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Aliases for PCDH9 Gene

Aliases for PCDH9 Gene

  • Protocadherin 9 2 3
  • Cadherin Superfamily Protein VR4-11 3
  • Protocadherin-9 3

External Ids for PCDH9 Gene

Previous GeneCards Identifiers for PCDH9 Gene

  • GC13M065766
  • GC13M061794
  • GC13M065597
  • GC13M064677
  • GC13M065774
  • GC13M066876
  • GC13M047575

Summaries for PCDH9 Gene

Entrez Gene Summary for PCDH9 Gene

  • This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Nov 2012]

GeneCards Summary for PCDH9 Gene

PCDH9 (Protocadherin 9) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH7.

UniProtKB/Swiss-Prot for PCDH9 Gene

  • Potential calcium-dependent cell-adhesion protein

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDH9 Gene

Genomics for PCDH9 Gene

Regulatory Elements for PCDH9 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for PCDH9 Gene

66,302,834 bp from pter
67,230,445 bp from pter
927,612 bases
Minus strand

Genomic View for PCDH9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PCDH9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDH9 Gene

Proteins for PCDH9 Gene

  • Protein details for PCDH9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • A2A6U1
    • Q5VT83
    • Q7Z3U0
    • Q8N3K7

    Protein attributes for PCDH9 Gene

    1237 amino acids
    Molecular mass:
    136064 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PCDH9 Gene

    Alternative splice isoforms for PCDH9 Gene


neXtProt entry for PCDH9 Gene

Proteomics data for PCDH9 Gene at MOPED

Post-translational modifications for PCDH9 Gene

  • Glycosylation at Asn48, Asn148, Asn306, Asn307, Asn347, Asn368, Asn450, Asn511, Asn630, Asn681, Asn734, Asn754, Asn775, and Asn780
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDH9 Gene

No data available for DME Specific Peptides for PCDH9 Gene

Domains for PCDH9 Gene

Gene Families for PCDH9 Gene

Protein Domains for PCDH9 Gene

Suggested Antigen Peptide Sequences for PCDH9 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 7 cadherin domains.
  • Contains 7 cadherin domains.
genes like me logo Genes that share domains with PCDH9: view

Function for PCDH9 Gene

Molecular function for PCDH9 Gene

GENATLAS Biochemistry:
BH protocadherin 9 cadherin-related neuronal receptor,predominantly expressed in brain,localizing to synaptic junctions and putatively involved in specific neuronal connections and signal transduction,also expressed in other tissues with a developmentally regulated expression pattern,cadherin superfamily of calcium dependant cell-cell adhesion glycoproteins
UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein

Gene Ontology (GO) - Molecular Function for PCDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding --
genes like me logo Genes that share ontologies with PCDH9: view

Phenotypes for PCDH9 Gene

genes like me logo Genes that share phenotypes with PCDH9: view

Animal Model Products

miRNA for PCDH9 Gene

miRTarBase miRNAs that target PCDH9

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PCDH9

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDH9 Gene

Localization for PCDH9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDH9 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for PCDH9 Gene COMPARTMENTS Subcellular localization image for PCDH9 gene
Compartment Confidence
plasma membrane 5
cytosol 1
endoplasmic reticulum 1
extracellular 1
golgi apparatus 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for PCDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
GO:0030426 growth cone IEA --
GO:0044291 cell-cell contact zone IEA --
genes like me logo Genes that share ontologies with PCDH9: view

Pathways for PCDH9 Gene

SuperPathways for PCDH9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0030900 forebrain development IEA --
genes like me logo Genes that share ontologies with PCDH9: view

No data available for Pathways by source for PCDH9 Gene

Drugs for PCDH9 Gene

(1) HMDB Compounds for PCDH9 Gene

Compound Synonyms Cas Number PubMed IDs
  • Ca
genes like me logo Genes that share compounds with PCDH9: view

Transcripts for PCDH9 Gene

Unigene Clusters for PCDH9 Gene

Protocadherin 9:
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PCDH9

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDH9 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c
SP1: -
SP2: - -
SP3: - - -

Relevant External Links for PCDH9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDH9 Gene

mRNA expression in normal human tissues for PCDH9 Gene

mRNA differential expression in normal tissues according to GTEx for PCDH9 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (5.1), Brain - Amygdala (4.5), Brain - Anterior cingulate cortex (BA24) (4.4), Brain - Hippocampus (4.3), and Brain - Substantia nigra (4.2).

Protein differential expression in normal tissues for PCDH9 Gene

This gene is overexpressed in Frontal cortex (28.7), Brain (26.9), and Fetal Brain (7.9).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PCDH9 Gene

SOURCE GeneReport for Unigene cluster for PCDH9 Gene Hs.654709

genes like me logo Genes that share expressions with PCDH9: view

Expression partners for PCDH9 Gene

* - Elite partner

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for PCDH9 Gene

Orthologs for PCDH9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDH9 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PCDH9 35
  • 95.63 (n)
  • 99.19 (a)
PCDH9 36
  • 98 (a)
(Canis familiaris)
Mammalia PCDH9 35
  • 96.42 (n)
  • 99.6 (a)
PCDH9 36
  • 99 (a)
(Mus musculus)
Mammalia Pcdh9 35
  • 92.51 (n)
  • 98.22 (a)
Pcdh9 16
Pcdh9 36
  • 98 (a)
(Pan troglodytes)
Mammalia PCDH9 35
  • 99.49 (n)
  • 99.68 (a)
PCDH9 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Pcdh9 35
  • 92.7 (n)
  • 98.54 (a)
(Monodelphis domestica)
Mammalia PCDH9 36
  • 97 (a)
(Gallus gallus)
Aves PCDH9 35
  • 86.99 (n)
  • 96.24 (a)
PCDH9 36
  • 97 (a)
(Anolis carolinensis)
Reptilia PCDH9 36
  • 97 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcdh9 35
  • 80.25 (n)
  • 91.19 (a)
(Danio rerio)
Actinopterygii pcdh9 35
  • 74.4 (n)
  • 84.71 (a)
PCDH9 36
  • 86 (a)
Species with no ortholog for PCDH9:
  • 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PCDH9 Gene

