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Aliases for PCDHGA1 Gene

Aliases for PCDHGA1 Gene

  • Protocadherin Gamma Subfamily A, 1 2 3 5
  • PCDH-GAMMA-A1 3 4
  • Protocadherin Gamma-A1 3

External Ids for PCDHGA1 Gene

Previous GeneCards Identifiers for PCDHGA1 Gene

  • GC05P140526
  • GC05P141293
  • GC05P140693
  • GC05P140738
  • GC05P140690
  • GC05P141047
  • GC05P135855
  • GC05P141240
  • GC05P141288
  • GC05P141367
  • GC05P141440
  • GC05P141515
  • GC05P141622
  • GC05P141724

Summaries for PCDHGA1 Gene

Entrez Gene Summary for PCDHGA1 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 PCDHGA1 Gene

PCDHGA1 (Protocadherin Gamma Subfamily A, 1) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA2.

UniProtKB/Swiss-Prot for PCDHGA1 Gene

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

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGA1 Gene

Genomics for PCDHGA1 Gene

Regulatory Elements for PCDHGA1 Gene

Enhancers for PCDHGA1 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
GH05F141968 0.5 ENCODE 12.4 +639.0 638996 3.0 HDGF PKNOX1 ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 PCDHB5 KIAA0141 HDAC3 PCDHGA5 PCDHB12 RNF14 PCDHB11 PCDHB4 PCDHB19P PCDHB18P
GH05F141325 0.2 ENCODE 9.7 -4.4 -4399 1.1 TBP ATF1 CBX3 PKNOX1 ZNF48 RAD21 GATA2 CBX5 ETV6 CREM PCDHB15 PCDHGA1 IK PCDHA11 ENSG00000272070 TAF7
GH05F141429 0.6 ENCODE 5.2 +100.2 100191 1.5 CTCF POLR2A ZNF143 SMC3 TRIM22 RAD21 MYC PCDHGA1 HDAC3 PCDHGA12 PCDHGB9P
GH05F141592 0.6 Ensembl ENCODE 5.1 +261.7 261730 0.6 CTCF SAP130 ARID4B RAD21 ZNF121 ZNF664 NCOR1 GATAD1 ZNF143 SMC3 FCHSD1 LOC102723915 DIAPH1 HDAC3 RELL2 PCDHGA1 GC05P141898 RPS27AP10
GH05F141597 1.8 FANTOM5 Ensembl ENCODE 5.1 +273.3 273330 13.8 PKNOX1 ARNT ARID4B SIN3A YY1 CBX5 ZNF143 ZNF263 JUNB TBX21 RELL2 HDAC3 FCHSD1 DIAPH1 LOC100505658 PCDHGA6 PCDHGB6 KIAA0141 PCDHGA8 PCDHB17P
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PCDHGA1 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHGA1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001874442 129 601 BCOR CTCF ZNF223 ZMYM3 ZNF384 BCL11B RAD21 ZNF324 ZNF335 SMC3

Genomic Location for PCDHGA1 Gene

Chromosome:
5
Start:
141,330,571 bp from pter
End:
141,512,981 bp from pter
Size:
182,411 bases
Orientation:
Plus strand

Genomic View for PCDHGA1 Gene

Genes around PCDHGA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGA1 Gene

Proteins for PCDHGA1 Gene

  • Protein details for PCDHGA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5H4-PCDG1_HUMAN
    Recommended name:
    Protocadherin gamma-A1
    Protein Accession:
    Q9Y5H4
    Secondary Accessions:
    • Q2M273
    • Q9Y5D6

    Protein attributes for PCDHGA1 Gene

    Size:
    931 amino acids
    Molecular mass:
    101226 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGA1 Gene

Post-translational modifications for PCDHGA1 Gene

  • Glycosylation at Asn 265, Asn 419, Asn 545, and Asn 685
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGA1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGA1 Gene

Domains & Families for PCDHGA1 Gene

Gene Families for PCDHGA1 Gene

Protein Domains for PCDHGA1 Gene

Suggested Antigen Peptide Sequences for PCDHGA1 Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y5H4

UniProtKB/Swiss-Prot:

PCDG1_HUMAN :
  • Contains 6 cadherin domains.
Domain:
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHGA1: view

Function for PCDHGA1 Gene

Molecular function for PCDHGA1 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 PCDHGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGA1: view
genes like me logo Genes that share phenotypes with PCDHGA1: view

Animal Models for PCDHGA1 Gene

MGI Knock Outs for PCDHGA1:

Animal Model Products

miRNA for PCDHGA1 Gene

miRTarBase miRNAs that target PCDHGA1

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PCDHGA1 Gene

Localization for PCDHGA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGA1 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDHGA1 Gene COMPARTMENTS Subcellular localization image for PCDHGA1 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytosol 1
endoplasmic reticulum 1
lysosome 1
peroxisome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for PCDHGA1 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 PCDHGA1: view

