Tbio RNF40 E3 ubiquitin-protein ligase BRE1B

Protein Summary

Description

Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role in histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes. The protein encoded by this gene contains a RING finger, a motif known to be involved in protein-protein and protein-DNA interactions. This protein was reported to interact with the tumor suppressor protein RB1. Studies of the rat counterpart suggested that this protein may function as an E3 ubiquitin-protein ligase, and facilitate the ubiquitination and degradation of syntaxin 1, which is an essential component of the neurotransmitter release machinery. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

Uniprot Accession IDs

• O75150
• A0A024QZG0
• Q6AHZ6
• Q6N005
• Q7L3T6
• Q8N615
• Q96T18
• Q9BSV9
• Q9HC82
• BRE1-B

Gene Name

• RNF40

Ensembl ID

• ENST00000324685
• ENSP00000325677
• ENSG00000103549
• ENST00000357890
• ENSP00000350563

Symbol

• BRE1B
• KIAA0661
• BRE1B
• RBP95
• STARING

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
molecular function	0.94
disease perturbation	0.83
biological process	0.73
microRNA	0.67
tissue sample	0.63

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: 15.46   (req: < 5)

Gene RIFs: 10   (req: <= 3)

Antibodies: 245   (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: 15.46   (req: >= 5)

Gene RIFs: 10   (req: > 3)

Antibodies: 245   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 17

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

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Target Illumination GWAS Analytics (TIGA)

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GENEVA

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GlyGen

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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 (139)

Explore Interacting Targets

1 – 10 of 139

• See Interactions on String-DB

WAC

Tbio

Novelty:  0.02189388

p_int:  0.99999978

p_ni:  2.2e-7

Score:  0.975

Data Source:  BioPlex,STRINGDB

SYCE1

Tbio

Novelty:  0.05038876

p_int:  0.999905562

p_ni:  0.000094438

Data Source:  BioPlex

TCP10L

Tbio

Novelty:  0.24089479

p_int:  0.999862005

p_ni:  0.000137995

Data Source:  BioPlex

IL36A

Tbio

Novelty:  0.03569425

p_int:  0.999802081

p_ni:  0.000197919

Score:  0.207

Data Source:  BioPlex,STRINGDB

DISC1

Tbio

Novelty:  0.00183442

p_int:  0.999755269

p_ni:  0.000244731

Data Source:  BioPlex

OLFM2

Tbio

Novelty:  0.06929963

p_int:  0.99973586

p_ni:  0.00026414

Data Source:  BioPlex

BRK1

Tbio

Novelty:  0.02289534

p_int:  0.998083808

p_ni:  0.001916192

Data Source:  BioPlex

COG6

Tbio

Novelty:  0.02874093

p_int:  0.996712143

p_ni:  0.003287857

Score:  0.203

Data Source:  BioPlex,STRINGDB

EPS15L1

Tbio

Novelty:  0.06929299

p_int:  0.994436027

p_ni:  0.005563973

Data Source:  BioPlex

NUP62

Tbio

Novelty:  0.01432724

p_int:  0.989976525

p_ni:  0.010023475

Data Source:  BioPlex

Nearest Tclin Targets

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

Pathways (14)

Reactome (4)

UniProt (1)

WikiPathways (9)

E3 ubiquitin ligases ubiquitinate target proteins (R-HSA-8866654)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	E3 ubiquitin ligases ubiquitinate target proteins	110 targets	R-HSA-8866654
Reactome	Metabolism of proteins	2050 targets	R-HSA-392499
Reactome	Post-translational protein modification	1450 targets	R-HSA-597592
Reactome	Protein ubiquitination	130 targets	R-HSA-8852135

Name	Explore in Pharos	Explore in Source
E3 ubiquitin ligases ubiquitinate target proteins	110 targets	R-HSA-8866654
Metabolism of proteins	2050 targets	R-HSA-392499
Post-translational protein modification	1450 targets	R-HSA-597592
Protein ubiquitination	130 targets	R-HSA-8852135

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (26)

Functions (8)

Components (9)

Processes (9)

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1 – 8 of 8

GO Term	Evidence	Assigned by
mRNA 3'-UTR binding	Inferred from Direct Assay (IDA)	UniProtKB
protein homodimerization activity	Inferred from Physical Interaction (IPI)	UniProtKB
ubiquitin protein ligase binding	Inferred from Physical Interaction (IPI)	UniProtKB
metal ion binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW
protein-containing complex binding	Inferred from Electronic Annotation (IEA)	Ensembl
syntaxin-1 binding	Inferred from Electronic Annotation (IEA)	Ensembl
ubiquitin conjugating enzyme binding	Inferred from Electronic Annotation (IEA)	Ensembl
ubiquitin-protein transferase activity	Inferred from Electronic Annotation (IEA)	Ensembl

Disease Associations ()

No disease associations found

GWAS Traits (10)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 10

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
serum non-albumin protein measurement	EFO_0004568	1	1	1		71.3
comparative body size at age 10, self-reported	EFO_0009819	1	1	1		54.4
HbA1c measurement	EFO_0004541	1	1	1		52
testosterone measurement	EFO_0004908	2	2	2		46.5
HMG CoA reductase inhibitor use measurement	EFO_0009932	1	1	1		33.1

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 10

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
serum non-albumin protein measurement	EFO_0004568	1		71.3
comparative body size at age 10, self-reported	EFO_0009819	1		54.4
HbA1c measurement	EFO_0004541	1		52
testosterone measurement	EFO_0004908	2		46.5
HMG CoA reductase inhibitor use measurement	EFO_0009932	1		33.1

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UniProt Keyword Find Similar Targets

No Header	No Header
Acetylation
Alternative splicing
Chromatin regulator
Coiled coil
Complete proteome
Isopeptide bond
Metal-binding
Nucleus
Phosphoprotein
Polymorphism

GWAS Trait Find Similar Targets

No Header	No Header
comparative body size at age 10, self-reported
HbA1c measurement
HMG CoA reductase inhibitor use measurement
IGF-1 measurement
leukocyte count
Lewy body dementia
mean platelet volume
multiple myeloma
serum non-albumin protein measurement
testosterone measurement

IDG Resources

No IDG generated resources found

Orthologs (14)

1 – 5 of 14

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	ring finger protein 40	VGNC:9101	454054
Macaque	ring finger protein 40		713148
Mouse	ring finger protein 40	MGI:2142048	233900
Rat	ring finger protein 40	RGD:628638	266712
Dog	ring finger protein 40	VGNC:45669	489913

Species	Name	OMA	EggNOG	Inparanoid
Chimp	ring finger protein 40
Macaque	ring finger protein 40
Mouse	ring finger protein 40
Rat	ring finger protein 40
Dog	ring finger protein 40

Publication Statistics

PubMed Score 15.46

PubMed score by year

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PubTator Score 14.12

PubTator score by year

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Related Publications

Text Mined References (29)

GeneRif Annotations (10)

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PMID	Year	Title