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Aliases for PCDHA1 Gene

Aliases for PCDHA1 Gene

  • Protocadherin Alpha 1 2 3
  • KIAA0345-Like 13 2 3
  • PCDH-Alpha-1 3 4
  • Protocadherin Alpha-1 3
  • PCDH-ALPHA1 3

External Ids for PCDHA1 Gene

Summaries for PCDHA1 Gene

Entrez Gene Summary for PCDHA1 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 PCDHA1 Gene

PCDHA1 (Protocadherin Alpha 1) 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 PCDHA1 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 PCDHA1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA1 Gene

Genomics for PCDHA1 Gene

Genomic Location for PCDHA1 Gene

Start:
140,786,136 bp from pter
End:
141,012,347 bp from pter
Size:
226,212 bases
Orientation:
Plus strand

Genomic View for PCDHA1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PCDHA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA1 Gene

Regulatory Elements for PCDHA1 Gene

Proteins for PCDHA1 Gene

  • Protein details for PCDHA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5I3-PCDA1_HUMAN
    Recommended name:
    Protocadherin alpha-1
    Protein Accession:
    Q9Y5I3
    Secondary Accessions:
    • O75288
    • Q9NRT7

    Protein attributes for PCDHA1 Gene

    Size:
    950 amino acids
    Molecular mass:
    102952 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHA1 Gene

Proteomics data for PCDHA1 Gene at MOPED

Post-translational modifications for PCDHA1 Gene

  • Glycosylation at Asn257, Asn265, and Asn548

Other Protein References for PCDHA1 Gene

No data available for DME Specific Peptides for PCDHA1 Gene

Domains for PCDHA1 Gene

Gene Families for PCDHA1 Gene

HGNC:
  • PCDHC :Cadherins / Protocadherins : Clustered

Protein Domains for PCDHA1 Gene

UniProtKB/Swiss-Prot:

PCDA1_HUMAN
Domain:
  • Contains 6 cadherin domains.:
    • Q9Y5I3
genes like me logo Genes that share domains with PCDHA1: view

Function for PCDHA1 Gene

Molecular function for PCDHA1 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 PCDHA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHA1: view

Phenotypes for PCDHA1 Gene

MGI mutant phenotypes for PCDHA1:
inferred from 1 alleles
GenomeRNAi human phenotypes for PCDHA1:
genes like me logo Genes that share phenotypes with PCDHA1: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for PCDHA1 Gene

Localization for PCDHA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA1 Gene

Isoform 1: Cell membrane; Single-pass type I membrane protein.
Isoform 2: Secreted.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDHA1 Gene COMPARTMENTS Subcellular localization image for PCDHA1 gene
Compartment Confidence
plasma membrane 5
extracellular 3

Gene Ontology (GO) - Cellular Components for PCDHA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005886 plasma membrane IDA --
GO:0005887 integral component of plasma membrane TAS 10380929
GO:0016020 membrane --
genes like me logo Genes that share ontologies with PCDHA1: view

Pathways for PCDHA1 Gene

SuperPathways for PCDHA1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 10380929
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007399 nervous system development TAS 10380929
genes like me logo Genes that share ontologies with PCDHA1: view

No data available for Pathways by source for PCDHA1 Gene

Compounds for PCDHA1 Gene

(1) HMDB Compounds for PCDHA1 Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2
genes like me logo Genes that share compounds with PCDHA1: view

Transcripts for PCDHA1 Gene

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA1 Gene

No ASD Table

Relevant External Links for PCDHA1 Gene

GeneLoc Exon Structure for
PCDHA1
ECgene alternative splicing isoforms for
PCDHA1

Expression for PCDHA1 Gene

mRNA expression in normal human tissues for PCDHA1 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHA1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (5.7) and Brain - Cerebellar Hemisphere (4.2).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for PCDHA1 Gene

