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Aliases for PCDHA9 Gene

Aliases for PCDHA9 Gene

  • Protocadherin Alpha 9 2 3 5
  • KIAA0345-Like 5 2 3
  • PCDH-Alpha-9 3 4
  • KIAA0345 4

External Ids for PCDHA9 Gene

Previous GeneCards Identifiers for PCDHA9 Gene

  • GC05P140043
  • GC05P140756
  • GC05P140158
  • GC05P140213
  • GC05P140220
  • GC05P140175
  • GC05P140229
  • GC05P140234
  • GC05P140241
  • GC05P140250
  • GC05P140259
  • GC05P140268
  • GC05P140278
  • GC05P140288
  • GC05P140299
  • GC05P140308
  • GC05P140317
  • GC05P140333
  • GC05P140336
  • GC05P135372
  • GC05P140355
  • GC05P140370
  • GC05P140385
  • GC05P140399
  • GC05P140415
  • GC05P140428
  • GC05P140447
  • GC05P141271
  • GC05P141493

Summaries for PCDHA9 Gene

Entrez Gene Summary for PCDHA9 Gene

  • This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHA9 Gene

PCDHA9 (Protocadherin Alpha 9) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA5.

UniProtKB/Swiss-Prot for PCDHA9 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 PCDHA9 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA9 Gene

Genomics for PCDHA9 Gene

Regulatory Elements for PCDHA9 Gene

Enhancers for PCDHA9 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PCDHA9 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHA9 Gene

140,847,463 bp from pter
141,012,344 bp from pter
164,882 bases
Plus strand

Genomic View for PCDHA9 Gene

Genes around PCDHA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA9 Gene

Proteins for PCDHA9 Gene

  • Protein details for PCDHA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin alpha-9
    Protein Accession:
    Secondary Accessions:
    • O15053
    • Q2M3S5

    Protein attributes for PCDHA9 Gene

    950 amino acids
    Molecular mass:
    102402 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAA20803.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PCDHA9 Gene


neXtProt entry for PCDHA9 Gene

Proteomics data for PCDHA9 Gene at MOPED

Post-translational modifications for PCDHA9 Gene

  • Glycosylation at Asn 254, Asn 265, and Asn 548
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHA9 Gene

Domains & Families for PCDHA9 Gene

Gene Families for PCDHA9 Gene

Protein Domains for PCDHA9 Gene

Suggested Antigen Peptide Sequences for PCDHA9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 6 cadherin domains.
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHA9: view

Function for PCDHA9 Gene

Molecular function for PCDHA9 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 for PCDHA9 Gene

GenomeRNAi human phenotypes for PCDHA9:
genes like me logo Genes that share phenotypes with PCDHA9: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHA9 Gene

Localization for PCDHA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA9 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for PCDHA9 Gene COMPARTMENTS Subcellular localization image for PCDHA9 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PCDHA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHA9: view

Pathways & Interactions for PCDHA9 Gene

SuperPathways for PCDHA9 Gene

No Data Available

Interacting Proteins for PCDHA9 Gene

Gene Ontology (GO) - Biological Process for PCDHA9 Gene


No data available for Pathways by source and SIGNOR curated interactions for PCDHA9 Gene

Drugs & Compounds for PCDHA9 Gene

(1) Drugs for PCDHA9 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 PCDHA9: view

Transcripts for PCDHA9 Gene

mRNA/cDNA for PCDHA9 Gene

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA9 Gene

No ASD Table

Relevant External Links for PCDHA9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHA9 Gene

mRNA expression in normal human tissues for PCDHA9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCDHA9 Gene

This gene is overexpressed in Testis (x11.6), Brain - Cerebellum (x6.6), and Brain - Cerebellar Hemisphere (x5.9).

Protein differential expression in normal tissues from HIPED for PCDHA9 Gene

This gene is overexpressed in Adipocyte (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHA9 Gene

