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Aliases for PCDHB9 Gene

Aliases for PCDHB9 Gene

  • Protocadherin Beta 9 2 3 5
  • Protocadherin-3h 2 3
  • PCDH-Beta-9 3 4
  • PCDH3H 3 4
  • Protocadherin Beta-9 3
  • Protocadherin-3H 4
  • PCDH-BETA9 3

External Ids for PCDHB9 Gene

Previous GeneCards Identifiers for PCDHB9 Gene

  • GC05P140383
  • GC05P141149
  • GC05P140550
  • GC05P140601
  • GC05P140604
  • GC05P140547
  • GC05P135711
  • GC05P140575
  • GC05P140581
  • GC05P140689
  • GC05P141282
  • GC05P141364
  • GC05P141424
  • GC05P141509
  • GC05P141615
  • GC05P141718
  • GC05P141817
  • GC05P141916
  • GC05P142024
  • GC05P142131

Summaries for PCDHB9 Gene

Entrez Gene Summary for PCDHB9 Gene

  • This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHB9 Gene

PCDHB9 (Protocadherin Beta 9) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB10.

UniProtKB/Swiss-Prot for PCDHB9 Gene

  • Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Gene Wiki entry for PCDHB9 Gene

Additional gene information for PCDHB9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB9 Gene

Genomics for PCDHB9 Gene

GeneHancer (GH) Regulatory Elements for PCDHB9 Gene

Promoters and enhancers for PCDHB9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 17.9 +782.4 782440 3 CLOCK DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC GLIS1 RNF14 PCDH12 LOC102723915 HDAC3 PCDHB18P PCDHGA6 PCDHGA7 DELE1 PCDHGA5 ENSG00000271871
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 22 -468.0 -467991 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
GH05J141563 Enhancer 1.4 Ensembl ENCODE dbSUPER 13.3 +377.3 377286 1.4 FOXA2 PKNOX1 ARNT SIN3A DMAP1 ZNF2 IRF4 YY1 ZNF213 ZNF207 HARS2 IK PCDHB8 PCDHB3 PCDHA6 PCDHB9 PCDHB7 ENSG00000272108 PCDHB15 PCDHGC3
GH05J140710 Promoter/Enhancer 1.6 Ensembl ENCODE 10.5 -476.1 -476143 1.9 CLOCK FEZF1 IRF4 YY1 ZNF213 ZNF143 SP3 SSRP1 ZNF610 GLIS1 GC05P142295 LOC105378198 VTRNA1-1 HARS2 ANKHD1 WDR55 LOC102723915 HDAC3 PCDHB18P PURA
GH05J140725 Promoter/Enhancer 1.6 Ensembl ENCODE 10.5 -461.1 -461145 1.1 PKNOX1 ARNT ARID4B SIN3A ZNF2 IRF4 YY1 POLR2B ZNF766 ZNF213 GC05P142300 VTRNA1-3 ANKHD1 LOC102723915 WDR55 HDAC3 HARS2 TMCO6 FCHSD1 PCDHA4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHB9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHB9 gene promoter:
  • LCR-F1
  • AREB6
  • Egr-1
  • Pax-2a
  • Pax-2
  • Arnt
  • AhR
  • FOXD1

Genomic Locations for PCDHB9 Gene

Genomic Locations for PCDHB9 Gene
4,415 bases
Plus strand
4,219 bases
Plus strand

Genomic View for PCDHB9 Gene

Genes around PCDHB9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB9 Gene

Proteins for PCDHB9 Gene

  • Protein details for PCDHB9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin beta-9
    Protein Accession:
    Secondary Accessions:
    • Q2M2U8
    • Q496X9
    • Q9NRJ8

    Protein attributes for PCDHB9 Gene

    797 amino acids
    Molecular mass:
    87099 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB9 Gene

Post-translational modifications for PCDHB9 Gene

  • Glycosylation at isoforms=567, isoforms=418, and Asn169
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB9 Gene

Domains & Families for PCDHB9 Gene

Gene Families for PCDHB9 Gene

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

Protein Domains for PCDHB9 Gene

Suggested Antigen Peptide Sequences for PCDHB9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHB9: view

No data available for UniProtKB/Swiss-Prot for PCDHB9 Gene

Function for PCDHB9 Gene

Molecular function for PCDHB9 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 PCDHB9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB9: view
genes like me logo Genes that share phenotypes with PCDHB9: 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 PCDHB9 Gene

Localization for PCDHB9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB9 Gene

Cell membrane; Single-pass type I membrane protein.