genes like me logo Genes that share expressions with PCDHA1: view

Orthologs for PCDHA1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHA1 37
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdha1 36
  • 83.91 (n)
  • 84.79 (a)
Pcdha1 16
oppossum
(Monodelphis domestica)
Mammalia -- 37
  • 64 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 37
  • 66 (a)
ManyToMany
-- 37
  • 68 (a)
ManyToMany
-- 37
  • 69 (a)
ManyToMany
rat
(Rattus norvegicus)
Mammalia Pcdha1 36
  • 83.39 (n)
  • 84.69 (a)
chicken
(Gallus gallus)
Aves -- 37
  • 47 (a)
ManyToMany
PCDHA11 37
  • 53 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 37
  • 52 (a)
ManyToMany
-- 37
  • 54 (a)
ManyToMany
-- 37
  • 54 (a)
ManyToMany
-- 37
  • 52 (a)
ManyToMany
-- 37
  • 55 (a)
ManyToMany
-- 37
  • 56 (a)
ManyToMany
-- 37
  • 54 (a)
ManyToMany
-- 37
  • 55 (a)
ManyToMany
-- 37
  • 55 (a)
ManyToMany
-- 37
  • 55 (a)
ManyToMany
-- 37
  • 55 (a)
ManyToMany
-- 37
  • 56 (a)
ManyToMany
-- 37
  • 56 (a)
ManyToMany
-- 37
  • 55 (a)
ManyToMany
-- 37
  • 51 (a)
ManyToMany
-- 37
  • 54 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii CR847851.6 37
  • 41 (a)
ManyToMany
CR847851.8 37
  • 40 (a)
ManyToMany
CT573264.4 37
  • 41 (a)
ManyToMany
CT573264.5 37
  • 40 (a)
ManyToMany
Dr.19866 36
pcdh1a6 37
  • 42 (a)
ManyToMany
pcdh2ab1 37
  • 42 (a)
ManyToMany
pcdh2ab10 37
  • 40 (a)
ManyToMany
pcdh2ab11 37
  • 41 (a)
ManyToMany
pcdh2ab12 37
  • 41 (a)
ManyToMany
pcdh2ab2 37
  • 40 (a)
ManyToMany
pcdh2ab2 37
  • 40 (a)
ManyToMany
pcdh2ab3 37
  • 41 (a)
ManyToMany
pcdh2ab6 37
  • 41 (a)
ManyToMany
pcdh2ab7 37
  • 41 (a)
ManyToMany
pcdh2ab8 37
  • 42 (a)
ManyToMany
pcdh2ab9 37
  • 39 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 32 (a)
ManyToMany
CSA.7308 37
  • 20 (a)
ManyToMany
Species with no ortholog for PCDHA1:
  • 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)
  • 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)
  • 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 PCDHA1 Gene

ENSEMBL:
Gene Tree for PCDHA1 (if available)
TreeFam:
Gene Tree for PCDHA1 (if available)

Paralogs for PCDHA1 Gene

genes like me logo Genes that share paralogs with PCDHA1: view

Variants for PCDHA1 Gene

Sequence variations from dbSNP and Humsavar for PCDHA1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type MAF
rs1548699 -- 140,785,333(-) ATATA(A/G)TCCAT upstream-variant-2KB
rs1548700 -- 140,785,304(-) AATCT(A/T)ATGCA upstream-variant-2KB
rs1548701 -- 140,784,972(-) TTTAT(A/G)TATTT upstream-variant-2KB
rs2240695 - 140,788,566(-) TAGAG(A/C)ACACC reference, missense, intron-variant
rs2240696 - 140,788,485(-) GCACA(C/T)ACGCA reference, missense, intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHA1 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
dgv970n67 CNV Gain 20364138
nsv330045 CNV Loss 16902084
esv8310 CNV Loss 19470904
esv2659321 CNV Deletion 23128226
nsv882956 CNV Loss 21882294
nsv882957 CNV Loss 21882294
dgv6345n71 CNV Loss 21882294
nsv882960 CNV Gain 21882294
esv2730838 CNV Deletion 23290073
nsv10752 CNV Gain+Loss 18304495
dgv6346n71 CNV Loss 21882294
esv21596 CNV Gain 19812545
nsv882965 CNV Gain+Loss 21882294
nsv436885 CNV Insertion 17901297
esv27071 CNV Loss 19812545
esv33939 CNV Gain+Loss 17666407
dgv6347n71 CNV Loss 21882294
nsv823251 CNV Gain 20364138
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
dgv972n67 CNV Gain 20364138
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

Relevant External Links for PCDHA1 Gene

HapMap Linkage Disequilibrium report
PCDHA1

Disorders for PCDHA1 Gene

(1) University of Copenhagen DISEASES for PCDHA1 Gene

Relevant External Links for PCDHA1

Genetic Association Database (GAD)
PCDHA1
Human Genome Epidemiology (HuGE) Navigator
PCDHA1
genes like me logo Genes that share disorders with PCDHA1: view

No data available for UniProtKB/Swiss-Prot for PCDHA1 Gene

Publications for PCDHA1 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 DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J. … Rubin E.M. (Nature 2004) 3 4
  3. Analysis of protocadherin alpha gene deletion variant in bipolar disorder and schizophrenia. (PMID: 18496207) Lachman H.M. … Stopkova P. (Psychiatr. Genet. 2008) 3 49
  4. 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
  5. CTCF/cohesin-mediated DNA looping is required for protocadherin I+ promoter choice. (PMID: 23204437) Guo Y. … Wu Q. (Proc. Natl. Acad. Sci. U.S.A. 2012) 3

Products for PCDHA1 Gene

Sources for PCDHA1 Gene

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