Tbio TRIM28 Transcription intermediary factor 1-beta

Protein Summary

Description

Nuclear corepressor for KRAB domain-containing zinc finger proteins (KRAB-ZFPs). Mediates gene silencing by recruiting CHD3, a subunit of the nucleosome remodeling and deacetylation (NuRD) complex, and SETDB1 (which specifically methylates histone H3 at 'Lys-9' (H3K9me)) to the promoter regions of KRAB target genes. Enhances transcriptional repression by coordinating the increase in H3K9me, the decrease in histone H3 'Lys-9 and 'Lys-14' acetylation (H3K9ac and H3K14ac, respectively) and the disposition of HP1 proteins to silence gene expression. Recruitment of SETDB1 induces heterochromatinization. May play a role as a coactivator for CEBPB and NR3C1 in the transcriptional activation of ORM1. Also corepressor for ERBB4. Inhibits E2F1 activity by stimulating E2F1-HDAC1 complex formation and inhibiting E2F1 acetylation. May serve as a partial backup to prevent E2F1-mediated apoptosis in the absence of RB1. Important regulator of CDKN1A/p21(CIP1). Has E3 SUMO-protein ligase activity toward itself via its PHD-type zinc finger. Also specifically sumoylates IRF7, thereby inhibiting its transactivation activity. Ubiquitinates p53/TP53 leading to its proteosomal degradation; the function is enhanced by MAGEC2 and MAGEA2, and possibly MAGEA3 and MAGEA6. Mediates the nuclear localization of KOX1, ZNF268 and ZNF300 transcription factors. In association with isoform 2 of ZFP90, is required for the transcriptional repressor activity of FOXP3 and the suppressive function of regulatory T-cells (Treg) (PubMed:23543754). Probably forms a corepressor complex required for activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) or other tumor-related genes in colorectal cancer (CRC) cells (PubMed:24623306). Also required to maintain a transcriptionally repressive state of genes in undifferentiated embryonic stem cells (ESCs) (PubMed:24623306). Associates at promoter regions of tumor suppressor genes (TSGs) leading to their gene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complex may play a role in recruiting ATRX to the 3'-exons of zinc-finger coding genes with atypical chromatin signatures to establish or maintain/protect H3K9me3 at these transcriptionally active regions (PubMed:27029610). Acts as a corepressor for ZFP568 (By similarity). (Microbial infection) Plays a critical role in the shutdown of lytic gene expression during the early stage of herpes virus 8 primary infection. This inhibition is mediated through interaction with herpes virus 8 protein LANA1. The protein encoded by this gene mediates transcriptional control by interaction with the Kruppel-associated box repression domain found in many transcription factors. The protein localizes to the nucleus and is thought to associate with specific chromatin regions. The protein is a member of the tripartite motif family. This tripartite motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• Q13263
• O00677
• Q7Z632
• Q93040
• Q96IM1
• TIF1-beta

Gene Name

• TRIM28

Ensembl ID

• ENST00000253024
• ENSP00000253024
• ENSG00000130726
• ENST00000341753
• ENSP00000342232

Symbol

• KAP1
• RNF96
• TIF1B
• KAP1
• TF1B
• RNF96
• TIF1B
• PPP1R157

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
drug perturbation	1
hub protein	1
interacting protein	1
co-expressed gene	0.99
protein domain	0.99

Protein Classes

PANTHER Classes

Protein / ... / Transcription Cofactor / Transcription Intermediary Factor 1-beta

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: 177.31   (req: < 5)

Gene RIFs: 107   (req: <= 3)

Antibodies: 661   (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: 177.31   (req: >= 5)

Gene RIFs: 107   (req: > 3)

Antibodies: 661   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 40

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)

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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 (510)