Gene Ontology (GO) - Cellular Components for PCDHB9 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 NAS 11322959
genes like me logo Genes that share ontologies with PCDHB9: view

No data available for Subcellular locations from COMPARTMENTS and Subcellular locations from the Human Protein Atlas (HPA) for PCDHB9 Gene

Pathways & Interactions for PCDHB9 Gene

SuperPathways for PCDHB9 Gene

No Data Available

Interacting Proteins for PCDHB9 Gene

Gene Ontology (GO) - Biological Process for PCDHB9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA,IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007268 chemical synaptic transmission TAS 12231349
GO:0007416 synapse assembly TAS 12231349
genes like me logo Genes that share ontologies with PCDHB9: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB9 Gene

Drugs & Compounds for PCDHB9 Gene

(1) Drugs for PCDHB9 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 PCDHB9: view

Transcripts for PCDHB9 Gene

mRNA/cDNA for PCDHB9 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(13) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCDHB9 Gene

Protocadherin beta 9:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB9 Gene

No ASD Table

Relevant External Links for PCDHB9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHB9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHB9 Gene

Protein differential expression in normal tissues from HIPED for PCDHB9 Gene

This gene is overexpressed in Adipocyte (65.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHB9 Gene

Protein tissue co-expression partners for PCDHB9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHB9 Gene:


SOURCE GeneReport for Unigene cluster for PCDHB9 Gene:

genes like me logo Genes that share expression patterns with PCDHB9: 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 PCDHB9 Gene

Orthologs for PCDHB9 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for PCDHB9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHB9 33
  • 98.37 (n)
Species where no ortholog for PCDHB9 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)
  • dog (Canis familiaris)
  • 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)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 PCDHB9 Gene

Gene Tree for PCDHB9 (if available)
Gene Tree for PCDHB9 (if available)
Evolutionary constrained regions (ECRs) for PCDHB9: view image

Paralogs for PCDHB9 Gene

genes like me logo Genes that share paralogs with PCDHB9: view

Variants for PCDHB9 Gene

Sequence variations from dbSNP and Humsavar for PCDHB9 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1001120297 -- 141,191,202(+) C/T 3_prime_UTR_variant
rs1002301962 -- 141,190,540(+) C/G 3_prime_UTR_variant
rs1002393428 -- 141,189,972(+) A/G 3_prime_UTR_variant
rs1002637169 -- 141,187,738(+) A/T coding_sequence_variant, missense_variant
rs1002730418 -- 141,187,570(+) G/A coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHB9 Gene

Variant ID Type Subtype PubMed ID
dgv958e201 CNV deletion 23290073
esv2664767 CNV deletion 23128226
esv2730844 CNV deletion 23290073
esv2730845 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv2763501 CNV loss 21179565
esv3606971 CNV loss 21293372
esv3606972 CNV gain 21293372
nsv1024594 CNV loss 25217958
nsv1031792 CNV loss 25217958
nsv428127 CNV loss 18775914
nsv471634 CNV gain+loss 15918152
nsv499084 CNV gain 21111241
nsv5031 CNV insertion 18451855
nsv509092 CNV insertion 20534489
nsv599908 CNV loss 21841781
nsv599919 CNV loss 21841781
nsv823266 CNV gain 20364138
nsv823275 CNV gain 20364138
nsv964958 CNV duplication 23825009

Additional Variant Information for PCDHB9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for PCDHB9 Gene

Disorders for PCDHB9 Gene

Additional Disease Information for PCDHB9

No disorders were found for PCDHB9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB9 Gene

Publications for PCDHB9 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. 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) 3 4 58
  3. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PMID: 11322959) Vanhalst K … van Roy F (FEBS letters 2001) 3 4 58
  4. Overexpression of PCDHB9 promotes peritoneal metastasis and correlates with poor prognosis in patients with gastric cancer. (PMID: 28671736) Mukai S … Yasui W (The Journal of pathology 2017) 3 58
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K … Sugano S (Genome research 2006) 3 58

Products for PCDHB9 Gene

Sources for PCDHB9 Gene

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