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Aliases for PCDHB16 Gene

Aliases for PCDHB16 Gene

  • Protocadherin Beta 16 2 3
  • Protocadherin-3x 2 3 4
  • Cadherin ME1 2 3
  • PCDH3X 3 4
  • Protocadherin Beta 8a 3
  • Protocadherin Beta-16 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

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. Among its related pathways are Metabolism and Metabolism. GO annotations related to this gene include calcium ion binding.

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

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for PCDHB16 Gene

Start:
141,181,399 bp from pter
End:
141,186,399 bp from pter
Size:
5,001 bases
Orientation:
Plus strand

Genomic View for PCDHB16 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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:
    Q9NRJ7-PCDBG_HUMAN
    Recommended name:
    Protocadherin beta-16
    Protein Accession:
    Q9NRJ7
    Secondary Accessions:
    • B3KPK5
    • Q8IYD5
    • Q96SE9
    • Q9HCF1

    Protein attributes for PCDHB16 Gene

    Size:
    776 amino acids
    Molecular mass:
    84983 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • 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 Asn418, Asn436, and Asn567
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB16 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB16 Gene

Domains for PCDHB16 Gene

Gene Families for PCDHB16 Gene

HGNC:
  • PCDHC :Cadherins / Protocadherins : Clustered

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

Q9NRJ7

UniProtKB/Swiss-Prot:

PCDBG_HUMAN :
  • Q9NRJ7
Domain:
  • 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

Gene Ontology (GO) - Molecular Function for PCDHB16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB16: view

Animal Model Products

CRISPR Products

miRNA for PCDHB16 Gene

miRTarBase miRNAs that target PCDHB16

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PCDHB16

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting 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

COMPARTMENTS
Jensen Localization Image for PCDHB16 Gene COMPARTMENTS Subcellular localization image for PCDHB16 gene
Compartment Confidence
plasma membrane 3
cytoskeleton 1
cytosol 1
endoplasmic reticulum 1
extracellular 1
golgi apparatus 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PCDHB16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane --
GO:0016021 integral component of membrane NAS 11322959
genes like me logo Genes that share ontologies with PCDHB16: view

Pathways for PCDHB16 Gene

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

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 --
GO:0007268 synaptic transmission TAS 12231349
GO:0007416 synapse assembly TAS 12231349
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS 11322959
genes like me logo Genes that share ontologies with PCDHB16: view

Compounds for PCDHB16 Gene

(1) HMDB Compounds for PCDHB16 Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2
genes like me logo Genes that share compounds with PCDHB16: view

Transcripts for PCDHB16 Gene

mRNA/cDNA for PCDHB16 Gene

(38) Selected AceView cDNA sequences:
(7) Additional mRNA sequences :
(1) REFSEQ mRNAs :
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCDHB16 Gene

Protocadherin beta 16:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PCDHB16

Primer Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for PCDHB16 Gene

GeneLoc Exon Structure for
PCDHB16
ECgene alternative splicing isoforms for
PCDHB16

Expression for PCDHB16 Gene

mRNA expression in normal human tissues for PCDHB16 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB and MOPED for PCDHB16 Gene

SOURCE GeneReport for Unigene cluster for PCDHB16 Gene Hs.147674

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

In Situ Assay 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
chimpanzee
(Pan troglodytes)
Mammalia PCDHB16 35
  • 98.63 (n)
  • 98.2 (a)
cow
(Bos Taurus)
Mammalia PCDHB16 35
  • 85.98 (n)
  • 83.87 (a)
dog
(Canis familiaris)
Mammalia PCDHB8 35
  • 77.21 (n)
  • 73.05 (a)
mouse
(Mus musculus)
Mammalia Pcdhb17 35
  • 79.75 (n)
  • 76.68 (a)
Pcdhb17 16
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

ENSEMBL:
Gene Tree for PCDHB16 (if available)
TreeFam:
Gene Tree for PCDHB16 (if available)

Paralogs for PCDHB16 Gene

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

No data available for Paralogs for PCDHB16 Gene

Variants for PCDHB16 Gene

Sequence variations from dbSNP and Humsavar for PCDHB16 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type MAF
rs2204704 -- 141,182,408(-) TTCTT(C/T)TGCTT utr-variant-5-prime
rs2697532 - 141,184,153(-) GGCGC(C/T)CACGC missense, reference
rs2697533 -- 141,184,083(-) TTGTC(C/T)GCGTT synonymous-codon, reference
rs2697534 -- 141,183,999(-) GTGCC(C/T)GAGTC synonymous-codon, reference
rs2697535 -- 141,182,077(-) ACCAG(A/G)CATAG utr-variant-5-prime

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

Relevant External Links for PCDHB16 Gene

HapMap Linkage Disequilibrium report
PCDHB16
Human Gene Mutation Database (HGMD)
PCDHB16

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

Disorders for PCDHB16 Gene

No disorders were found for PCDHB16 Gene.

No data available for UniProtKB/Swiss-Prot 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
  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 4
  3. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. (PMID: 12665801) Gevaert K. … Vandekerckhove J. (Nat. Biotechnol. 2003) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  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 4

Products for PCDHB16 Gene

Sources for PCDHB16 Gene

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