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Aliases for PCDHB16 Gene

Aliases for PCDHB16 Gene

  • Protocadherin Beta 16 2 3 5
  • Protocadherin-3x 2 3 4
  • Cadherin ME1 2 3
  • PCDH3X 3 4
  • Protocadherin Beta 8a 3
  • PCDH-Beta-16 4
  • PCDHbeta 16 2
  • PCDH-BETA16 3
  • KIAA1621 4
  • PCDHB8a 3
  • ME1 3

External Ids for PCDHB16 Gene

Previous GeneCards Identifiers for PCDHB16 Gene

  • GC05P140377
  • GC05P141143
  • GC05P140544
  • GC05P140599
  • GC05P140605
  • GC05P140542
  • GC05P135706
  • GC05P140561
  • GC05P140563
  • GC05P141354
  • GC05P141504

Summaries for PCDHB16 Gene

Entrez Gene Summary for PCDHB16 Gene

  • This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHB16 Gene

PCDHB16 (Protocadherin Beta 16) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA11.

UniProtKB/Swiss-Prot for PCDHB16 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 PCDHB16 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB16 Gene

Genomics for PCDHB16 Gene

Regulatory Elements for PCDHB16 Gene

Enhancers for PCDHB16 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 PCDHB16 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHB16 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PCDHB16 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHB16 Gene

141,181,399 bp from pter
141,186,399 bp from pter
5,001 bases
Plus strand

Genomic View for PCDHB16 Gene

Genes around PCDHB16 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB16 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB16 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB16 Gene

Proteins for PCDHB16 Gene

  • Protein details for PCDHB16 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin beta-16
    Protein Accession:
    Secondary Accessions:
    • B3KPK5
    • Q8IYD5
    • Q96SE9
    • Q9HCF1

    Protein attributes for PCDHB16 Gene

    776 amino acids
    Molecular mass:
    84983 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAB13447.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

neXtProt entry for PCDHB16 Gene

Proteomics data for PCDHB16 Gene at MOPED

Post-translational modifications for PCDHB16 Gene

  • Glycosylation at Asn 418, Asn 436, and Asn 567
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB16 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for PCDHB16

No data available for DME Specific Peptides for PCDHB16 Gene

Domains & Families for PCDHB16 Gene

Gene Families for PCDHB16 Gene

Protein Domains for PCDHB16 Gene

Suggested Antigen Peptide Sequences for PCDHB16 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 PCDHB16: view

Function for PCDHB16 Gene

Molecular function for PCDHB16 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 PCDHB16 Gene

GenomeRNAi human phenotypes for PCDHB16:
genes like me logo Genes that share phenotypes with PCDHB16: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDHB16

CRISPR Products

miRNA for PCDHB16 Gene

miRTarBase miRNAs that target PCDHB16

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHB16 Gene

Localization for PCDHB16 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB16 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for PCDHB16 Gene COMPARTMENTS Subcellular localization image for PCDHB16 gene
Compartment Confidence
plasma membrane 4
cytoskeleton 1
cytosol 1
endoplasmic reticulum 1
extracellular 1
golgi apparatus 1
mitochondrion 1
peroxisome 1

No data available for Gene Ontology (GO) - Cellular Components for PCDHB16 Gene

Pathways & Interactions for PCDHB16 Gene

SuperPathways for PCDHB16 Gene

No Data Available

Interacting Proteins for PCDHB16 Gene

Gene Ontology (GO) - Biological Process for PCDHB16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
genes like me logo Genes that share ontologies with PCDHB16: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB16 Gene

Drugs & Compounds for PCDHB16 Gene

(1) Drugs for PCDHB16 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 PCDHB16: view

Transcripts for PCDHB16 Gene

mRNA/cDNA for PCDHB16 Gene

Unigene Clusters for PCDHB16 Gene

Protocadherin beta 16:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB16 Gene

No ASD Table

Relevant External Links for PCDHB16 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHB16 Gene

mRNA expression in normal human tissues for PCDHB16 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDHB16 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (48.0) and Platelet (13.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHB16 Gene

SOURCE GeneReport for Unigene cluster for PCDHB16 Gene Hs.147674

genes like me logo Genes that share expression patterns with PCDHB16: view

Protein tissue co-expression partners for PCDHB16 Gene

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PCDHB16 Gene

Orthologs for PCDHB16 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHB16 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PCDHB16 35
  • 85.98 (n)
  • 83.87 (a)
(Canis familiaris)
Mammalia PCDHB8 35
  • 77.21 (n)
  • 73.05 (a)
(Mus musculus)
Mammalia Pcdhb17 35
  • 79.75 (n)
  • 76.68 (a)
Pcdhb17 16
(Pan troglodytes)
Mammalia PCDHB16 35
  • 98.63 (n)
  • 98.2 (a)
Species with no ortholog for PCDHB16:
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 PCDHB16 Gene

Gene Tree for PCDHB16 (if available)
Gene Tree for PCDHB16 (if available)

Paralogs for PCDHB16 Gene

genes like me logo Genes that share paralogs with PCDHB16: view

Variants for PCDHB16 Gene

Sequence variations from dbSNP and Humsavar for PCDHB16 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs17844651 - 141,184,133(+) CCTGC(A/G)GGAGT reference, missense
rs2697532 - 141,184,153(-) GGCGC(C/T)CACGC reference, missense
rs17096969 - 141,182,832(+) CTAGA(G/T)CGAGA reference, missense
rs28664170 - 141,183,598(+) CACAG(C/G/T)TGACC reference, missense
VAR_061069 -

Structural Variations from Database of Genomic Variants (DGV) for PCDHB16 Gene

Variant ID Type Subtype PubMed ID
dgv1857e1 CNV Complex 17122850
nsv428127 CNV Loss 18775914
dgv6348n71 CNV Loss 21882294
nsv471634 CNV Gain+Loss 15918152
dgv6349n71 CNV Loss 21882294
dgv1858e1 CNV Complex 17122850
dgv6350n71 CNV Loss 21882294
nsv509092 CNV Insertion 20534489
nsv823266 CNV Gain 20364138
dgv1005e201 CNV Deletion 23290073
nsv10756 CNV Gain 18304495
nsv499084 CNV Gain 21111241
esv2664767 CNV Deletion 23128226
nsv5031 CNV Insertion 18451855
nsv882981 CNV Gain 21882294
esv2730844 CNV Deletion 23290073

Variation tolerance for PCDHB16 Gene

Residual Variation Intolerance Score: 71% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 20.29; 99.06% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHB16 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB16 Gene

Disorders for PCDHB16 Gene

Relevant External Links for PCDHB16

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for PCDHB16 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB16 Gene

Publications for PCDHB16 Gene

  1. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 2 3 4 67
  2. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PMID: 11322959) Vanhalst K. … van Roy F. (FEBS Lett. 2001) 2 3
  3. Postsynaptic and differential localization to neuronal subtypes of protocadherin beta16 in the mammalian central nervous system. (PMID: 18279309) Junghans D. … Kemler R. (Eur. J. Neurosci. 2008) 23
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 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 PCDHB16 Gene

Sources for PCDHB16 Gene