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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TRIM28 Gene

protein-coding   GIFtS: 62
GCID: GC19P059055

Tripartite Motif Containing 28

(Previous name: tripartite motif-containing 28)
Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Tripartite Motif Containing 281 2     TIF1B2 3
Tripartite Motif-Containing 281 2     E3 SUMO-Protein Ligase TRIM282 3
Nuclear Corepressor KAP-12 3     KRAB-Associated Protein 12 3
Tripartite Motif-Containing Protein 282 3     KRAB-Interacting Protein 12 3
KAP-12 3     RING Finger Protein 962 3
KAP12 3     TF1B2
KRIP-12 3     Transcription Intermediary Factor 1-Beta2
RNF962 3     Transcriptional Intermediary Factor 1-Beta2
TIF1-beta2 3     EC 6.3.2.-3

External Ids:    HGNC: 163841   Entrez Gene: 101552   Ensembl: ENSG000001307267   OMIM: 6017425   UniProtKB: Q132633   

Export aliases for TRIM28 gene to outside databases

Previous GC identifers: GC19P059954 GC19P059509 GC19P063731 GC19P063747 GC19P063553 GC19P055366


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for TRIM28 Gene:
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)

GeneCards Summary for TRIM28 Gene: 
TRIM28 (tripartite motif containing 28) is a protein-coding gene. Diseases associated with TRIM28 include parotitis, and kaposi's sarcoma, and among its related super-pathways are Gene Expression and Cell Cycle / Checkpoint Control. GO annotations related to this gene include ubiquitin-protein ligase activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is TRIM33.

UniProtKB/Swiss-Prot: TIF1B_HUMAN, Q13263
Function: 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

Gene Wiki entry for TRIM28 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NT_011109.16  NC_018930.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TRIM28 gene promoter:
         SRF   SRF (504 AA)   AP-4   CUTL1   HNF-4alpha1   MZF-1   PPAR-gamma1   Pax-3   PPAR-gamma2   MRF-2   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for TRIM28

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TRIM28


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.4   Ensembl cytogenetic band:  19q13.43   HGNC cytogenetic band: 19q13.4

TRIM28 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRIM28 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P059055:  view genomic region     (about GC identifiers)

Start:
59,055,458 bp from pter      End:
59,062,089 bp from pter
Size:
6,632 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: TIF1B_HUMAN, Q13263 (See protein sequence)
Recommended Name: Transcription intermediary factor 1-beta  
Size: 835 amino acids; 88550 Da
Subunit: Oligomer; the RBCC domain homotrimerizes and interacts with one molecule of KRAB to form the KRAB-KAP1
corepressor complex. Binding to a KRAB domain is an absolute requirement for silencing gene expression. Interacts
with CEBPB and NR3C1 (By similarity). Interacts with a number of KRAB-ZFP proteins including ZNF10, ZFP53, ZFP68,
ZNF382 and ZNF256. Interacts with NCOR1, NR3C1 and CHD3. Interacts with CEBPB (via the RING-type and PHD-type
zinc fingers). Component of a ternary complex that includes TRIM28, a HP1 protein (CBX1, CBX3 OR CBX5), a KRAB
domain-containing protein, and DNA. Interacts with CBX5 (via the PxVxL motif); the interaction occurs in
interphase nuclei and competes for binding POGZ. Interacts with POGZ; the interaction competes for interaction
with CBX5. Interacts with SETDB1; the interaction is enhanced by KAP1 sumoylation, stimulates SETB1 histone
methyltransferase activity and gene silencing. Interacts (via the PHD-type zinc finger) with UBE2I; the
interaction is required for sumoylation and repressor activity. Component of the TRIM28/KAP1-ERBB4-MDM2 complex
involved in connecting growth factor and DNA damage responses. Interacts directly with ERBB4; the interaction
represses ERBB4-mediated transcription activity. Interacts with MDM2; the interaction contributes to p53/TP53
inactivation. Component of the TRIM28/KAP1-MDM2-p53/TP53; involved in regulating p53/TP53 stabilization and
activity. Interacts (via the leucine zipper alpha helical coiled-coil) with E2F1 (central region); the
interaction inhibits E2F1 acetylation and transcriptional activity. Interacts with PPP1CA; the interaction
dephosphorylates TRIM28 at Ser-824 and forms a complex at the p21 promoter site. Interacts with PPP1CB; the
interaction is weak but is increased on dephosphorylation at Ser-824. Interacts with FES/FPS. Interacts with
SMARCAD1. Interacts with, and sumoylates IRF7. Interacts with MAGEC2. Part of a complex composed of TRIM28,
HDAC1, HDAC2 and EHMT2
Subcellular location: Nucleus. Note=Associated with centromeric heterochromatin during cell differentiation
through CBX1 (By similarity)
3 PDB 3D structures from and Proteopedia for TRIM28:
1FP0 (3D)        2RO1 (3D)        2YVR (3D)    
Secondary accessions: O00677 Q7Z632 Q93040 Q96IM1
Alternative splicing: 2 isoforms:  Q13263-1   Q13263-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TRIM28: NX_Q13263

