Tdark PCDHGB4 Protocadherin gamma-B4

Protein Summary

Description

Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain. This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. This particular family member is expressed in fibroblasts and is thought to play a role in wound healing in response to injury. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• Q9UN71
• O15099
• Q2M267
• Q9UN64
• PCDH-gamma-B4

Gene Name

• PCDHGB4

Ensembl ID

• ENST00000519479
• ENSP00000428288
• ENSG00000253953
• ENST00000615384
• ENSP00000484560

Symbol

• CDH20
• FIB2
• FIB2
• CDH20
• PCDH-GAMMA-B4

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
cell type or tissue	0.81
tissue sample	0.66
protein domain	0.58
cell line	0.48
pathway	0.47

Protein Classes

No PANTHER Classes or DTO Classes found

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 3.8   (req: < 5)

Gene RIFs: 0   (req: <= 3)

Antibodies: 107   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 3.8   (req: >= 5)

Gene RIFs: 0   (req: > 3)

Antibodies: 107   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 4

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Expression Data (0 Tissues)

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No expression data found

Related Tools

Target Illumination GWAS Analytics (TIGA)

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (69)

Explore Interacting Targets

1 – 10 of 69

• See Interactions on String-DB

PCDHGB5

Tdark

Novelty:  4.39427151

p_int:  1

Score:  0.634

Data Source:  BioPlex,STRINGDB

PCDHGB1

Tdark

Novelty:  0.60440805

p_int:  0.999999998

p_wrong:  2e-9

Score:  0.266

Data Source:  BioPlex,STRINGDB

PCDHGB3

Tdark

Novelty:  1.9379995

p_int:  0.99999998

p_ni:  2e-8

Score:  0.586

Data Source:  BioPlex,STRINGDB

PCDHGB2

Tdark

Novelty:  1.16587709

p_int:  0.99999998

p_ni:  4e-9

p_wrong:  1.7e-8

Data Source:  BioPlex

GRAMD1B

Tbio

Novelty:  0.2994102

p_int:  0.999705759

p_ni:  0.000294201

p_wrong:  4e-8

Data Source:  BioPlex

GRAMD1A

Tbio

Novelty:  0.15461113

p_int:  0.999309207

p_ni:  0.000690793

Data Source:  BioPlex

DAG1

Tbio

Family:  Enzyme

Novelty:  0.00149278

p_int:  0.999233509

p_ni:  0.000766491

Data Source:  BioPlex

EMILIN2

Tbio

Novelty:  0.2816786

p_int:  0.998748427

p_ni:  0.001247986

p_wrong:  0.000003588

Data Source:  BioPlex

AREL1

Tdark

Family:  Enzyme

Novelty:  0.31082841

p_int:  0.998673702

p_ni:  0.000736843

p_wrong:  0.000589454

Score:  0.152

Data Source:  BioPlex,STRINGDB

PCDH10

Tbio

Novelty:  0.01058382

p_int:  0.998439769

p_ni:  0.001560189

p_wrong:  4.2e-8

Score:  0.184

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (2)

PathwayCommons (2)

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5

1 – 2 of 2

Data Source	Name	Explore in Pharos	Explore in Source
PathwayCommons: panther	Cadherin signaling pathway	150 targets	PathwayCommons: panther
PathwayCommons: panther	Wnt signaling pathway	264 targets	PathwayCommons: panther

Name	Explore in Pharos	Explore in Source
Cadherin signaling pathway	150 targets	PathwayCommons: panther
Wnt signaling pathway	264 targets	PathwayCommons: panther

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (6)

Functions (1)

Components (2)

Processes (3)

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Items per page:

10

1 – 1 of 1

GO Term	Evidence	Assigned by
calcium ion binding	Inferred from Electronic Annotation (IEA)	InterPro

Disease Associations ()

No disease associations found

GWAS Traits (6)

• Explore on Target Illumination GWAS Analytics (TIGA)

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1 – 5 of 6

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
mean platelet volume	EFO_0004584	3	4	6		93.5
self reported educational attainment	EFO_0004784	2	2	2		57.1
triglyceride measurement	EFO_0004530	1	1	1		47.7
allergy	EFO_0003785	1	1	0	1	46.5
age at first birth measurement	EFO_0009101	1	1	1		24.5

• Explore on Target Illumination GWAS Analytics (TIGA)

Items per page:

5

1 – 5 of 6

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
mean platelet volume	EFO_0004584	6		93.5
self reported educational attainment	EFO_0004784	2		57.1
triglyceride measurement	EFO_0004530	1		47.7
allergy	EFO_0003785	0	1	46.5
age at first birth measurement	EFO_0009101	1		24.5

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Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
Alternative splicing
Calcium
Cell adhesion
Cell membrane
Complete proteome
Glycoprotein
Membrane
Reference proteome
Repeat
Signal

GWAS Trait Find Similar Targets

No Header	No Header
age at first birth measurement
allergy
mathematical ability
mean platelet volume
self reported educational attainment
triglyceride measurement

IDG Resources

No IDG generated resources found

Orthologs (1)

1 – 1 of 1

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Pig	protocadherin gamma-B4-like		106509590

Species	Name	OMA	EggNOG	Inparanoid
Pig	protocadherin gamma-B4-like

Publication Statistics

PubMed Score 3.80

PubMed score by year

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PubTator Score 7.78

PubTator score by year

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Related Publications

Text Mined References (8)

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10

0 of 0

PMID	Year	Title