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Aliases for PCDHGA9 Gene

Aliases for PCDHGA9 Gene

  • Protocadherin Gamma Subfamily A, 9 2 3 5
  • PCDH-GAMMA-A9 3 4
  • Protocadherin Gamma-A9 3

External Ids for PCDHGA9 Gene

Previous GeneCards Identifiers for PCDHGA9 Gene

  • GC05P140588
  • GC05P141312
  • GC05P140708
  • GC05P140767
  • GC05P140787
  • GC05P140726
  • GC05P140806
  • GC05P140829
  • GC05P140846
  • GC05P140871
  • GC05P140878
  • GC05P140898
  • GC05P140931
  • GC05P140953
  • GC05P140974
  • GC05P140998
  • GC05P141026
  • GC05P141044
  • GC05P141072
  • GC05P135927
  • GC05P141110
  • GC05P141152
  • GC05P141169
  • GC05P141205
  • GC05P141245
  • GC05P141332
  • GC05P141387
  • GC05P141455
  • GC05P141533
  • GC05P141635
  • GC05P141737
  • GC05P141836
  • GC05P141939

Summaries for PCDHGA9 Gene

Entrez Gene Summary for PCDHGA9 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 PCDHGA9 Gene

PCDHGA9 (Protocadherin Gamma Subfamily A, 9) is a Protein Coding gene. GO annotations related to this gene include poly(A) RNA binding and calcium ion binding. An important paralog of this gene is PCDHGA8.

UniProtKB/Swiss-Prot for PCDHGA9 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 PCDHGA9 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGA9 Gene

Genomics for PCDHGA9 Gene

Regulatory Elements for PCDHGA9 Gene

Enhancers for PCDHGA9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H142221 1.6 Ensembl ENCODE dbSUPER 16 +819.7 819722 3 FOXA2 FEZF1 ZNF2 FOS SP3 JUNB ZNF662 KAT8 ZNF610 SMARCA4 PCDHB18P PCDHGA7 PCDHGA6 PCDHB15 PCDHGB3 PCDHB19P PCDHGB4 PCDHGA8 PCDHGB8P PCDHGA5
GH05H142278 1.7 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +877.6 877593 3 HDAC1 PKNOX1 ATF1 NFIB FEZF1 GLI4 ZNF2 ZNF366 SCRT2 FOS PCDHGA9 PCDHGB7 PCDHGB3 PCDHGA2 PCDHGA5 PCDHGB4 ENSG00000277968 ENSG00000280047
GH05H141563 1.6 Ensembl ENCODE dbSUPER 10.7 +161.5 161481 1 FOXA2 PKNOX1 ARNT DMAP1 ZNF2 YY1 ZNF143 ZNF207 FOS SP3 HARS2 IK PCDHB8 PCDHB3 PCDHA6 PCDHB9 PCDHB7 ENSG00000272108 PCDHB15 PCDHGC3
GH05H141968 1.1 ENCODE 14.7 +566.6 566635 2 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9 LOC102723915 HDAC3 KIAA0141 PCDHGA5 PCDHB12 RNF14 PCDHB11 PCDHB18P PCDHB4 PCDHB15
GH05H140717 1.2 ENCODE 10.6 -683.8 -683796 2 MLX ZNF416 ZNF143 SP3 PPARGC1A MEF2D GLIS1 RCOR2 NBN KDM1A ANKHD1 HARS2 PURA HDAC3 WDR55 PCDHB18P PCDHB19P TMCO6 PCDHB12 HARS
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDHGA9 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHGA9 Gene

Chromosome:
5
Start:
141,402,932 bp from pter
End:
141,512,979 bp from pter
Size:
110,048 bases
Orientation:
Plus strand

Genomic View for PCDHGA9 Gene

Genes around PCDHGA9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGA9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGA9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGA9 Gene

Proteins for PCDHGA9 Gene

  • Protein details for PCDHGA9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5G4-PCDG9_HUMAN
    Recommended name:
    Protocadherin gamma-A9
    Protein Accession:
    Q9Y5G4
    Secondary Accessions:
    • A2RU65
    • Q9Y5C9

    Protein attributes for PCDHGA9 Gene

    Size:
    932 amino acids
    Molecular mass:
    101687 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGA9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGA9 Gene

Post-translational modifications for PCDHGA9 Gene

  • Glycosylation at Asn47, posLast=127127, Asn389, posLast=419419, and Asn545
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGA9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGA9 Gene

Domains & Families for PCDHGA9 Gene

Gene Families for PCDHGA9 Gene

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

Protein Domains for PCDHGA9 Gene

Suggested Antigen Peptide Sequences for PCDHGA9 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGA9: view