Explore proteomics data for TRIM28 at MOPED 

Post-translational modifications:

  • UniProtKB: ATM-induced phosphorylation on Ser-824 represses sumoylation leading to the de-repression of expression of a
    subset of genes involved in cell cycle control and apoptosis in response to genotoxic stress. Dephosphorylation
    by the phosphatases, PPP1CA and PP1CB forms, allows sumoylation and expression of TRIM28 target genes
  • UniProtKB: Sumoylation/desumoylation events regulate TRIM28-mediated transcriptional repression. Sumoylation is required for
    interaction with CHD3 and SETDB1 and the corepressor activity. Represses and is repressed by Ser-824
    phosphorylation. Enhances the TRIM28 corepressor activity, inhibiting transcriptional activity of a number of
    genes including GADD45A and CDKN1A/p21. Lys-554, Lys-779 and Lys-804 are the major sites of sumoylation. In
    response to Dox-induced DNA damage, enhanced phosphorylation on Ser-824 prevents sumoylation and allows
    de-repression of CDKN1A/p21
  • UniProtKB: Auto-ubiquitinated; enhanced by MAGEA2 and MAGEC2
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q13263

  • TRIM28 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    TRIM28 Protein Expression
    REFSEQ proteins: NP_005753.1  
    ENSEMBL proteins: 
     ENSP00000472586   ENSP00000473126   ENSP00000253024   ENSP00000342232   ENSP00000470503  
     ENSP00000471303  
    Reactome Protein details: Q13263
    Human Recombinant Protein Products for TRIM28: 
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    Novus Biologicals TRIM28 Proteins
    Novus Biologicals TRIM28 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 5/6 cellular component terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000785chromatin ----
    GO:0005622intracellular ----
    GO:0005634nucleus ISS--
    GO:0005654nucleoplasm TAS--
    GO:0005719nuclear euchromatin IEA--

    TRIM28 for ontologies           About GeneDecksing



    TRIM28 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of TRIM28
    R&D Systems Antibodies for TRIM28 (KAP1)
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    Abcam antibodies for TRIM28
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    LSBio Antibodies in human, mouse, rat for TRIM28 

    Assay Products for TRIM28: 
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    Browse ELISAs at Cloud-Clone Corp. 
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    TRIM: Tripartite motif containing / Tripartite motif containing
    RNF: RING-type (C3HC4) zinc fingers
    PHF: Zinc fingers, PHD-type

    IUPHAR Guide to PHARMACOLOGY protein family classification: tripartite motif containing 28 
    TIF1 family

    5/9 InterPro protein domains (see all 9):
     IPR003649 Bbox_C
     IPR019786 Zinc_finger_PHD-type_CS
     IPR001841 Znf_RING
     IPR001965 Znf_PHD
     IPR001487 Bromodomain

    Graphical View of Domain Structure for InterPro Entry Q13263

    ProtoNet protein and cluster: Q13263

    4 Blocks protein domains:
    IPB000315 B-box zinc finger signature
    IPB001841 Zn-finger
    IPB001965 Zn-finger-like
    IPB003649 B-box


    UniProtKB/Swiss-Prot: TIF1B_HUMAN, Q13263
    Domain: The HP1 box is both necessary and sufficient for HP1 binding
    Domain: The PHD-type zinc finger enhances CEBPB transcriptional activity. The PHD-type zinc finger, the HP1 box
    and the bromo domain, function together to assemble the machinery required for repression of KRAB
    domain-containing proteins. Acts as an intramolecular SUMO E3 ligase for autosumoylation of bromodomain
    Domain: The RING-finger-B Box-coiled-coil/tripartite motif (RBCC/TRIM motif) is required for interaction with the
    KRAB domain of KRAB-zinc finger proteins. Binds four zinc ions per molecule. The RING finger and the N-terminal
    of the leucine zipper alpha helical coiled-coil region of RBCC are required for oligomerization
    Domain: Contains one Pro-Xaa-Val-Xaa-Leu (PxVxL) motif, which is required for interaction with chromoshadow
    domains. This motif requires additional residues -7, -6, +4 and +5 of the central Val which contact the
    chromoshadow domain
    Similarity: Belongs to the TRIM/RBCC family
    Similarity: Contains 2 B box-type zinc fingers
    Similarity: Contains 1 bromo domain
    Similarity: Contains 1 PHD-type zinc finger
    Similarity: Contains 1 RING-type zinc finger


    TRIM28 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: TIF1B_HUMAN, Q13263
    Function: 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

         Enzyme Number (IUBMB): EC 6.3.2.-1

         Gene Ontology (GO): 5/12 molecular function terms (GO ID links to tree view) (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IDA9016654
    GO:0003700contributes to sequence-specific DNA binding transcription factor activity ISS--
    GO:0003713transcription coactivator activity IEA--
    GO:0003714transcription corepressor activity IDA8769649
    GO:0004672protein kinase activity IEA--
         
