PCDHB9 Gene (Protein Coding)

Protocadherin Beta 9

GC05P143044
GIFtS:
28
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 ... See more...

Aliases for PCDHB9 Gene

Aliases for PCDHB9 Gene

  • Protocadherin Beta 9 2 3 5
  • PCDH3H 2 3 4
  • Protocadherin Beta-9 3 4
  • Protocadherin-3h 2 3
  • PCDH-Beta-9 3 4
  • PCDH-BETA9 2 3
  • Protocadherin-3H 4
  • PCDHB9 5

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
  • GC05P142436
  • GC05P142540
  • GC05P142651
  • GC05P142850
  • GC05P141615
  • GC05P141718
  • GC05P141817
  • GC05P141916
  • GC05P142024
  • GC05P142131
  • GC05P142230
  • GC05P142332

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 Summary 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 , Rfam classification and piRNA Summary for PCDHB9 Gene

Genomics for PCDHB9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PCDHB9 Gene
- 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 the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDHB9

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

Genomic Locations for PCDHB9 Gene

Genomic Locations for PCDHB9 Gene
chr5:141,187,127-141,191,541
(GRCh38/hg38)
Size:
4,415 bases
Orientation:
Plus strand
chr5:140,566,893-140,571,111
(GRCh37/hg19)
Size:
4,219 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for PCDHB9 Gene

Proteins for PCDHB9 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    Q9Y5E1-PCDB9_HUMAN
    Recommended name:
    Protocadherin beta-9
    Protein Accession:
    Q9Y5E1
    Secondary Accessions:
    • Q2M2U8
    • Q496X9
    • Q9NRJ8

    Protein attributes for PCDHB9 Gene

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

neXtProt entry for PCDHB9 Gene

Protein Expression for PCDHB9 Gene

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

Post-translational modifications for PCDHB9 Gene

  • Glycosylation at Asn169, Asn418, and Asn567
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PCDB9_HUMAN (1685)

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

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

Protein Domains for PCDHB9 Gene

InterPro:
Blocks:
  • Cadherin
ProtoNet:

Suggested Antigen Peptide Sequences for PCDHB9 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin-3H (PCDB9_HUMAN)
  • PCDHB9 protein (Q3ZB85_HUMAN)
genes like me logo Genes that share domains with PCDHB9: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCDHB9 Gene

Function for PCDHB9 Gene

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  2. CRISPR
  3. miRNA
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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.

Phenotypes From GWAS Catalog for PCDHB9 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB9

No data available for Enzyme Numbers (IUBMB) , 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.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PCDHB9 gene
Compartment Confidence
plasma membrane 3
extracellular 1
nucleus 1

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 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 11322959
GO:0045202 synapse IEA --
genes like me logo Genes that share ontologies with PCDHB9: view

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

Pathways & Interactions for PCDHB9 Gene

PathCards logo

SuperPathways for PCDHB9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHB9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,IBA 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007268 chemical synaptic transmission TAS 12231349
GO:0007416 synapse assembly TAS 12231349
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS 11322959
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

Products:

  1. Drug

(1) Drugs for PCDHB9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6556
genes like me logo Genes that share compounds with PCDHB9: view

Transcripts for PCDHB9 Gene

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

mRNA/cDNA for PCDHB9 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB9

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

No ASD Table

Relevant External Links for PCDHB9 Gene

GeneLoc Exon Structure for
PCDHB9

Expression for PCDHB9 Gene

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  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for PCDHB9 Gene
mRNA expression by GTEx 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDHB9

SOURCE GeneReport for Unigene cluster for PCDHB9 Gene:

Hs.662726
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
Chimpanzee
(Pan troglodytes)
 Mammalia PCDHB9 30
  • 98.37 (n)
Species where no ortholog for PCDHB9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

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

Paralogs for PCDHB9 Gene

Paralogs for PCDHB9 Gene

(72) SIMAP similar genes for PCDHB9 Gene using alignment to 3 proteins:

  • PCDB9_HUMAN
  • L8E8J0_HUMAN
  • Q3ZB85_HUMAN
genes like me logo Genes that share paralogs with PCDHB9: view

Variants for PCDHB9 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDHB9 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs10040383 - p.Lys414Glu
rs11167742 - p.Ser174Pro
rs11167743 - p.Ala239Val
rs17844512 - p.Ser185Gly
rs2697530 - p.Leu426Met

Additional dbSNP identifiers (rs#s) for PCDHB9 Gene

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
PCDHB9

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

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

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
  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
  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
  4. Protocadherin B9 promotes resistance to bicalutamide and is associated with the survival of prostate cancer patients. (PMID: 30324761) Sekino Y … Yasui W (The Prostate 2019) 3
  5. 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

ExternalLinks

View latest publications for PCDHB9 gene in Mastermind

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