Tdark PCDHGA11 Protocadherin gamma-A11

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. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• Q9Y5H2
• B7ZVY8
• Q9Y5D8
• Q9Y5D9
• PCDH-gamma-A11

Gene Name

• PCDHGA11

Ensembl ID

• ENST00000398587
• ENSP00000381589
• ENSG00000253873
• ENST00000518882
• ENSP00000428333
• ENST00000622044
• ENSP00000480917

Symbol

• PCDH-GAMMA-A11

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
microRNA	0.69
tissue sample	0.62
PubMedID	0.6
protein domain	0.58
transcription factor binding site profile	0.51

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: 1.86   (req: < 5)

Gene RIFs: 2   (req: <= 3)

Antibodies: 10   (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: 1.86   (req: >= 5)

Gene RIFs: 2   (req: > 3)

Antibodies: 10   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 3

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

Expression Data (0 Tissues)

tutorial

No expression data found

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Related Tools (4)

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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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 (14)

Explore Interacting Targets

1 – 10 of 14

• See Interactions on String-DB

PCDHGB1

Tdark

Novelty:  0.60440805

p_int:  0.999999901

p_ni:  9.9e-8

Score:  0.202

Data Source:  BioPlex,STRINGDB

TMEM30B

Tbio

Novelty:  0.26735006

p_int:  0.999995618

p_ni:  0.000004382

Data Source:  BioPlex

PCDH12

Tbio

Novelty:  0.06268895

p_int:  0.999991974

p_ni:  0.000008025

p_wrong:  1e-9

Score:  0.185

Data Source:  BioPlex,STRINGDB

DKKL1

Tbio

Novelty:  0.00544618

p_int:  0.999989959

p_ni:  0.000010041

Data Source:  BioPlex

C2orf48

Tdark

Novelty:  1

p_int:  0.999900168

p_ni:  0.000099806

p_wrong:  2.6e-8

Score:  0.719

Data Source:  BioPlex,STRINGDB

UPK2

Tbio

Novelty:  0.01066132

p_int:  0.999886655

p_ni:  0.000112145

p_wrong:  0.0000012

Data Source:  BioPlex

FCGRT

Tclin

Novelty:  0.00105713

p_int:  0.999870457

p_ni:  0.000129541

p_wrong:  2e-9

Data Source:  BioPlex

CEACAM21

Tdark

Novelty:  0.46116153

p_int:  0.999869489

p_ni:  0.000130466

p_wrong:  4.6e-8

Score:  0.201

Data Source:  BioPlex,STRINGDB

CLEC4A

Tbio

Novelty:  0.01821643

p_int:  0.999753083

p_ni:  0.000241878

p_wrong:  0.000005039

Data Source:  BioPlex

PCDHGB2

Tdark

Novelty:  1.16587709

p_int:  0.99778615

p_ni:  0.00202855

p_wrong:  0.0001853

Score:  0.168

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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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 (4)

Functions (1)

Components (1)

Processes (2)

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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 (null)

No disease associations found

GWAS Traits (6)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

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
Polymorphism
Reference proteome
Repeat

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
Rat	protocadherin gamma subfamily A, 11 [Source:HGNC Symbol;Acc:HGNC:8698]

Species	Name	OMA	EggNOG	Inparanoid
Rat	protocadherin gamma subfamily A, 11 [Source:HGNC Symbol;Acc:HGNC:8698]

Publication Statistics

PubMed Score 1.86

PubMed score by year

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PubTator Score 1.50

PubTator score by year

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Related Publications

Text Mined References (12)

GeneRif Annotations (2)

Items per page:

10

0 of 0

PMID	Year	Title