Gene Tree for PCDH9 (if available)
Gene Tree for PCDH9 (if available)

Paralogs for PCDH9 Gene

genes like me logo Genes that share paralogs with PCDH9: view

Variants for PCDH9 Gene

Sequence variations from dbSNP and Humsavar for PCDH9 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type MAF
rs155008 -- 67,018,184(+) TTATA(C/T)TGGAG intron-variant
rs155009 -- 67,017,933(+) ATAAC(A/G)TTATT intron-variant
rs155010 -- 67,017,360(+) AATTA(C/T)ACCAT intron-variant
rs155013 -- 67,028,117(+) atgca(A/C)acata intron-variant
rs155014 -- 67,028,128(+) tgttt(A/C)ttgcg intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDH9 Gene

Variant ID Type Subtype PubMed ID
nsv900352 CNV Loss 21882294
nsv900388 CNV Loss 21882294
nsv900389 CNV Loss 21882294
esv2672074 CNV Deletion 23128226
nsv900390 CNV Loss 21882294
dgv567e1 CNV Complex 17122850
nsv9084 CNV Gain 18304495
essv4340 CNV CNV 17122850
nsv1074 CNV Insertion 18451855
esv2422196 CNV Deletion 17116639
nsv832639 CNV Gain 17160897
esv2747551 CNV Deletion 23290073
nsv900391 CNV Loss 21882294
dgv1658n71 CNV Loss 21882294
nsv471142 CNV Loss 18288195
dgv228n27 CNV Loss 19166990
nsv455926 CNV Loss 19166990
esv2747553 CNV Deletion 23290073
esv2661300 CNV Deletion 23128226
esv2747554 CNV Deletion 23290073
nsv511510 CNV Loss 21212237
nsv512325 CNV Loss 21212237
esv2747555 CNV Deletion 23290073
esv2667555 CNV Deletion 23128226
esv28367 CNV Loss 19812545
nsv900398 CNV Loss 21882294
nsv455928 CNV Loss 19166990
esv2664008 CNV Deletion 23128226
nsv826687 CNV Loss 20364138
nsv455929 CNV Loss 19166990
nsv826688 CNV Loss 20364138
esv34348 CNV Loss 17911159
dgv568e1 CNV Complex 17122850
nsv455931 CNV Loss 19166990
dgv1659n71 CNV Loss 21882294
nsv900400 CNV Loss 21882294
nsv455932 CNV Loss 19166990
nsv471143 CNV Loss 18288195
nsv523360 CNV Loss 19592680
nsv900403 CNV Loss 21882294
nsv900404 CNV Loss 21882294
esv2747556 CNV Deletion 23290073
esv2657997 CNV Deletion 23128226
nsv900405 CNV Loss 21882294
nsv528416 CNV Loss 19592680
nsv455933 CNV Loss 19166990
esv2660269 CNV Deletion 23128226
nsv64575 CNV Loss 16902084
nsv900406 CNV Loss 21882294
nsv900407 CNV Loss 21882294
esv2678519 CNV Deletion 23128226
nsv832640 CNV Gain 17160897
nsv437166 CNV Loss 16327808
nsv507708 CNV Insertion 20534489
dgv1660n71 CNV Loss 21882294
nsv818971 CNV Loss 17921354
dgv1661n71 CNV Loss 21882294
esv2667447 CNV Deletion 23128226
nsv900412 CNV Loss 21882294
nsv438254 CNV Loss 16468122
nsv900414 CNV Loss 21882294
nsv900415 CNV Loss 21882294
nsv518201 CNV Loss 19592680
nsv832641 CNV Loss 17160897
esv267821 CNV Insertion 20981092
esv269191 CNV Insertion 20981092
nsv522396 CNV Loss 19592680

Relevant External Links for PCDH9 Gene

HapMap Linkage Disequilibrium report

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDH9 Gene

Disorders for PCDH9 Gene

Relevant External Links for PCDH9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator

No disorders were found for PCDH9 Gene.

No data available for MalaCards , OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES , Novoseek inferred disease relationships and Genatlas for PCDH9 Gene

Publications for PCDH9 Gene

  1. Characterization of two novel protocadherins (PCDH8 and PCDH9) localized on human chromosome 13 and mouse chromosome 14. (PMID: 9787079) Strehl S. … Lalande M. (Genomics 1998) 2 3 23
  2. The DNA sequence and analysis of human chromosome 13. (PMID: 15057823) Dunham A. … Ross M.T. (Nature 2004) 3 4
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 48
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 48
  5. A genome-wide association study on obesity and obesity-related traits. (PMID: 21552555) Wang K. … Price R.A. (PLoS ONE 2011) 3 48

Products for PCDH9 Gene

Sources for PCDH9 Gene

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