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PCDHGB5 Gene(Protein Coding)

Protocadherin Gamma Subfamily B, 5

GCID:
GC05P142150
GIFtS:
36
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
  • GC05P141938
  • GC05P142042

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. Diseases associated with PCDHGB5 include Protocadherin-Gamma Gene Cluster. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB4.

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.

Additional gene information for PCDHGB5 Gene

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

GeneHancer (GH) Regulatory Elements for PCDHGB5 Gene

Promoters and enhancers for PCDHGB5 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH05I141398 Promoter 1.4 EPDnew Ensembl 550.8 +0.3 313 0.6 ZNF639 CTCF ZBTB6 NRF1 ZNF2 ZNF335 ZNF217 ZNF610 ZBTB33 ZNF600 PCDHGB5 PCDHGB6 PCDHGA9 PCDHGA8 PCDHGB4 PCDHGA7 PCDHGA6 PCDHGB3 PCDHGA5 PCDHGB2
GH05I141397 Promoter 0.9 EPDnew 550.8 -0.1 -62 0.1 ZNF639 CTCF ZNF654 ZBTB6 NRF1 ZNF2 RAD21 ZNF335 ZNF217 ZNF610 PCDHGB5 PCDHGA8 PCDHGB4 PCDHGA7 PCDHGA6 PCDHGB3 PCDHGA5 PCDHGB2 PCDHGA4 PCDHGB1
GH05I141402 Promoter 0.8 EPDnew 0.8 +4.9 4897 0.1 CTCF SMC3 ZSCAN29 RAD21 PCDHGA9 PCDHGB5 PCDHGA8 PCDHGB4 PCDHGA7 PCDHGA6 PCDHGB3 PCDHGA5 PCDHGB2 PCDHGA4
GH05I141417 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 0.4 +19.7 19740 1.3 SMARCA5 CTCF NRF1 TRIM22 RAD21 ZNF592 IKZF1 ZNF143 SMC3 MLLT1 PCDHGB7 PCDHGB6 NDUFA2 PCDHGA10 PCDHGA11 PCDHGA9 PCDHGB5 PCDHGA8 PCDHGA7 PCDHGB4
GH05I141412 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 0.4 +15.3 15251 0.7 SMARCA5 CTCF NRF1 TRIM22 RAD21 ZNF592 YY1 IKZF1 ZNF143 SMC3 PCDHGA10 NDUFA2 PCDHGB7 PCDHGB6 PCDHGA9 PCDHGB5 PCDHGA8 PCDHGB4 PCDHGA7 PCDHGA6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHGB5 on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for PCDHGB5 Gene

Genomic Locations for PCDHGB5 Gene
chr5:141,397,987-141,512,979
(GRCh38/hg38)
Size:
114,993 bases
Orientation:
Plus strand
chr5:140,777,695-140,892,546
(GRCh37/hg19)

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 Asn415 and isoforms=2541

Other Protein References for PCDHGB5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB5 Gene

Domains & Families for PCDHGB5 Gene

Gene Families for PCDHGB5 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins

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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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.

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
  • Plasma membrane (2)
  • Vesicles (2)
See all subcellular structures

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 HDA,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 Approved 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 :

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

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 33
  • 99.24 (n)
cow
(Bos Taurus)
 Mammalia PCDHGB5 33
  • 87.51 (n)
dog
(Canis familiaris)
 Mammalia PCDHGB5 33
  • 86.38 (n)
mouse
(Mus musculus)
 Mammalia Pcdhgb5 33 16
  • 83.19 (n)
rat
(Rattus norvegicus)
 Mammalia Pcdhgb5 33
  • 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 Variation AA Info Type
rs386352347 uncertain-significance, not provided 141,485,635(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000014772 -- 141,409,727(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000022316 -- 141,472,751(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000136303 -- 141,452,887(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000138324 -- 141,499,091(+) A/C genic_downstream_transcript_variant, 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

Additional Variant Information 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

MalaCards: The human disease database

(1) MalaCards diseases for PCDHGB5 Gene - From: GeneCards

Disorder Aliases PubMed IDs
protocadherin-gamma gene cluster
  • pcdhg@
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHGB5

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PCDHGB5: view

No data available for 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 58
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  3. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). (PMID: 19199708) Gonzalez-Begne M … Yates JR (Journal of proteome research 2009) 3 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 4 58
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58

Products for PCDHGB5 Gene

Sources for PCDHGB5 Gene

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