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Aliases for PCDHB13 Gene

Aliases for PCDHB13 Gene

  • Protocadherin Beta 13 2 3
  • Protocadherin Beta-13 3
  • PCDH-Beta-13 4
  • PCDH-BETA13 3

External Ids for PCDHB13 Gene

Summaries for PCDHB13 Gene

Entrez Gene Summary for PCDHB13 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 PCDHB13 Gene

PCDHB13 (Protocadherin Beta 13) 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 PCDHB13 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 PCDHB13 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB13 Gene

Genomics for PCDHB13 Gene

Genomic Location for PCDHB13 Gene

Start:
141,213,919 bp from pter
End:
141,218,979 bp from pter
Size:
5,061 bases
Orientation:
Plus strand

Genomic View for PCDHB13 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PCDHB13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB13 Gene

Regulatory Elements for PCDHB13 Gene

Proteins for PCDHB13 Gene

  • Protein details for PCDHB13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5F0-PCDBD_HUMAN
    Recommended name:
    Protocadherin beta-13
    Protein Accession:
    Q9Y5F0
    Secondary Accessions:
    • A8K9V6

    Protein attributes for PCDHB13 Gene

    Size:
    798 amino acids
    Molecular mass:
    87552 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB13 Gene

Proteomics data for PCDHB13 Gene at MOPED

Post-translational modifications for PCDHB13 Gene

  • Modification sites at PhosphoSitePlus
  • Glycosylation at Asn418, Asn436, and Asn567

Other Protein References for PCDHB13 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB13 Gene

Domains for PCDHB13 Gene

Gene Families for PCDHB13 Gene

HGNC:
  • PCDHC :Cadherins / Protocadherins : Clustered

Protein Domains for PCDHB13 Gene

Suggested Antigen Peptide Sequences for PCDHB13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y5F0

UniProtKB/Swiss-Prot:

PCDBD_HUMAN
Domain:
  • Contains 6 cadherin domains.:
    • Q9Y5F0
genes like me logo Genes that share domains with PCDHB13: view

Function for PCDHB13 Gene

Molecular function for PCDHB13 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 PCDHB13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB13: view

Phenotypes for PCDHB13 Gene

GenomeRNAi human phenotypes for PCDHB13:
genes like me logo Genes that share phenotypes with PCDHB13: view

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for PCDHB13 Gene

Localization for PCDHB13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB13 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PCDHB13 Gene COMPARTMENTS Subcellular localization image for PCDHB13 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 1
extracellular 1
golgi apparatus 1
lysosome 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PCDHB13 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 PCDHB13: view

Pathways for PCDHB13 Gene

SuperPathways for PCDHB13 Gene

No Data Available

Interacting Proteins for PCDHB13 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.ENSP00000345491%0d%0a9606.ENSP00000346155%0d%0a9606.ENSP00000344456%0d%0a9606.ENSP00000311113%0d%0a9606.ENSP00000362481%0d%0a
Selected Interacting proteins: ENSP00000345491 for PCDHB13 Gene via STRING

Gene Ontology (GO) - Biological Process for PCDHB13 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 PCDHB13: view

No data available for Pathways by source for PCDHB13 Gene

Compounds for PCDHB13 Gene

(1) HMDB Compounds for PCDHB13 Gene

Compound Synonyms Cas Number PubMed IDs
Calcium
  • Ca
7440-70-2
genes like me logo Genes that share compounds with PCDHB13: view

Transcripts for PCDHB13 Gene

mRNA/cDNA for PCDHB13 Gene

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

Unigene Clusters for PCDHB13 Gene

Protocadherin beta 13:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB13 Gene

No ASD Table

Relevant External Links for PCDHB13 Gene

GeneLoc Exon Structure for
PCDHB13
ECgene alternative splicing isoforms for
PCDHB13

Expression for PCDHB13 Gene

mRNA expression in normal human tissues for PCDHB13 Gene

SOURCE GeneReport for Unigene cluster for PCDHB13 Gene Hs.283803

genes like me logo Genes that share expressions with PCDHB13: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein expression and mRNA Expression by UniProt/SwissProt for PCDHB13 Gene

Orthologs for PCDHB13 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHB13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHB13 35
  • 98.58 (n)
  • 98.5 (a)
PCDHB13 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia -- 36
  • 82 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Pcdhb16 36
  • 74 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 36
  • 64 (a)
ManyToMany
-- 36
  • 64 (a)
ManyToMany
-- 36
  • 64 (a)
ManyToMany
-- 36
  • 64 (a)
ManyToMany
-- 36
  • 64 (a)
ManyToMany
-- 36
  • 64 (a)
ManyToMany
-- 36
  • 64 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 60 (a)
ManyToMany
-- 36
  • 63 (a)
ManyToMany
-- 36
  • 63 (a)
ManyToMany
Species with no ortholog for PCDHB13:
  • 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)
  • dog (Canis familiaris)
  • 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)
  • 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 PCDHB13 Gene

ENSEMBL:
Gene Tree for PCDHB13 (if available)
TreeFam:
Gene Tree for PCDHB13 (if available)

Paralogs for PCDHB13 Gene

genes like me logo Genes that share paralogs with PCDHB13: view

Variants for PCDHB13 Gene

Sequence variations from dbSNP and Humsavar for PCDHB13 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type MAF
rs584459 -- 141,216,515(-) TCACT(A/G)AATAT reference, stop-gained
rs628301 -- 141,213,684(-) GGGCA(A/G)AAAGG upstream-variant-2KB
rs2338531 -- 141,214,112(+) TGAAT(C/T)CAGCA utr-variant-5-prime
rs2860677 -- 141,214,610(-) GCCTA(C/T)ATCTA missense, reference
rs2860678 -- 141,214,577(-) AAACG(C/T)AGTCC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PCDHB13 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
nsv823266 CNV Gain 20364138
dgv1005e201 CNV Deletion 23290073
nsv823277 CNV Gain 20364138
nsv10757 CNV Gain 18304495
nsv823278 CNV Gain 20364138
esv26005 CNV Gain 19812545

Relevant External Links for PCDHB13 Gene

HapMap Linkage Disequilibrium report
PCDHB13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB13 Gene

Disorders for PCDHB13 Gene

No disorders were found for PCDHB13 Gene.

No data available for UniProtKB/Swiss-Prot for PCDHB13 Gene

Publications for PCDHB13 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. 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) 3 4
  3. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 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 PCDHB13 Gene

Sources for PCDHB13 Gene

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