Pathways & Interactions for PCDHGA1 Gene

SuperPathways for PCDHGA1 Gene

No Data Available

Interacting Proteins for PCDHGA1 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see 8)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000431083%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000344456%0d%0a9606.ENSP00000362481%0d%0a9606.ENSP00000311113%0d%0a
Selected Interacting proteins: ENSP00000431083 Q9Y5H4-PCDG1_HUMAN for PCDHGA1 Gene via STRING IID

Gene Ontology (GO) - Biological Process for PCDHGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,IBA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development IBA --
genes like me logo Genes that share ontologies with PCDHGA1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGA1 Gene

Drugs & Compounds for PCDHGA1 Gene

(1) Drugs for PCDHGA1 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 PCDHGA1: view

Transcripts for PCDHGA1 Gene

mRNA/cDNA for PCDHGA1 Gene

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGA1 Gene

No ASD Table

Relevant External Links for PCDHGA1 Gene

GeneLoc Exon Structure for
PCDHGA1
ECgene alternative splicing isoforms for
PCDHGA1

Expression for PCDHGA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHGA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDHGA1 Gene

This gene is overexpressed in Heart (38.8) and Peripheral blood mononuclear cells (30.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHGA1 Gene



Protein tissue co-expression partners for PCDHGA1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGA1 Gene:

PCDHGA1
genes like me logo Genes that share expression patterns with PCDHGA1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PCDHGA1 Gene

Orthologs for PCDHGA1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGA1 34
  • 98.62 (n)
rat
(Rattus norvegicus)
Mammalia Pcdhga1 34
  • 82.42 (n)
mouse
(Mus musculus)
Mammalia Pcdhga1 34 16
  • 81.66 (n)
dog
(Canis familiaris)
Mammalia PCDHGA1 35
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 67 (a)
ManyToMany
-- 35
  • 65 (a)
ManyToMany
-- 35
  • 65 (a)
ManyToMany
-- 35
  • 64 (a)
ManyToMany
-- 35
  • 64 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 66 (a)
ManyToMany
-- 35
  • 63 (a)
ManyToMany
-- 35
  • 63 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 35
  • 50 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 54 (a)
ManyToMany
-- 35
  • 54 (a)
ManyToMany
-- 35
  • 54 (a)
ManyToMany
-- 35
  • 53 (a)
ManyToMany
-- 35
  • 53 (a)
ManyToMany
-- 35
  • 53 (a)
ManyToMany
-- 35
  • 52 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.11957 34
African clawed frog
(Xenopus laevis)
Amphibia LOC398725 34
Species where no ortholog for PCDHGA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • cow (Bos Taurus)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PCDHGA1 Gene

ENSEMBL:
Gene Tree for PCDHGA1 (if available)
TreeFam:
Gene Tree for PCDHGA1 (if available)

Paralogs for PCDHGA1 Gene

genes like me logo Genes that share paralogs with PCDHGA1: view

Variants for PCDHGA1 Gene

Sequence variations from dbSNP and Humsavar for PCDHGA1 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
rs1002519 -- 141,489,436(-) GCCCA(A/G)TTGCA intron-variant, reference, synonymous-codon
rs10035418 -- 141,437,664(+) CGAAG(A/G)GATGT intron-variant
rs10038103 -- 141,414,849(+) CTGGA(C/T)CAGAA intron-variant, reference, synonymous-codon
rs10040701 -- 141,508,490(+) TTTCC(A/G)TATCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGA1 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv3422812 CNV insertion 20981092
esv3570470 CNV loss 25503493
esv3606980 CNV loss 21293372
esv3606981 CNV gain 21293372
esv3606982 CNV loss 21293372
esv3606983 CNV gain 21293372
esv3606984 CNV loss 21293372
esv3606985 CNV gain 21293372
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
nsv599921 CNV loss 21841781
nsv599922 CNV loss 21841781
nsv599923 CNV loss 21841781
nsv823279 CNV gain 20364138
nsv823280 CNV loss 20364138
nsv964962 CNV duplication 23825009
nsv968258 CNV duplication 23825009
nsv968259 CNV duplication 23825009
nsv980739 CNV duplication 23825009
nsv980740 CNV duplication 23825009

Variation tolerance for PCDHGA1 Gene

Residual Variation Intolerance Score: 48.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.73; 66.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHGA1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGA1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGA1 Gene

Disorders for PCDHGA1 Gene

Relevant External Links for PCDHGA1

Genetic Association Database (GAD)
PCDHGA1
Human Genome Epidemiology (HuGE) Navigator
PCDHGA1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHGA1

No disorders were found for PCDHGA1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGA1 Gene

Publications for PCDHGA1 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 64
  2. 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 46 64
  3. 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) 4 64
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3 64
  5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 3 64

Products for PCDHGA1 Gene

Sources for PCDHGA1 Gene

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