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Aliases for PCDHB1 Gene

Aliases for PCDHB1 Gene

  • Protocadherin Beta 1 2 3
  • PCDH-Beta-1 3 4
  • Protocadherin Beta-1 3
  • PCDH-BETA1 3

External Ids for PCDHB1 Gene

Summaries for PCDHB1 Gene

Entrez Gene Summary for PCDHB1 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 PCDHB1 Gene

PCDHB1 (Protocadherin Beta 1) 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 PCDHB1 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 Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB1 Gene

Genomics for PCDHB1 Gene

Genomic Location for PCDHB1 Gene

Start:
141,051,135 bp from pter
End:
141,059,344 bp from pter
Size:
8,210 bases
Orientation:
Plus strand

Genomic View for PCDHB1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PCDHB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB1 Gene

Regulatory Elements for PCDHB1 Gene

Proteins for PCDHB1 Gene

  • Protein details for PCDHB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5F3-PCDB1_HUMAN
    Recommended name:
    Protocadherin beta-1
    Protein Accession:
    Q9Y5F3
    Secondary Accessions:
    • Q2M257

    Protein attributes for PCDHB1 Gene

    Size:
    818 amino acids
    Molecular mass:
    90491 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB1 Gene

Proteomics data for PCDHB1 Gene at MOPED

Post-translational modifications for PCDHB1 Gene

  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn169, Asn209, Asn257, Asn419, and Asn568

Other Protein References for PCDHB1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB1 Gene

Domains for PCDHB1 Gene

Gene Families for PCDHB1 Gene

HGNC:
  • PCDHC :Cadherins / Protocadherins : Clustered

Protein Domains for PCDHB1 Gene

UniProtKB/Swiss-Prot:

PCDB1_HUMAN
Domain:
  • Contains 6 cadherin domains.:
    • Q9Y5F3
genes like me logo Genes that share domains with PCDHB1: view

Function for PCDHB1 Gene

Molecular function for PCDHB1 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 PCDHB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB1: view

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for PCDHB1 Gene

Localization for PCDHB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB1 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDHB1 Gene COMPARTMENTS Subcellular localization image for PCDHB1 gene
Compartment Confidence
plasma membrane 5
cytosol 1
endoplasmic reticulum 1
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PCDHB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHB1: view

Pathways for PCDHB1 Gene

SuperPathways for PCDHB1 Gene

No Data Available

Interacting Proteins for PCDHB1 Gene

STRING Interaction Network Preview (showing 4 interactants - click image to see details)
http://string-db.org/version_10/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000307234%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000344456%0d%0a9606.ENSP00000311113%0d%0a9606.ENSP00000362481%0d%0a
Selected Interacting proteins: ENSP00000307234 for PCDHB1 Gene via STRING

Gene Ontology (GO) - Biological Process for PCDHB1 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 PCDHB1: view

No data available for Pathways by source for PCDHB1 Gene

Compounds for PCDHB1 Gene

(1) HMDB Compounds for PCDHB1 Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2
genes like me logo Genes that share compounds with PCDHB1: view

Transcripts for PCDHB1 Gene

mRNA/cDNA for PCDHB1 Gene

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

Unigene Clusters for PCDHB1 Gene

Protocadherin beta 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB1 Gene

No ASD Table

Relevant External Links for PCDHB1 Gene

GeneLoc Exon Structure for
PCDHB1
ECgene alternative splicing isoforms for
PCDHB1

Expression for PCDHB1 Gene

mRNA expression in normal human tissues for PCDHB1 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHB1 Gene

This gene is overexpressed in Testis (12.5) and Pituitary (8.5).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for PCDHB1 Gene

SOURCE GeneReport for Unigene cluster for PCDHB1 Gene Hs.278950

genes like me logo Genes that share expressions with PCDHB1: view

Orthologs for PCDHB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCDHB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHB1 36
  • 99.39 (n)
  • 99.27 (a)
PCDHB1 37
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PCDHB1 36
  • 88.26 (n)
  • 88.51 (a)
PCDHB1 37
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PCDHB1 37
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdhb1 36
  • 85.04 (n)
  • 88.02 (a)
Pcdhb1 16
Pcdhb1 37
  • 88 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PCDHB1 37
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PCDHB1 37
  • 71 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pcdhb1 36
  • 84.39 (n)
  • 88.39 (a)
fruit fly
(Drosophila melanogaster)
Insecta Cad89D 38
  • 26 (a)
Species with no ortholog for PCDHB1:
  • 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)
  • 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 PCDHB1 Gene

ENSEMBL:
Gene Tree for PCDHB1 (if available)
TreeFam:
Gene Tree for PCDHB1 (if available)

Paralogs for PCDHB1 Gene

genes like me logo Genes that share paralogs with PCDHB1: view

Variants for PCDHB1 Gene

Sequence variations from dbSNP and Humsavar for PCDHB1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type MAF
VAR_048541 -
VAR_048542 -
VAR_048543 -
VAR_048544 -
VAR_048545 -

Structural Variations from Database of Genomic Variants (DGV) for PCDHB1 Gene

Variant ID Type Subtype PubMed ID
dgv1857e1 CNV Complex 17122850
nsv428127 CNV Loss 18775914
nsv818387 CNV Gain 17921354

Relevant External Links for PCDHB1 Gene

HapMap Linkage Disequilibrium report
PCDHB1

Disorders for PCDHB1 Gene

No disorders were found for PCDHB1 Gene.

No data available for UniProtKB/Swiss-Prot for PCDHB1 Gene

Publications for PCDHB1 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
  2. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PMID: 10716726) Wu Q. … Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000) 3
  3. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PMID: 10817752) Yagi T. … Takeichi M. (Genes Dev. 2000) 3
  4. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. (PMID: 10835267) Nollet F. … van Roy F. (J. Mol. Biol. 2000) 3
  5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 3

Products for PCDHB1 Gene

Sources for PCDHB1 Gene

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