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Aliases for PCDHA13 Gene

Aliases for PCDHA13 Gene

  • Protocadherin Alpha 13 2 3 5
  • Ortholog Of Mouse CNR5 2 3
  • KIAA0345-Like 1 2 3
  • PCDH-Alpha-13 3 4
  • CNRS5 3 4
  • Protocadherin Alpha-13 3
  • PCDH-ALPHA13 3
  • CNRN5 3
  • CRNR5 3
  • CNR5 3

External Ids for PCDHA13 Gene

Previous HGNC Symbols for PCDHA13 Gene

  • CNRS5

Previous GeneCards Identifiers for PCDHA13 Gene

  • GC05P140078
  • GC05P140760
  • GC05P140205
  • GC05P140198
  • GC05P140169
  • GC05P140242
  • GC05P140251
  • GC05P140260
  • GC05P140270
  • GC05P140279
  • GC05P140289
  • GC05P140300
  • GC05P140309
  • GC05P140330
  • GC05P140337
  • GC05P135406
  • GC05P140353
  • GC05P140374
  • GC05P140393
  • GC05P140407
  • GC05P140423
  • GC05P140440
  • GC05P140458
  • GC05P141436
  • GC05P141571
  • GC05P141673
  • GC05P141774
  • GC05P141875

Summaries for PCDHA13 Gene

Entrez Gene Summary for PCDHA13 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 PCDHA13 Gene

PCDHA13 (Protocadherin Alpha 13) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHA3.

UniProtKB/Swiss-Prot for PCDHA13 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 CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHA13 Gene

Genomics for PCDHA13 Gene

Regulatory Elements for PCDHA13 Gene

Enhancers for PCDHA13 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
GH05G140965 1 ENCODE 16.8 +84.3 84309 1.3 PKNOX1 ARID4B SIN3A DMAP1 ZNF48 GLIS2 ZNF263 SP3 MXD4 TSHZ1 PCDHA11 PCDHA13 LOC102723915 ENSG00000279028 PCDHACT
GH05G141725 0.7 ENCODE 6.4 +843.9 843867 1.4 SCRT1 MAX GTF3C2 MAFF POLR3A SCRT2 NFE2L1 RCOR1 NFE2 MAFK HDAC3 LOC102723915 PCDH1 PCDHA13 ARAP3 ENSG00000278925
GH05G140943 0.6 FANTOM5 3.9 +61.2 61180 0.1 JUND BHLHE40 NRF1 SIN3A FOS ZNF600 NFE2L2 PCDHA13 PCDHA3 PCDHGA6 PCDHA2 PCDHA1 PCDHAC2 PCDHA7 PCDHA4 PCDHA5 PCDHB15
GH05G140996 0.5 FANTOM5 3.1 +114.4 114368 0.3 ZNF121 ZNF512 ZSCAN5C PCDHGC4 PCDHA13 PCDHGA6 PCDHA3 PCDHA2 PCDHB12 PCDHA4 PCDHGA8 PCDHB15 PCDHA6
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDHA13 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHA13 Gene

Chromosome:
5
Start:
140,882,208 bp from pter
End:
141,012,344 bp from pter
Size:
130,137 bases
Orientation:
Plus strand

Genomic View for PCDHA13 Gene

Genes around PCDHA13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHA13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHA13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHA13 Gene

Proteins for PCDHA13 Gene

  • Protein details for PCDHA13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5I0-PCDAD_HUMAN
    Recommended name:
    Protocadherin alpha-13
    Protein Accession:
    Q9Y5I0
    Secondary Accessions:
    • O75277

    Protein attributes for PCDHA13 Gene

    Size:
    950 amino acids
    Molecular mass:
    102483 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHA13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHA13 Gene

Post-translational modifications for PCDHA13 Gene

  • Glycosylation at posLast=257257, Asn265, and posLast=548548
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHA13 Gene

No data available for DME Specific Peptides for PCDHA13 Gene

Domains & Families for PCDHA13 Gene

Gene Families for PCDHA13 Gene

Suggested Antigen Peptide Sequences for PCDHA13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHA13: view

No data available for UniProtKB/Swiss-Prot for PCDHA13 Gene

Function for PCDHA13 Gene

Molecular function for PCDHA13 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 PCDHA13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHA13: view
genes like me logo Genes that share phenotypes with PCDHA13: view

Animal Model Products

CRISPR Products

miRNA for PCDHA13 Gene

miRTarBase miRNAs that target PCDHA13

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHA13 Gene

Localization for PCDHA13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHA13 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 PCDHA13 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PCDHA13 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 PCDHA13: view

Pathways & Interactions for PCDHA13 Gene

SuperPathways for PCDHA13 Gene

No Data Available

Interacting Proteins for PCDHA13 Gene

Gene Ontology (GO) - Biological Process for PCDHA13 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:0007399 nervous system development IBA --
genes like me logo Genes that share ontologies with PCDHA13: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHA13 Gene

Drugs & Compounds for PCDHA13 Gene

(1) Drugs for PCDHA13 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 PCDHA13: view

Transcripts for PCDHA13 Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHA13 Gene

No ASD Table

Relevant External Links for PCDHA13 Gene

GeneLoc Exon Structure for
PCDHA13
ECgene alternative splicing isoforms for
PCDHA13

Expression for PCDHA13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHA13 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHA13 Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x7.4) and Brain - Cerebellum (x4.7).

