TRIM28 tripartite motif containing 28 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TRIM28provided by HGNC
Official Full Name: tripartite motif containing 28provided by HGNC
Primary source: HGNC:HGNC:16384
See related: Ensembl:ENSG00000130726 MIM:601742; AllianceGenome:HGNC:16384
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: KAP1; TF1B; RNF96; TIF1B; PPP1R157; TIF1beta
Summary: 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]
Expression: Ubiquitous expression in ovary (RPKM 89.1), testis (RPKM 80.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.43

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (58544064..58550715)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (61641740..61648391)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (59055431..59062082)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Functional Analysis of KAP1/TRIM28 Requirements for HIV-1 Transcription Activation.
Title: Functional Analysis of KAP1/TRIM28 Requirements for HIV-1 Transcription Activation.
TRIM28 suppresses cancer stem-like characteristics in gastric cancer cells through Wnt/beta-catenin signaling pathways.
Title: TRIM28 suppresses cancer stem-like characteristics in gastric cancer cells through Wnt/β-catenin signaling pathways.
TRIM28 inactivation in epithelial nephroblastoma is frequent and often associated with predisposing TRIM28 germline variants.
Title: TRIM28 inactivation in epithelial nephroblastoma is frequent and often associated with predisposing TRIM28 germline variants.
ATM, KAP1 and the Epstein-Barr virus polymerase processivity factor direct traffic at the intersection of transcription and replication.
Title: ATM, KAP1 and the Epstein-Barr virus polymerase processivity factor direct traffic at the intersection of transcription and replication.
E3 ligase TRIM28 promotes anti-PD-1 resistance in non-small cell lung cancer by enhancing the recruitment of myeloid-derived suppressor cells.
Title: E3 ligase TRIM28 promotes anti-PD-1 resistance in non-small cell lung cancer by enhancing the recruitment of myeloid-derived suppressor cells.
A TIAM1-TRIM28 complex mediates epigenetic silencing of protocadherins to promote migration of lung cancer cells.
Title: A TIAM1-TRIM28 complex mediates epigenetic silencing of protocadherins to promote migration of lung cancer cells.
Children with Chronic Immune Thrombocytopenia Exhibit High Expression of Human Endogenous Retroviruses TRIM28 and SETDB1.
Title: Children with Chronic Immune Thrombocytopenia Exhibit High Expression of Human Endogenous Retroviruses TRIM28 and SETDB1.
N6-methyladenosine hypomethylation of circGPATCH2L regulates DNA damage and apoptosis through TRIM28 in intervertebral disc degeneration.
Title: N6-methyladenosine hypomethylation of circGPATCH2L regulates DNA damage and apoptosis through TRIM28 in intervertebral disc degeneration.
WDR4/TRIM28 is a novel molecular target linked to lenvatinib resistance that helps retain the stem characteristics in hepatocellular carcinomas.
Title: WDR4/TRIM28 is a novel molecular target linked to lenvatinib resistance that helps retain the stem characteristics in hepatocellular carcinomas.
Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells.
Title: Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells.

Submit: New GeneRIF Correction See all GeneRIFs (169)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify tripartite motif containing 28 (TRIM28), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify tripartite motif containing 28 (TRIM28), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify tripartite motif containing 28 (TRIM28), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify tripartite motif containing 28 (TRIM28), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
integrase	gag-pol	KAP1 inhibits HIV-1 integration via HIV-1 IN acetylation-dependent mechanism through HDAC1	PubMed
	gag-pol	The interaction between HIV-1 IN and KAP1 is highly favored by HAT/p300-mediated IN acetylation	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D5S2433 (e-PCR)
- UniSTS:18444

MARC_7281-7282:992008298:1 (e-PCR)
- UniSTS:231311

MARC_7281-7282:996687721:1 (e-PCR)
- UniSTS:231311

Cda0zf05 (e-PCR)
- UniSTS:90045

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables Krueppel-associated box domain binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables SUMO transferase activity	EXP Inferred from Experiment more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromo shadow domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activity	IEA Inferred from Electronic Annotation more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in convergent extension involved in axis elongation	IEA Inferred from Electronic Annotation more info
involved_in embryo implantation	IEA Inferred from Electronic Annotation more info
involved_in embryonic placenta morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in epigenetic programming of gene expression	IEA Inferred from Electronic Annotation more info
involved_in epithelial to mesenchymal transition	ISS Inferred from Sequence or Structural Similarity more info
involved_in genomic imprinting	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in innate immune response	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA demethylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA methylation-dependent heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA methylation-dependent heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA repair	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of protein import into nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in protein sumoylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein sumoylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein sumoylation	IEA Inferred from Electronic Annotation more info
involved_in protein sumoylation	TAS Traceable Author Statement more info
involved_in suppression of viral release by host	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase II transcription regulator complex	ISS Inferred from Sequence or Structural Similarity more info
part_of euchromatin	IEA Inferred from Electronic Annotation more info
part_of heterochromatin	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: transcription intermediary factor 1-beta

Names: E3 SUMO-protein ligase TRIM28; KAP-1; KRAB [Kruppel-associated box domain]-associated protein 1; KRAB-interacting protein 1; KRIP-1; RING finger protein 96; RING-type E3 ubiquitin transferase TIF1-beta; TIF1-beta; nuclear corepressor KAP-1; protein phosphatase 1, regulatory subunit 157; transcriptional intermediary factor 1-beta

NP_005753.1

EC 2.3.2.27

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_046945.1 RefSeqGene

Range

4596..11247

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_005762.3 → NP_005753.1 transcription intermediary factor 1-beta

See identical proteins and their annotated locations for NP_005753.1

Status: REVIEWED

Source sequence(s)

AC016630, BC004978

Consensus CDS

CCDS12985.1

UniProtKB/Swiss-Prot

O00677, Q13263, Q7Z632, Q93040, Q96IM1

UniProtKB/TrEMBL

B2R8R5

Related

ENSP00000253024.4, ENST00000253024.10

Conserved Domains (7) summary

cd05502
Location:696 → 802

Bromo_tif1_like; Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or ...

smart00502
Location:252 → 378

BBC; B-Box C-terminal domain

cd15623
Location:627 → 669

PHD_TIF1beta; PHD finger found in transcription intermediary factor 1-beta (TIF1-beta)

cd16765
Location:62 → 124

RING-HC_TIF1beta; RING finger, HC subclass, found in transcription inknown asiary factor 1-beta (TIF1-beta)

cd19829
Location:206 → 249

Bbox2_TIF1b_C-VI; B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta)

cd19846
Location:148 → 199

Bbox1_TIF1b_C-VI; B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta)

NF033761
Location:526 → 626

gliding_GltJ; adventurous gliding motility protein GltJ