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PCDHGB5 Gene(Protein Coding)

Protocadherin Gamma Subfamily B, 5

GCID:
GC05P141938
GIFtS:
37
Genes Participants
UDN Logo

Aliases for PCDHGB5 Gene

Aliases for PCDHGB5 Gene

  • Protocadherin Gamma Subfamily B, 5 2 3 5
  • PCDH-GAMMA-B5 3 4
  • Protocadherin Gamma-B5 3

External Ids for PCDHGB5 Gene

Previous GeneCards Identifiers for PCDHGB5 Gene

  • GC05P140594
  • GC05P141311
  • GC05P140713
  • GC05P140771
  • GC05P140792
  • GC05P140731
  • GC05P140808
  • GC05P140828
  • GC05P140845
  • GC05P140870
  • GC05P140877
  • GC05P140897
  • GC05P140930
  • GC05P140952
  • GC05P140973
  • GC05P140995
  • GC05P141025
  • GC05P141043
  • GC05P141070
  • GC05P141090
  • GC05P141109
  • GC05P141151
  • GC05P141168
  • GC05P141204
  • GC05P141244
  • GC05P141327
  • GC05P141386
  • GC05P141454
  • GC05P141531
  • GC05P141634
  • GC05P141736
  • GC05P141835

Summaries for PCDHGB5 Gene

Entrez Gene Summary for PCDHGB5 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 PCDHGB5 Gene

PCDHGB5 (Protocadherin Gamma Subfamily B, 5) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB1.

UniProtKB/Swiss-Prot for PCDHGB5 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 CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGB5 Gene

Genomics for PCDHGB5 Gene

Products:

  1. Regulatory Element

Regulatory Elements for PCDHGB5 Gene


Promoters for PCDHGB5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187857 172 600 CTCF ZNF610 NRF1 SMC3 ZNF600 ZBTB33 ZNF2
ENSR00000187857 313 600 CTCF ZNF610 NRF1 SMC3 ZNF600 ZBTB33 ZNF2

Transcription factor binding sites by QIAGEN in the PCDHGB5 gene promoter:

Genomic Location for PCDHGB5 Gene

Chromosome:
5
Start:
141,397,987 bp from pter
End:
141,512,979 bp from pter
Size:
114,993 bases
Orientation:
Plus strand

Genomic View for PCDHGB5 Gene

Genes around PCDHGB5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGB5 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PCDHGB5 Gene

Proteins for PCDHGB5 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for PCDHGB5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5G0-PCDGH_HUMAN
    Recommended name:
    Protocadherin gamma-B5
    Protein Accession:
    Q9Y5G0
    Secondary Accessions:
    • Q52LK8
    • Q9Y5C6

    Protein attributes for PCDHGB5 Gene

    Size:
    923 amino acids
    Molecular mass:
    99875 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGB5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB5 Gene

Protein Expression for PCDHGB5 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PCDHGB5 Gene

  • Glycosylation at posLast=415415 and posLast=541541
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGB5 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for PCDHGB5

No data available for DME Specific Peptides for PCDHGB5 Gene

Domains & Families for PCDHGB5 Gene

Gene Families for PCDHGB5 Gene

HGNC:

Protein Domains for PCDHGB5 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PCDHGB5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGB5: view

No data available for UniProtKB/Swiss-Prot for PCDHGB5 Gene

Function for PCDHGB5 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PCDHGB5 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 PCDHGB5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGB5: view

Phenotypes for PCDHGB5 Gene

GenomeRNAi human phenotypes for PCDHGB5:
genes like me logo Genes that share phenotypes with PCDHGB5: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGB5 Gene

Localization for PCDHGB5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB5 Gene

Cell membrane; Single-pass type I membrane protein.

Gene Ontology (GO) - Cellular Components for PCDHGB5 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:0070062 extracellular exosome IDA 19199708
genes like me logo Genes that share ontologies with PCDHGB5: view

No data available for Subcellular locations from COMPARTMENTS for PCDHGB5 Gene

Pathways & Interactions for PCDHGB5 Gene

SuperPathways for PCDHGB5 Gene

PathCards logo More details on SuperPathways for PCDHGB5
No Data Available

Interacting Proteins for PCDHGB5 Gene

Selected Interacting proteins: Q9Y5G0-PCDGH_HUMAN for PCDHGB5 Gene via IID

Gene Ontology (GO) - Biological Process for PCDHGB5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development IBA --
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with PCDHGB5: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB5 Gene

Drugs & Compounds for PCDHGB5 Gene

Products:

  1. Drug

(1) Drugs for PCDHGB5 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 PCDHGB5: view

Transcripts for PCDHGB5 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PCDHGB5 Gene

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

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB5 Gene

No ASD Table

Relevant External Links for PCDHGB5 Gene

GeneLoc Exon Structure for
PCDHGB5
ECgene alternative splicing isoforms for
PCDHGB5

Expression for PCDHGB5 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGB5 Gene

mRNA expression in normal human tissues for PCDHGB5 Gene
mRNA expression by BioGPS for PCDHGB5 Gene

Protein differential expression in normal tissues from HIPED for PCDHGB5 Gene

This gene is overexpressed in Breast (68.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCDHGB5 Gene



Protein tissue co-expression partners for PCDHGB5 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHGB5 Gene:

PCDHGB5
genes like me logo Genes that share expression patterns with PCDHGB5: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGB5 Gene

Orthologs for PCDHGB5 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHGB5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PCDHGB5 34
  • 99.24 (n)
cow
(Bos Taurus)
 Mammalia PCDHGB5 34
  • 87.51 (n)
dog
(Canis familiaris)
 Mammalia PCDHGB5 34
  • 86.38 (n)
mouse
(Mus musculus)
 Mammalia Pcdhgb5 34 16
  • 83.19 (n)
rat
(Rattus norvegicus)
 Mammalia Pcdhgb5 34
  • 81.94 (n)
Species where no ortholog for PCDHGB5 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 PCDHGB5 Gene

ENSEMBL:
Gene Tree for PCDHGB5 (if available)
TreeFam:
Gene Tree for PCDHGB5 (if available)

Paralogs for PCDHGB5 Gene

Paralogs for PCDHGB5 Gene

(61) SIMAP similar genes for PCDHGB5 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for PCDHGB5 Gene

genes like me logo Genes that share paralogs with PCDHGB5: view

Variants for PCDHGB5 Gene

Sequence variations from dbSNP and Humsavar for PCDHGB5 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
rs1000014772 -- 141,409,727(+) TGAGC(A/G)CGCAG intron-variant, reference, missense
rs1000022316 -- 141,472,751(+) GAGGC(A/G)GAGGC intron-variant
rs1000136303 -- 141,452,887(+) TTATT(C/T)CACTT intron-variant
rs1000138324 -- 141,499,091(+) GGCAC(A/C)TGCTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGB5 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv3422812 CNV insertion 20981092
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
nsv968259 CNV duplication 23825009
nsv980740 CNV duplication 23825009

Relevant External Links for PCDHGB5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGB5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for PCDHGB5 Gene

Disorders for PCDHGB5 Gene

Relevant External Links for PCDHGB5

Genetic Association Database (GAD)
PCDHGB5
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHGB5

No disorders were found for PCDHGB5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGB5 Gene

Publications for PCDHGB5 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. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). (PMID: 19199708) Gonzalez-Begne M. … Yates J.R. (J. Proteome Res. 2009) 3 64
  3. 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
  4. 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
  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 PCDHGB5 Gene

Sources for PCDHGB5 Gene

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