Protein differential expression in normal tissues from HIPED for PCDHA13 Gene

This gene is overexpressed in Tlymphocyte (49.6) and Heart (19.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHA13 Gene



Protein tissue co-expression partners for PCDHA13 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHA13 Gene:

PCDHA13

Evidence on tissue expression from TISSUES for PCDHA13 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHA13: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHA13 Gene

Orthologs for PCDHA13 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHA13 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PCDHA13 34 35
  • 87.37 (n)
mouse
(Mus musculus)
Mammalia Pcdha12 16 34
  • 83.68 (n)
rat
(Rattus norvegicus)
Mammalia Pcdha13 34
  • 82.98 (n)
dog
(Canis familiaris)
Mammalia -- 35
  • 74 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 68 (a)
ManyToMany
-- 35
  • 68 (a)
ManyToMany
-- 35
  • 67 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 64 (a)
OneToMany
chicken
(Gallus gallus)
Aves PCDHA11 35
  • 53 (a)
ManyToMany
-- 35
  • 47 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 58 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 55 (a)
ManyToMany
-- 35
  • 53 (a)
ManyToMany
-- 35
  • 52 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
zebrafish
(Danio rerio)
Actinopterygii pcdh2ab1 35
  • 43 (a)
ManyToMany
pcdh2ab12 35
  • 43 (a)
ManyToMany
pcdh2ab8 35
  • 43 (a)
ManyToMany
CR847851.6 35
  • 42 (a)
ManyToMany
CR847851.8 35
  • 42 (a)
ManyToMany
pcdh1a6 35
  • 42 (a)
ManyToMany
pcdh2ab11 35
  • 42 (a)
ManyToMany
pcdh2ab2 35 35
  • 42 (a)
ManyToMany
pcdh2ab3 35
  • 42 (a)
ManyToMany
pcdh2ab6 35
  • 42 (a)
ManyToMany
pcdh2ab7 35
  • 42 (a)
ManyToMany
CT573264.5 35
  • 42 (a)
ManyToMany
CT573264.4 35
  • 42 (a)
ManyToMany
pcdh2ab10 35
  • 41 (a)
ManyToMany
pcdh2ab9 35
  • 41 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 33 (a)
ManyToMany
CSA.7308 35
  • 20 (a)
ManyToMany
Species where no ortholog for PCDHA13 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • 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 PCDHA13 Gene

ENSEMBL:
Gene Tree for PCDHA13 (if available)
TreeFam:
Gene Tree for PCDHA13 (if available)

Paralogs for PCDHA13 Gene

genes like me logo Genes that share paralogs with PCDHA13: view

Variants for PCDHA13 Gene

Sequence variations from dbSNP and Humsavar for PCDHA13 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs386352346 Uncertain significance 140,929,288(+) GATTC(A/G)GAATA intron-variant, reference, missense
rs1000122176 -- 140,965,777(+) TTTGC(C/T)TACAG intron-variant, upstream-variant-2KB
rs1000158608 -- 140,908,533(+) GTTTC(C/T)ACCAA intron-variant
rs1000222500 -- 140,957,863(+) TTTCC(G/T)ATTTT intron-variant
rs1000356638 -- 140,999,029(+) TGATA(C/T)TTCGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHA13 Gene

Variant ID Type Subtype PubMed ID
esv2505753 CNV deletion 19546169
esv2759382 CNV gain 17122850
esv3606959 CNV gain 21293372
nsv1031849 CNV loss 25217958
nsv10754 CNV gain 18304495
nsv599904 CNV loss 21841781
nsv823264 CNV gain 20364138
nsv968252 CNV duplication 23825009
nsv968992 CNV duplication 23825009

Variation tolerance for PCDHA13 Gene

Residual Variation Intolerance Score: 42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.51; 43.87% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHA13 Gene

Human Gene Mutation Database (HGMD)
PCDHA13
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHA13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHA13 Gene

Disorders for PCDHA13 Gene

Relevant External Links for PCDHA13

Genetic Association Database (GAD)
PCDHA13
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHA13

No disorders were found for PCDHA13 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHA13 Gene

Publications for PCDHA13 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. The DNA sequence and comparative analysis of human chromosome 5. (PMID: 15372022) Schmutz J. … Rubin E.M. (Nature 2004) 3 4 64
  3. Genomic organization of the family of CNR cadherin genes in mice and humans. (PMID: 10662547) Sugino H. … Yagi T. (Genomics 2000) 2 3 64
  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 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 PCDHA13 Gene

Sources for PCDHA13 Gene

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