1: view

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGB1 Gene

Publications for PCDHGB1 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 67
  2. 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) 67
  3. 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) 67
  4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 67
  5. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PMID: 10835267) Nollet F. … van Roy F. (J. Mol. Biol. 2000) 67

Products for PCDHGB1 Gene

Sources for PCDHGB1 Gene

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