Explore Interacting Targets

1 – 10 of 510

• See Interactions on String-DB

POGK

Tbio

Novelty:  0.17276635

p_int:  0.999999959

p_ni:  3.9e-8

p_wrong:  2e-9

Data Source:  BioPlex

ZNF30

Tdark

Family:  TF

Novelty:  1.40379259

p_int:  0.999999194

p_ni:  8.06e-7

Score:  0.935

Data Source:  BioPlex,STRINGDB

ZNF28

Tdark

Family:  TF

Novelty:  0.60861294

p_int:  0.999998704

p_ni:  0.000001209

p_wrong:  8.7e-8

Score:  0.92

Data Source:  BioPlex,STRINGDB

ZNF573

Tdark

Family:  TF

Novelty:  2.6663167

p_int:  0.99999825

p_wrong:  0.000001749

Score:  0.934

Data Source:  BioPlex,STRINGDB

ZNF250

Tdark

Family:  TF

Novelty:  2.37207478

p_int:  0.999998171

p_ni:  0.000001829

Score:  0.944

Data Source:  BioPlex,STRINGDB

ZNF274

Tbio

Family:  TF

Novelty:  0.01432522

p_int:  0.999997858

p_ni:  0.000002142

Score:  0.981

Data Source:  BioPlex,STRINGDB

ZNF112

Tdark

Family:  TF

Novelty:  0.9242381

p_int:  0.999994182

p_wrong:  0.000005817

Score:  0.942

Data Source:  BioPlex,STRINGDB

ZNF620

Tdark

Family:  TF

Novelty:  2.57179565

p_int:  0.999990924

p_ni:  0.000009074

p_wrong:  3e-9

Score:  0.917

Data Source:  BioPlex,STRINGDB

ZNF268

Tbio

Family:  TF

Novelty:  0.0471762

p_int:  0.99998964

p_ni:  0.000010345

p_wrong:  1.5e-8

Score:  0.937

Data Source:  BioPlex,STRINGDB

ZNF721

Tdark

Family:  TF

Novelty:  0.47000061

p_int:  0.999988077

p_ni:  1.02e-7

p_wrong:  0.000011821

Score:  0.933

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

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

Pathways (29)

Reactome (8)

PathwayCommons (4)

UniProt (1)

WikiPathways (16)

Gene expression (Transcription) (R-HSA-74160)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Gene expression (Transcription)	1452 targets	R-HSA-74160
Reactome	Generic Transcription Pathway	1195 targets	R-HSA-212436
Reactome	Metabolism of proteins	2050 targets	R-HSA-392499
Reactome	Post-translational protein modification	1450 targets	R-HSA-597592
Reactome	RNA Polymerase II Transcription	1314 targets	R-HSA-73857

Name	Explore in Pharos	Explore in Source
Gene expression (Transcription)	1452 targets	R-HSA-74160
Generic Transcription Pathway	1195 targets	R-HSA-212436
Metabolism of proteins	2050 targets	R-HSA-392499
Post-translational protein modification	1450 targets	R-HSA-597592
RNA Polymerase II Transcription	1314 targets	R-HSA-73857

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (46)

Functions (15)

Components (6)

Processes (25)

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1 – 10 of 15

GO Term	Evidence	Assigned by
SUMO transferase activity	Inferred from Experiment (EXP)	Reactome
chromatin binding	Inferred from Direct Assay (IDA)	UniProtKB
DNA binding	Inferred from Direct Assay (IDA)	UniProtKB
Krueppel-associated box domain binding	Inferred from Direct Assay (IDA)	UniProtKB
promoter-specific chromatin binding	Inferred from Direct Assay (IDA)	UniProtKB
transcription corepressor activity	Inferred from Direct Assay (IDA)	UniProtKB
ubiquitin protein ligase binding	Inferred from Direct Assay (IDA)	UniProtKB
ubiquitin-protein transferase activity	Inferred from Direct Assay (IDA)	UniProtKB
zinc ion binding	Inferred from Direct Assay (IDA)	UniProtKB
chromo shadow domain binding	Inferred from Physical Interaction (IPI)	BHF-UCL

Disease Associations (null)

No disease associations found

GWAS Traits (11)

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1 – 5 of 11

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
sex hormone-binding globulin measurement	EFO_0004696	3	2	3		78.7
mathematical ability	EFO_0004875	3	2	3		64
mean reticulocyte volume	EFO_0010701	1	1	1		49.5
red blood cell distribution width	EFO_0005192	1	1	1		49.5
mean platelet volume	EFO_0004584	1	1	1		44.2

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
sex hormone-binding globulin measurement	EFO_0004696	3		78.7
mathematical ability	EFO_0004875	3		64
mean reticulocyte volume	EFO_0010701	1		49.5
red blood cell distribution width	EFO_0005192	1		49.5
mean platelet volume	EFO_0004584	1		44.2

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Acetylation
Alternative splicing
Chromatin regulator
Citrullination
Coiled coil
Complete proteome
Direct protein sequencing
Host-virus interaction
Isopeptide bond

GWAS Trait Find Similar Targets

No Header	No Header
cognitive function measurement
colorectal adenoma
colorectal cancer
heel bone mineral density
intelligence
mathematical ability
mean platelet volume
mean reticulocyte volume
puberty onset measurement
red blood cell distribution width

MGI Phenotype Find Similar Targets

No Header	No Header
cardiovascular system phenotype
cellular phenotype
digestive/alimentary phenotype
embryo phenotype
endocrine/exocrine gland phenotype
growth/size/body region phenotype
mortality/aging
nervous system phenotype
reproductive system phenotype

IDG Resources

No IDG generated resources found

Orthologs (7)

1 – 5 of 7

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Macaque	tripartite motif containing 28		711982
Mouse	tripartite motif-containing 28	MGI:109274	21849
Rat	tripartite motif-containing 28	RGD:620289	116698
Dog	tripartite motif containing 28	VGNC:47811	403689
Horse	tripartite motif containing 28	VGNC:24499	100064831

Species	Name	OMA	EggNOG	Inparanoid
Macaque	tripartite motif containing 28
Mouse	tripartite motif-containing 28
Rat	tripartite motif-containing 28
Dog	tripartite motif containing 28
Horse	tripartite motif containing 28

Publication Statistics

PubMed Score 177.31

PubMed score by year

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PubTator Score 184.38

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Related Publications

Text Mined References (161)

GeneRif Annotations (107)

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PMID	Year	Title