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Aliases for PCDHB2 Gene

Aliases for PCDHB2 Gene

  • Protocadherin Beta 2 2 3 5
  • Protocadherin Beta-2 3
  • PCDH-Beta-2 4
  • PCDH-BETA2 3

External Ids for PCDHB2 Gene

Previous GeneCards Identifiers for PCDHB2 Gene

  • GC05P140290
  • GC05P141057
  • GC05P140457
  • GC05P140502
  • GC05P140454
  • GC05P135618
  • GC05P140474
  • GC05P141276
  • GC05P141496
  • GC05P141603
  • GC05P141703
  • GC05P141805
  • GC05P141904
  • GC05P142012
  • GC05P142115

Summaries for PCDHB2 Gene

Entrez Gene Summary for PCDHB2 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 PCDHB2 Gene

PCDHB2 (Protocadherin Beta 2) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB3.

UniProtKB/Swiss-Prot for PCDHB2 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 PCDHB2 Gene

Additional gene information for PCDHB2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB2 Gene

Genomics for PCDHB2 Gene

GeneHancer (GH) Regulatory Elements for PCDHB2 Gene

Promoters and enhancers for PCDHB2 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
GH05J141094 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 660.5 +0.2 170 1.4 ARID4B SIN3A ZNF2 RAD21 ZNF48 ZSCAN9 ETS1 ZNF143 MIXL1 ZNF654 PCDHB2 GC05M141097 LOC101926905 PIR41040 PIR50728 PIR61536 PCDHB@
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 21.7 -375.4 -375442 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 14.1 +875.0 874989 3 CLOCK DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC GLIS1 RNF14 PCDH12 LOC102723915 HDAC3 PCDHB18P PCDHGA6 PCDHGA7 DELE1 PCDHGA5 ENSG00000271871
GH05J140725 Promoter/Enhancer 1.6 Ensembl ENCODE 11.3 -368.6 -368596 1.1 PKNOX1 ARNT ARID4B SIN3A ZNF2 IRF4 YY1 POLR2B ZNF766 ZNF213 GC05P142300 VTRNA1-3 ANKHD1 LOC102723915 WDR55 HDAC3 HARS2 TMCO6 FCHSD1 PCDHA4
GH05J140710 Promoter/Enhancer 1.6 Ensembl ENCODE 11.2 -383.6 -383594 1.9 CLOCK FEZF1 IRF4 YY1 ZNF213 ZNF143 SP3 SSRP1 ZNF610 GLIS1 GC05P142295 LOC105378198 VTRNA1-1 HARS2 ANKHD1 WDR55 LOC102723915 HDAC3 PCDHB18P PURA
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHB2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHB2 gene promoter:
  • Sox9
  • c-Jun
  • ATF-2
  • Pax-3
  • C/EBPalpha
  • AML1a
  • CUTL1
  • Tal-1beta

Genomic Locations for PCDHB2 Gene

Genomic Locations for PCDHB2 Gene
chr5:141,094,578-141,098,703
(GRCh38/hg38)
Size:
4,126 bases
Orientation:
Plus strand
chr5:140,474,227-140,476,964
(GRCh37/hg19)
Size:
2,738 bases
Orientation:
Plus strand

Genomic View for PCDHB2 Gene

Genes around PCDHB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB2 Gene

Proteins for PCDHB2 Gene

  • Protein details for PCDHB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5E7-PCDB2_HUMAN
    Recommended name:
    Protocadherin beta-2
    Protein Accession:
    Q9Y5E7
    Secondary Accessions:
    • Q4KMU1

    Protein attributes for PCDHB2 Gene

    Size:
    798 amino acids
    Molecular mass:
    87254 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB2 Gene

Post-translational modifications for PCDHB2 Gene

  • Glycosylation at isoforms=569, isoforms=438, Asn420, and isoforms=171
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB2 Gene

No data available for DME Specific Peptides for PCDHB2 Gene

Domains & Families for PCDHB2 Gene

Gene Families for PCDHB2 Gene

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

Protein Domains for PCDHB2 Gene

Suggested Antigen Peptide Sequences for PCDHB2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHB2: view

No data available for UniProtKB/Swiss-Prot for PCDHB2 Gene

Function for PCDHB2 Gene

Molecular function for PCDHB2 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 PCDHB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB2: view
genes like me logo Genes that share phenotypes with PCDHB2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PCDHB2

