Trim28 tripartite motif-containing 28 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Trim28provided by RGD
Official Full Name: tripartite motif-containing 28provided by RGD
Primary source: RGD:620289
See related: Ensembl:ENSRNOG00000027487 AllianceGenome:RGD:620289
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Kap1; Krip1; Tif1b
Summary: Predicted to enable several functions, including promoter-specific chromatin binding activity; protein domain specific binding activity; and ubiquitin-like protein transferase activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of DNA methylation-dependent heterochromatin assembly; and regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within several processes, including DNA methylation involved in embryo development; negative regulation of single stranded viral RNA replication via double stranded DNA intermediate; and regulation of nucleobase-containing compound metabolic process. Predicted to be located in euchromatin; heterochromatin; and nucleus. Predicted to be part of RNA polymerase II transcription regulator complex. Predicted to be active in chromatin and nucleoplasm. Orthologous to human TRIM28 (tripartite motif containing 28). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 532.0), Thymus (RPKM 470.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q21

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (82724842..82731566)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (73652441..73659388)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (65544369..65551043, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

KAP1 phosphorylation promotes the survival of neural stem cells after ischemia/reperfusion by maintaining the stability of PCNA.
Title: KAP1 phosphorylation promotes the survival of neural stem cells after ischemia/reperfusion by maintaining the stability of PCNA.

Submit: New GeneRIF Correction

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

RH143061 (e-PCR)
- UniSTS:232308

RH137168 (e-PCR)
- UniSTS:219256

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

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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 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	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 kinase activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
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 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 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryo implantation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic placenta morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epigenetic programming of gene expression	ISO Inferred from Sequence Orthology more info
involved_in epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in epithelial to mesenchymal transition	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within genomic imprinting	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within innate immune response	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA demethylation	ISO Inferred from Sequence Orthology 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	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of single stranded viral RNA replication via double stranded DNA intermediate	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA methylation-dependent heterochromatin formation	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
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	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 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	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	ISO Inferred from Sequence Orthology more info
part_of RNA polymerase II transcription regulator complex	ISS Inferred from Sequence or Structural Similarity more info
part_of chromatin	ISO Inferred from Sequence Orthology more info
part_of euchromatin	ISO Inferred from Sequence Orthology more info
part_of heterochromatin	ISO Inferred from Sequence Orthology more info
NOT located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity 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-associated protein 1; RING-type E3 ubiquitin transferase TIF1-beta; TIF1-beta; nuclear corepressor KAP-1; tripartite motif protein 28; tripartite motif-containing protein 28

NP_446368.1

EC 2.3.2.27

XP_063121963.1

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.

mRNA and Protein(s)

NM_053916.1 → NP_446368.1 transcription intermediary factor 1-beta

See identical proteins and their annotated locations for NP_446368.1

Status: VALIDATED

Source sequence(s)

BC166843

UniProtKB/Swiss-Prot

B2RYN5, O08629

UniProtKB/TrEMBL

A0A8I6ADF3

Related

ENSRNOP00000031061.2, ENSRNOT00000029996.3

Conserved Domains (6) summary

smart00502
Location:254 → 380

BBC; B-Box C-terminal domain

cd15623
Location:628 → 670

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

cd16765
Location:64 → 126

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

cd19829
Location:208 → 251

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

cd19846
Location:150 → 201

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

cl02556
Location:697 → 803

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