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

Gene ID: 21849, updated on 17-Jan-2023

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 and positive regulation of DNA methylation-dependent heterochromatin assembly. Acts 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. 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, Apr 2022]
Expression
Ubiquitous expression in ovary adult (RPKM 143.7), CNS E11.5 (RPKM 133.2) and 28 other tissues See more
Orthologs
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Genomic context

See Trim28 in Genome Data Viewer
Location:
7; 7 A1
Exon count:
17
Annotation release Status Assembly Chr Location
109 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_000073.7Genomic Context describing neighboring genes Neighboring gene zinc finger and BTB domain containing 45 Neighboring gene CRISPRi-validated cis-regulatory element for Slc27a5, Trim28, Ube2m, Zbtb45, Zfp324 and Zfp446 Neighboring gene predicted gene, 31649 Neighboring gene charged multivesicular body protein 2A Neighboring gene ubiquitin-conjugating enzyme E2M

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC102100

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 SUMO transferase activity ISO
Inferred from Sequence Orthology
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 metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables promoter-specific chromatin binding ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
enables ubiquitin protein ligase binding ISO
Inferred from Sequence Orthology
more info
 
enables ubiquitin-protein transferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables ubiquitin-protein transferase activity ISO
Inferred from Sequence Orthology
more info
 
enables zinc ion binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA methylation involved in embryo development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in DNA repair ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
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 
involved_in epithelial to mesenchymal transition IDA
Inferred from Direct Assay
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
PubMed 
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
 
acts_upstream_of_or_within negative regulation of DNA demethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 methylation-dependent heterochromatin formation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of DNA methylation-dependent heterochromatin formation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of DNA repair ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 binding ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of protein import into nucleus ISO
Inferred from Sequence Orthology
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
PubMed 
involved_in protein sumoylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of genetic imprinting IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
PubMed 
part_of RNA polymerase II transcription regulator complex IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in chromatin IBA
Inferred from Biological aspect of Ancestor
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 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
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 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

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

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)

  1. NM_011588.3NP_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
    Q62318, Q99PN4
    UniProtKB/TrEMBL
    Q5EBP9
    Related
    ENSMUSP00000005705.8, ENSMUST00000005705.8
    Conserved Domains (6) summary
    smart00502
    Location:253379
    BBC; B-Box C-terminal domain
    smart00336
    Location:149185
    BBOX; B-Box-type zinc finger
    cd00021
    Location:208246
    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:627669
    PHD_TIF1beta; PHD finger found in transcription intermediary factor 1-beta (TIF1-beta)
    pfam14634
    Location:65123
    zf-RING_5; zinc-RING finger domain
    cl02556
    Location:696802
    Bromodomain; Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    12758079..12764959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)