No data available for UniProtKB/Swiss-Prot for PCDHGA9 Gene

Function for PCDHGA9 Gene

Molecular function for PCDHGA9 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 PCDHGA9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22681889
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGA9: view
genes like me logo Genes that share phenotypes with PCDHGA9: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PCDHGA9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGA9 Gene

Localization for PCDHGA9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGA9 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 PCDHGA9 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PCDHGA9 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 --
genes like me logo Genes that share ontologies with PCDHGA9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHGA9 Gene

Pathways & Interactions for PCDHGA9 Gene

SuperPathways for PCDHGA9 Gene

No Data Available

Interacting Proteins for PCDHGA9 Gene

Gene Ontology (GO) - Biological Process for PCDHGA9 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:0007283 spermatogenesis IEA --
GO:0007399 nervous system development IBA --
genes like me logo Genes that share ontologies with PCDHGA9: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGA9 Gene

Drugs & Compounds for PCDHGA9 Gene

(1) Drugs for PCDHGA9 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 PCDHGA9: view

Transcripts for PCDHGA9 Gene

mRNA/cDNA for PCDHGA9 Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PCDHGA9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGA9 Gene

No ASD Table

Relevant External Links for PCDHGA9 Gene

GeneLoc Exon Structure for
PCDHGA9
ECgene alternative splicing isoforms for
PCDHGA9

Expression for PCDHGA9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGA9 Gene

Protein differential expression in normal tissues from HIPED for PCDHGA9 Gene

This gene is overexpressed in Testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHGA9 Gene



Protein tissue co-expression partners for PCDHGA9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGA9 Gene:

PCDHGA9

Evidence on tissue expression from TISSUES for PCDHGA9 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHGA9: view

Primer Products

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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGA9 Gene

Orthologs for PCDHGA9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGA9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGA9 33
  • 99.61 (n)
cow
(Bos Taurus)
Mammalia PCDHGA9 33
  • 84 (n)
mouse
(Mus musculus)
Mammalia Pcdhga9 33 16
  • 82.59 (n)
rat
(Rattus norvegicus)
Mammalia Pcdhga9 33
  • 82.1 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 68 (a)
ManyToMany
-- 34
  • 66 (a)
ManyToMany
-- 34
  • 65 (a)
ManyToMany
-- 34
  • 65 (a)
ManyToMany
-- 34
  • 65 (a)
ManyToMany
-- 34
  • 58 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 65 (a)
ManyToMany
-- 34
  • 64 (a)
ManyToMany
-- 34
  • 62 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 34
  • 51 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 55 (a)
ManyToMany
-- 34
  • 54 (a)
ManyToMany
-- 34
  • 54 (a)
ManyToMany
-- 34
  • 53 (a)
ManyToMany
-- 34
  • 53 (a)
ManyToMany
-- 34
  • 53 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
Species where no ortholog for PCDHGA9 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)
  • 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 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 PCDHGA9 Gene

ENSEMBL:
Gene Tree for PCDHGA9 (if available)
TreeFam:
Gene Tree for PCDHGA9 (if available)

Paralogs for PCDHGA9 Gene

genes like me logo Genes that share paralogs with PCDHGA9: view

Variants for PCDHGA9 Gene

Sequence variations from dbSNP and Humsavar for PCDHGA9 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs386352347 Uncertain significance 141,485,635(+) CCGTT(A/G)GAAAA intron-variant, reference, synonymous-codon
rs1000014772 -- 141,409,727(+) TGAGC(A/G)CGCAG intron-variant, reference, missense
rs1000022316 -- 141,472,751(+) GAGGC(A/G)GAGGC intron-variant
rs1000136303 -- 141,452,887(+) TTATT(C/T)CACTT intron-variant
rs1000138324 -- 141,499,091(+) GGCAC(A/C)TGCTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGA9 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
nsv980740 CNV duplication 23825009

Variation tolerance for PCDHGA9 Gene

Residual Variation Intolerance Score: 88.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.88; 48.42% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHGA9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGA9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGA9 Gene

Disorders for PCDHGA9 Gene

Relevant External Links for PCDHGA9

Genetic Association Database (GAD)
PCDHGA9
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHGA9

No disorders were found for PCDHGA9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGA9 Gene

Publications for PCDHGA9 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 60
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60
  3. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. (PMID: 22681889) Baltz AG … Landthaler M (Molecular cell 2012) 3 60
  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 60
  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 60

Products for PCDHGA9 Gene

Sources for PCDHGA9 Gene

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