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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
  • 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
  • GC05P141354
  • GC05P141504
  • GC05P141610
  • GC05P141713
  • GC05P141812
  • GC05P141911
  • GC05P142019

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. Diseases associated with PCDHB16 include Protocadherin-Beta Gene Cluster. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA7.

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

Additional gene information for PCDHB16 Gene

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

Genomics for PCDHB16 Gene

GeneHancer (GH) Regulatory Elements for PCDHB16 Gene

Promoters and enhancers for PCDHB16 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I141183 Promoter/Enhancer 1.1 EPDnew ENCODE 550.8 +1.0 953 0.1 SMARCA5 CTCF ZNF654 SIN3A RAD21 ZFHX2 CREB1 ZNF143 SMC3 ZNF444 ENSG00000279068 PIR41634 PCDHB16 ENSG00000279472 ENSG00000280029 PCDHB@
GH05I141182 Promoter 0.9 Ensembl 550.8 +1.2 1202 0.4 SMARCA5 CTCF ZNF654 SIN3A RAD21 ZFHX2 CREB1 ZNF143 SMC3 ZNF444 ENSG00000279068 PIR41634 PCDHB16 PCDHB7 PCDHB11 ENSG00000280029 PCDHB@
GH05I141039 Enhancer 1.4 FANTOM5 Ensembl ENCODE 21.9 -140.9 -140865 2.6 PKNOX1 CLOCK ATF1 ARID4B SIN3A ZNF48 YY1 CBX5 ELK1 ZNF143 ANKHD1 PCDHB16 HDAC3 WDR55 LOC102723915 TMCO6 HARS2 PCDHA4 PCDHA9 KIAA0141
GH05I141177 Promoter 0.7 EPDnew 36 -3.6 -3599 0.1 CTCF ZNF654 ENSG00000279472 PCDHB8 PCDHB16 ENSG00000280029 PCDHB@
GH05I140563 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 4.4 -616.5 -616473 3.1 HDGF PKNOX1 CLOCK ARNT ARID4B SIN3A YBX1 ZNF2 YY1 POLR2B APBB3 MIR6831 SLC35A4 CD14 WDR55 DND1 ENSG00000200051 ANKHD1 ANKHD1-EIF4EBP3 ENSG00000253965
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHB16 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHB16 gene promoter:

Genomic Locations for PCDHB16 Gene

Genomic Locations for PCDHB16 Gene
chr5:141,181,399-141,186,399
(GRCh38/hg38)
Size:
5,001 bases
Orientation:
Plus strand
chr5:140,560,980-140,565,796
(GRCh37/hg19)

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:
    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

Post-translational modifications for PCDHB16 Gene

  • Glycosylation at isoforms=418, Asn436, and isoforms=567
  • 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 & Families for PCDHB16 Gene

Gene Families for PCDHB16 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

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

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

No data available for UniProtKB/Swiss-Prot for PCDHB16 Gene

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 From GWAS Catalog for PCDHB16 Gene

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

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

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , 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

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 PCDHB16 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDHB16 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 NAS 11322959
genes like me logo Genes that share ontologies with PCDHB16: view

Pathways & Interactions for PCDHB16 Gene

SuperPathways for PCDHB16 Gene

No Data Available

Interacting Proteins for PCDHB16 Gene

Selected Interacting proteins: Q9NRJ7-PCDBG_HUMAN for PCDHB16 Gene via IID

Gene Ontology (GO) - Biological Process for PCDHB16 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA,IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007268 chemical 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

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 Approved 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:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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



Protein tissue co-expression partners for PCDHB16 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHB16 Gene:

PCDHB16

SOURCE GeneReport for Unigene cluster for PCDHB16 Gene:

Hs.147674

Evidence on tissue expression from TISSUES for PCDHB16 Gene

  • Nervous system(4.3)
  • Blood(4.1)
genes like me logo Genes that share expression patterns with PCDHB16: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33
  • 98.63 (n)
cow
(Bos Taurus)
Mammalia PCDHB16 33
  • 85.98 (n)
mouse
(Mus musculus)
Mammalia Pcdhb17 16 33
  • 79.75 (n)
dog
(Canis familiaris)
Mammalia PCDHB8 33
  • 77.21 (n)
Species where no ortholog for PCDHB16 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)
  • 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

Pseudogenes.org Pseudogenes 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 Variation AA Info Type
rs1002286752 -- 141,182,419(+) G/A 5_prime_UTR_variant
rs1002639545 -- 141,182,635(+) G/A coding_sequence_variant, missense_variant
rs1004339 -- 141,185,779(+) A/G/T 3_prime_UTR_variant
rs1005067984 -- 141,180,977(+) A/C upstream_transcript_variant
rs1005098977 -- 141,180,743(+) T/G upstream_transcript_variant

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

Variant ID Type Subtype PubMed ID
dgv958e201 CNV deletion 23290073
esv2664767 CNV deletion 23128226
esv2730844 CNV deletion 23290073
esv2759382 CNV gain 17122850
nsv1024594 CNV loss 25217958
nsv1031792 CNV loss 25217958
nsv10756 CNV gain 18304495
nsv428127 CNV loss 18775914
nsv471634 CNV gain+loss 15918152
nsv499084 CNV gain 21111241
nsv5031 CNV insertion 18451855
nsv509092 CNV insertion 20534489
nsv599908 CNV loss 21841781
nsv599919 CNV loss 21841781
nsv823266 CNV gain 20364138
nsv964957 CNV duplication 23825009

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)

Additional Variant Information for PCDHB16 Gene

Human Gene Mutation Database (HGMD)
PCDHB16
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHB16

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

Disorders for PCDHB16 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDHB16 Gene - From: HGMD and GeneCards

Disorder Aliases PubMed IDs
protocadherin-beta gene cluster
  • pcdhb@
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHB16

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

No data available for 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 research 2001) 2 3 4 58
  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 letters 2001) 2 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. (PMID: 12665801) Gevaert K … Vandekerckhove J (Nature biotechnology 2003) 3 4 58

Products for PCDHB16 Gene

Sources for PCDHB16 Gene

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