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHB2 Gene

Localization for PCDHB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB2 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 PCDHB2 gene
Compartment Confidence
plasma membrane 5
nucleus 2
endoplasmic reticulum 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PCDHB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS 10380929
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 11322959
genes like me logo Genes that share ontologies with PCDHB2: view

Pathways & Interactions for PCDHB2 Gene

SuperPathways for PCDHB2 Gene

No Data Available

Interacting Proteins for PCDHB2 Gene

Gene Ontology (GO) - Biological Process for PCDHB2 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:0007267 cell-cell signaling IBA --
GO:0007268 chemical synaptic transmission TAS 12231349
GO:0007399 nervous system development TAS 10380929
genes like me logo Genes that share ontologies with PCDHB2: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB2 Gene

Drugs & Compounds for PCDHB2 Gene

(1) Drugs for PCDHB2 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 PCDHB2: view

Transcripts for PCDHB2 Gene

mRNA/cDNA for PCDHB2 Gene

(1) REFSEQ mRNAs :
(11) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PCDHB2 Gene

Protocadherin beta 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB2 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c
SP1:
SP2: -

Relevant External Links for PCDHB2 Gene

GeneLoc Exon Structure for
PCDHB2
ECgene alternative splicing isoforms for
PCDHB2

Expression for PCDHB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHB2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCDHB2 Gene

This gene is overexpressed in Testis (x5.0).

Protein differential expression in normal tissues from HIPED for PCDHB2 Gene

This gene is overexpressed in Fetal heart (31.4), Brain (21.0), and CD8 Tcells (16.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHB2 Gene



Protein tissue co-expression partners for PCDHB2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHB2 Gene:

PCDHB2

SOURCE GeneReport for Unigene cluster for PCDHB2 Gene:

Hs.533023
genes like me logo Genes that share expression patterns with PCDHB2: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHB2 Gene

Orthologs for PCDHB2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHB2 34 33
  • 99 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PCDHB2 33
  • 85.15 (n)
PCDHB11 34
  • 71 (a)
ManyToMany
dog
(Canis familiaris)
Mammalia PCDHB2 34
  • 82 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdhb2 16 34 33
  • 80.2 (n)
rat
(Rattus norvegicus)
Mammalia Pcdhb2 33
  • 79.91 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 67 (a)
ManyToMany
-- 34
  • 67 (a)
ManyToMany
-- 34
  • 67 (a)
ManyToMany
-- 34
  • 67 (a)
ManyToMany
-- 34
  • 66 (a)
ManyToMany
-- 34
  • 63 (a)
ManyToMany
-- 34
  • 63 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 65 (a)
ManyToMany
-- 34
  • 63 (a)
ManyToMany
-- 34
  • 62 (a)
ManyToMany
chicken
(Gallus gallus)
Aves LOC100858025 33
  • 59.65 (n)
Species where no ortholog for PCDHB2 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)
  • 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)
  • 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 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 PCDHB2 Gene

ENSEMBL:
Gene Tree for PCDHB2 (if available)
TreeFam:
Gene Tree for PCDHB2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHB2: view image

Paralogs for PCDHB2 Gene

genes like me logo Genes that share paralogs with PCDHB2: view

Variants for PCDHB2 Gene

Sequence variations from dbSNP and Humsavar for PCDHB2 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1002976494 -- 141,097,777(+) G/A downstream_transcript_variant
rs1003028251 -- 141,097,326(+) T/G 3_prime_UTR_variant
rs1003365877 -- 141,094,591(+) C/G/T upstream_transcript_variant
rs1004200093 -- 141,097,293(+) T/G 3_prime_UTR_variant
rs1004599822 -- 141,094,143(+) C/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHB2 Gene

Variant ID Type Subtype PubMed ID
esv2759382 CNV gain 17122850
esv3606961 CNV loss 21293372
nsv428127 CNV loss 18775914
nsv516514 CNV gain 19592680
nsv599905 CNV gain 21841781
nsv599906 CNV loss 21841781
nsv980735 CNV duplication 23825009

Variation tolerance for PCDHB2 Gene

Residual Variation Intolerance Score: 62% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.40; 71.18% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHB2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHB2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB2 Gene

Disorders for PCDHB2 Gene

Additional Disease Information for PCDHB2

No disorders were found for PCDHB2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB2 Gene

Publications for PCDHB2 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 58
  2. 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
  3. 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) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Lysine acetylation targets protein complexes and co-regulates major cellular functions. (PMID: 19608861) Choudhary C … Mann M (Science (New York, N.Y.) 2009) 4 58

Products for PCDHB2 Gene

Sources for PCDHB2 Gene

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