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Aliases for PCDHGB1 Gene

Aliases for PCDHGB1 Gene

  • Protocadherin Gamma Subfamily B, 1 2 3 5
  • PCDH-GAMMA-B1 3 4
  • Protocadherin Gamma Subfamily B, 1, Isoform 2 2
  • Protocadherin Gamma-B1 3

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
  • GC05P141521
  • GC05P141627
  • GC05P141729

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 PCDHGB4.

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

Enhancers for PCDHGB1 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
GH05F140563 1.1 ENCODE 11.9 -785.2 -785176 3.1 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A YBX1 ZNF2 YY1 ZNF207 CD14 PCDHGB1 HARS PCDHGA9 WDR55 DND1 ENSG00000200051 ANKHD1 ANKHD1-EIF4EBP3 PCDHA5
GH05F141968 0.5 ENCODE 10.2 +619.5 619465 3.0 HDGF PKNOX1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 PCDHB5 KIAA0141 HDAC3 PCDHGA5 PCDHB12 RNF14 PCDHB11 PCDHB4 PCDHB19P PCDHB18P
GH05F141506 1.6 FANTOM5 Ensembl ENCODE 9.8 +166.4 166377 20.0 HDGF PKNOX1 MLX WRNIP1 ARID4B SIN3A FEZF1 ZNF2 YY1 ZNF207 DIAPH1 PCDHGB6 TMCO6 PCDHGA2 LOC102723915 PCDHGC5 PCDHGA11 HDAC3 PCDHGC4 RN7SL68P
GH05F141811 0.9 FANTOM5 Ensembl ENCODE 1.3 +461.8 461766 1.4 CTCF TEAD4 MAX ZNF2 RAD21 TEAD3 ZNF791 ZNF366 ZNF169 SMC3 HDAC3 KIAA0141 PCDHGC5 PCDHGA9 PCDHGA3 PCDHGC4 NDFIP1 PCDHGA6 PCDHGA8 PCDHGB2
GH05F141349 0.7 ENCODE 0.8 0.0 -34 0.2 ELF3 CTCF SAP130 ETV1 ARID4B SIN3A ZNF2 RAD21 ZNF7 POLR2A PCDHGB1 PCDHGA3
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PCDHGB1 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHGB1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001874445 298 800 ELF3 CTCF SAP130 ETV1 ARID4B ZNF2 RAD21 ZNF7 GATA3 POLR2A

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

Genes around PCDHGB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

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 --
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

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
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

STRING Interaction Network Preview (showing 5 interactants - click image to see 8)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000429273%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000344456%0d%0a9606.ENSP00000311113%0d%0a9606.ENSP00000362481%0d%0a
Selected Interacting proteins: ENSP00000429273 Q9Y5G3-PCDGD_HUMAN for PCDHGB1 Gene via STRING IID

Gene Ontology (GO) - Biological Process for PCDHGB1 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 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

Inhibitory RNA Products

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, MaxQB, and MOPED for PCDHGB1 Gene



Protein tissue co-expression partners for PCDHGB1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGB1 Gene:

PCDHGB1
genes like me logo Genes that share expression patterns with PCDHGB1: 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 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
chimpanzee
(Pan troglodytes)
Mammalia PCDHGB1 34
  • 99.53 (n)
mouse
(Mus musculus)
Mammalia Pcdhgb1 34 16
  • 83.17 (n)
dog
(Canis familiaris)
Mammalia PCDHGB1 35
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 64 (a)
ManyToMany
-- 35
  • 61 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 59 (a)
ManyToMany
-- 35
  • 58 (a)
ManyToMany
-- 35
  • 58 (a)
ManyToMany
-- 35
  • 58 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 53 (a)
ManyToMany
-- 35
  • 52 (a)
ManyToMany
-- 35
  • 52 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (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
fruit fly
(Drosophila melanogaster)
Insecta Cad89D 36
  • 28 (a)
Species where no ortholog for PCDHGB1 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)
  • 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

Sequence variations from dbSNP and Humsavar for PCDHGB1 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 PCDHGB1 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv3422812 CNV insertion 20981092
esv3606982 CNV loss 21293372
esv3606983 CNV gain 21293372
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
nsv980739 CNV duplication 23825009
nsv980740 CNV duplication 23825009

Variation tolerance for PCDHGB1 Gene

Residual Variation Intolerance Score: 33.2% 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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGB1

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

No disorders were found for PCDHGB1 Gene.

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 3 4 64
  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) 4 64
  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) 3 64
  4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 3 64
  5. 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 64

Products for PCDHGB1 Gene

Sources for PCDHGB1 Gene

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