genes like me logo Genes that share expression patterns with PCDHA9: view

Protein tissue co-expression partners for PCDHA9 Gene

- Elite partner

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for PCDHA9 Gene

Orthologs for PCDHA9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA9 Gene

Organism Taxonomy Gene Similarity Type Details
(Mus musculus)
Mammalia Pcdha8 35
  • 83.05 (n)
  • 84.14 (a)
Pcdha8 16
(Pan troglodytes)
Mammalia PCDHA9 35
  • 99.37 (n)
  • 99.05 (a)
(Rattus norvegicus)
Mammalia Pcdha9 35
  • 82.42 (n)
  • 82.98 (a)
(Bos Taurus)
Mammalia -- 36
  • 81 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 63 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 65 (a)
-- 36
  • 69 (a)
-- 36
  • 68 (a)
(Gallus gallus)
Aves -- 36
  • 47 (a)
PCDHA11 36
  • 54 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 53 (a)
-- 36
  • 55 (a)
-- 36
  • 54 (a)
-- 36
  • 53 (a)
-- 36
  • 56 (a)
-- 36
  • 56 (a)
-- 36
  • 55 (a)
-- 36
  • 56 (a)
-- 36
  • 56 (a)
-- 36
  • 56 (a)
-- 36
  • 56 (a)
-- 36
  • 57 (a)
-- 36
  • 55 (a)
-- 36
  • 56 (a)
-- 36
  • 50 (a)
-- 36
  • 55 (a)
(Danio rerio)
Actinopterygii CR847851.6 36
  • 40 (a)
CR847851.8 36
  • 40 (a)
CT573264.4 36
  • 40 (a)
CT573264.5 36
  • 41 (a)
pcdh1a6 36
  • 41 (a)
pcdh2ab1 36
  • 42 (a)
pcdh2ab10 36
  • 39 (a)
pcdh2ab11 36
  • 41 (a)
pcdh2ab12 36
  • 41 (a)
pcdh2ab2 36
  • 41 (a)
pcdh2ab2 36
  • 41 (a)
pcdh2ab3 36
  • 41 (a)
pcdh2ab6 36
  • 40 (a)
pcdh2ab7 36
  • 41 (a)
pcdh2ab8 36
  • 42 (a)
pcdh2ab9 36
  • 40 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 34 (a)
CSA.7308 36
  • 19 (a)
Species with no ortholog for PCDHA9:
  • 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)
  • 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)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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)

Evolution for PCDHA9 Gene

Gene Tree for PCDHA9 (if available)
Gene Tree for PCDHA9 (if available)

Paralogs for PCDHA9 Gene

genes like me logo Genes that share paralogs with PCDHA9: view

Variants for PCDHA9 Gene

Sequence variations from dbSNP and Humsavar for PCDHA9 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
VAR_048530 -
VAR_048531 -
VAR_048532 -
VAR_048533 -
VAR_048534 -

Structural Variations from Database of Genomic Variants (DGV) for PCDHA9 Gene

Variant ID Type Subtype PubMed ID
nsv830508 CNV Loss 17160897
nsv882950 CNV Loss 21882294
dgv6343n71 CNV Loss 21882294
dgv1856e1 CNV Complex 17122850
dgv1857e1 CNV Complex 17122850
nsv882952 CNV Loss 21882294
dgv6344n71 CNV Loss 21882294
nsv882956 CNV Loss 21882294
nsv882957 CNV Loss 21882294
dgv6346n71 CNV Loss 21882294
nsv882965 CNV Gain+Loss 21882294
esv33939 CNV Gain+Loss 17666407
dgv6347n71 CNV Loss 21882294
dgv1043e199 CNV Deletion 23128226
esv2730839 CNV Deletion 23290073
esv26168 CNV Gain 19812545
dgv971n67 CNV Loss 20364138
nsv820841 CNV Deletion 20802225
nsv10753 CNV Gain 18304495
nsv819207 CNV Gain 19587683
dgv1044e199 CNV Deletion 23128226
esv29977 CNV Gain 17803354
nsv514324 CNV Loss 21397061
esv2421858 CNV Deletion 20811451
nsv442962 CNV CNV 18776908
dgv724n27 CNV Loss 19166990
nsv437955 CNV Loss 16468122
nsv515909 CNV Loss 19592680
esv2657537 CNV Deletion 23128226
nsv823262 CNV Gain 20364138
nsv823263 CNV Gain 20364138
nsv823264 CNV Gain 20364138
nsv882970 CNV Loss 21882294
nsv10754 CNV Gain 18304495
esv2505753 CNV Deletion 19546169

Variation tolerance for PCDHA9 Gene

Residual Variation Intolerance Score: 99.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.60; 97.81% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for PCDHA9 Gene

Disorders for PCDHA9 Gene

Relevant External Links for PCDHA9

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

No disorders were found for PCDHA9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHA9 Gene

Publications for PCDHA9 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 67
  2. Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. (PMID: 22589738) Fox C.S. … Borecki I.B. (PLoS Genet. 2012) 3
  3. Systematic identification of SH3 domain-mediated human protein-protein interactions by peptide array target screening. (PMID: 17474147) Wu C. … Li S.S. (Proteomics 2007) 3
  4. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J. … Rubin E.M. (Nature 2004) 3
  5. 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) 3

Products for PCDHA9 Gene

Sources for PCDHA9 Gene