Trim28 tripartite motif-containing 28 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Trim28provided by MGI
Official Full Name: tripartite motif-containing 28provided by MGI
Primary source: MGI:MGI:109274
See related: Ensembl:ENSMUSG00000005566 AllianceGenome:MGI:109274
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: KAP-1; Tif1b; KRIP-1; MommeD9; Tif1beta
Summary: Enables DNA binding activity; protein kinase activity; and transcription coactivator activity. Involved in epithelial to mesenchymal transition; positive regulation of DNA methylation-dependent heterochromatin formation; and positive regulation of DNA-templated transcription. Acts upstream of or within several processes, including convergent extension involved in axis elongation; genomic imprinting; and negative regulation of RNA biosynthetic process. Located in euchromatin; heterochromatin; and nucleoplasm. Part of RNA polymerase II transcription regulator complex. Is expressed in several structures, including branchial arch; central nervous system; early conceptus; genitourinary system; and limb primordium. Orthologous to human TRIM28 (tripartite motif containing 28). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in ovary adult (RPKM 143.7), CNS E11.5 (RPKM 133.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 A1; 7 7.73 cM

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (12758079..12764959)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (13024152..13031032)

Chromosome 7 - NC_000073.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TRIM28 Fosters Microglia Ferroptosis via Autophagy Modulation to Enhance Neuropathic Pain and Neuroinflammation.
Title: TRIM28 Fosters Microglia Ferroptosis via Autophagy Modulation to Enhance Neuropathic Pain and Neuroinflammation.
TIF1beta activates leukemic transcriptional program in HSCs and promotes BCR::ABL1-induced myeloid leukemia.
Title: TIF1β activates leukemic transcriptional program in HSCs and promotes BCR::ABL1-induced myeloid leukemia.
Satellite cell-derived TRIM28 is pivotal for mechanical load- and injury-induced myogenesis.
Title: Satellite cell-derived TRIM28 is pivotal for mechanical load- and injury-induced myogenesis.
The correlation between TRIM28 expression and immune checkpoints in CRPC.
Title: The correlation between TRIM28 expression and immune checkpoints in CRPC.
Heat shock protein gp96 drives natural killer cell maturation and anti-tumor immunity by counteracting Trim28 to stabilize Eomes.
Title: Heat shock protein gp96 drives natural killer cell maturation and anti-tumor immunity by counteracting Trim28 to stabilize Eomes.
Co-option of endogenous retroviruses through genetic escape from TRIM28 repression.
Title: Co-option of endogenous retroviruses through genetic escape from TRIM28 repression.
Loss of Trim28 in muscle alters mitochondrial signalling but not systemic metabolism.
Title: Loss of Trim28 in muscle alters mitochondrial signalling but not systemic metabolism.
TRIM28 promotes the escape of gastric cancer cells from immune surveillance by increasing PD-L1 abundance.
Title: TRIM28 promotes the escape of gastric cancer cells from immune surveillance by increasing PD-L1 abundance.
Mitochondrial Glycerol-3-Phosphate Dehydrogenase Restricts HBV Replication via the TRIM28-Mediated Degradation of HBx.
Title: Mitochondrial Glycerol-3-Phosphate Dehydrogenase Restricts HBV Replication via the TRIM28-Mediated Degradation of HBx.
TRIM28 represses renal cell carcinoma cell proliferation by inhibiting TFE3/KDM6A-regulated autophagy.
Title: TRIM28 represses renal cell carcinoma cell proliferation by inhibiting TFE3/KDM6A-regulated autophagy.

Submit: New GeneRIF Correction See all GeneRIFs (83)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (3) 1 citation
Endonuclease-mediated (8) 1 citation
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126533 (e-PCR)
- UniSTS:209673

RH137168 (e-PCR)
- UniSTS:219256

Trim28 (e-PCR), detects polymorphism
- UniSTS:527586

Gene Ontology Provided by MGI

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

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in chromatin organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within convergent extension involved in axis elongation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryo implantation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic placenta morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epigenetic programming of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelial to mesenchymal transition	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within genomic imprinting	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within in utero embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within innate immune response	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within innate immune response	IGI Inferred from Genetic Interaction more info	PubMed
involved_in innate immune response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of DNA binding	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA repair	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA repair	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein import into nucleus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein import into nucleus	ISS Inferred from Sequence or Structural Similarity more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within protein autophosphorylation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within protein phosphorylation	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	IEA Inferred from Electronic Annotation more info
involved_in protein sumoylation	ISO Inferred from Sequence Orthology more info
involved_in suppression of viral release by host	IEA Inferred from Electronic Annotation more info
involved_in suppression of viral release by host	ISO Inferred from Sequence Orthology more info

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	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in euchromatin	IDA Inferred from Direct Assay more info	PubMed
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
NOT located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcription intermediary factor 1-beta

Names: E3 SUMO-protein ligase TRIM28; KRAB-A-interacting protein; RING-type E3 ubiquitin transferase TIF1-beta; TIF1-beta; transcriptional intermediary factor 1, beta; tripartite motif protein 28; tripartite motif-containing protein 28

NP_035718.2

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.

mRNA and Protein(s)

NM_011588.3 → NP_035718.2 transcription intermediary factor 1-beta

See identical proteins and their annotated locations for NP_035718.2

Status: VALIDATED

Source sequence(s)

BC089337

Consensus CDS

CCDS20823.1

UniProtKB/Swiss-Prot

P70391, Q62318, Q8C283, Q99PN4

UniProtKB/TrEMBL

Q5EBP9

Related

ENSMUSP00000005705.8, ENSMUST00000005705.8

Conserved Domains (6) summary

smart00502
Location:253 → 379

BBC; B-Box C-terminal domain

smart00336
Location:149 → 185

BBOX; B-Box-type zinc finger

cd00021
Location:208 → 246

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

cd15623
Location:627 → 669

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

pfam14634
Location:65 → 123

zf-RING_5; zinc-RING finger domain

cl02556
Location:696 → 802

Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.