    TRIM28 for ontologies           About GeneDecksing


    Phenotypes:
         5 GenomeRNAi human phenotypes for TRIM28:
     Decreased focal adhesion (FA)   Decreased influenza A virus in  Decreased number of cells in m  Increased cell death in HCC-19 
     Wnt reporter downregulated 

         8 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Trim28):
     cellular  embryogenesis  endocrine/exocrine gland  growth/size  mortality/aging 
     nervous system  normal  reproductive system 

    TRIM28 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Trim28tm1.2Ipc for TRIM28

       inGenious Targeting Laboratory - Custom generated mouse model solutions for TRIM28 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for TRIM28

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for TRIM28 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for TRIM28 

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat TRIM28
    6 QIAGEN miScript miRNA Assays for microRNAs that regulate TRIM28:
    hsa-miR-548am hsa-miR-548d-3p hsa-miR-548x hsa-miR-605 hsa-miR-3675-5p hsa-miR-548aa
    SwitchGear 3'UTR luciferase reporter plasmidTRIM28 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector: TRIM28 (NM_005762)
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for TRIM28 About   (see all 6)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Generic Transcription Pathway
    Gene Expression0.47
    Generic Transcription Pathway0.47
    2DNA Damage
    DNA Damage0.32
    Cell Cycle / Checkpoint Control0.32
    3p53 pathway
    p53 pathway
    4E2F transcription factor network
    E2F transcription factor network
    5C-MYB transcription factor network
    C-MYB transcription factor network

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    3 Cell Signaling Technology (CST) Pathways for TRIM28
        Chromatin Regulation / Acetylation
    Cell Cycle / Checkpoint Control
    DNA Damage

    3 BioSystems Pathways for TRIM28
        p53 pathway
    C-MYB transcription factor network
    E2F transcription factor network

    2        Reactome Pathways for TRIM28
        Generic Transcription Pathway
    Gene Expression


    UniProtKB/Swiss-Prot: TIF1B_HUMAN, Q13263
    Pathway: Protein modification; protein sumoylation


    TRIM28 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for TRIM28

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/1044 Interacting proteins for TRIM28 (Q132631, 2, 3 ENSP000002530244) via UniProtKB, MINT, STRING, and/or I2D (see all 1044)

    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H3AP684313, ENSP000003502754I2D: score=1 STRING: ENSP00000350275
    HIST1H3BP684313I2D: score=1 
    HIST1H3CP684313I2D: score=1 
    HIST1H3DP684313I2D: score=1 
    HIST1H3EP684313I2D: score=1 
    About this table

    Gene Ontology (GO): 5/16 biological process terms (GO ID links to tree view) (see all 16):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000122negative regulation of transcription from RNA polymerase II promoter IEA--
    GO:0001837epithelial to mesenchymal transition ISS--
    GO:0006281DNA repair IDA17178852
    GO:0006367transcription initiation from RNA polymerase II promoter TAS--
    GO:0006468protein phosphorylation ----

    TRIM28 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    TRIM28 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for TRIM28 (TIF1B)

    2 Novoseek inferred chemical compound relationships for TRIM28 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    zinc 65.9 23 11226167 (2), 14727140 (1), 15342492 (1), 12167632 (1) (see all 14)
    retinoic acid 17.9 2 10022127 (1), 10094499 (1)

    Search CenterWatch for drugs/clinical trials and news about TRIM28 / TIF1B

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TRIM28 gene: 
    NM_005762.2  

    Unigene Cluster for TRIM28:

    Tripartite motif containing 28
    Hs.467408  [show with all ESTs]
    Unigene Representative Sequence: X97548
    15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000593582 ENST00000594806 ENST00000253024(uc002qtg.1) ENST00000341753(uc010eut.1 uc002qth.1)
    ENST00000597968 ENST00000597618 ENST00000597423 ENST00000597172 ENST00000601150
    ENST00000597995 ENST00000597136 ENST00000595028 ENST00000595974 ENST00000600840
    ENST00000598355
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    SwitchGear 3'UTR luciferase reporter plasmidTRIM28 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AK131063.1 AK225760.1 AK313478.1 AL360114.1 AL360188.1 AL360189.1 BC004978.1 BC007390.2 
    BC052986.2 U31657.1 U78773.1 U95040.1 X97548.1 

    24/47 DOTS entries (see all 47):

    DT.320016  DT.100673748  DT.95143377  DT.91656083  DT.121473408  DT.100673731  DT.95164472  DT.100673745 
    DT.100673733  DT.99942398  DT.92023440  DT.100673728  DT.95251288  DT.121473526  DT.92020999  DT.100673737 
    DT.100866961  DT.100686449  DT.95164488  DT.100673744  DT.91783155  DT.92325778  DT.100673729  DT.100673730 

    24/1386 AceView cDNA sequences (see all 1386):

    BM710059 BU507412 BC004978 BE513513 AU125701 BU845210 CF127773 BU538844 
    BQ681409 BG257501 AW651654 BQ224915 CR613705 BQ890474 CB130768 BU849874 
    BM795255 BQ065964 CA424025 BQ682734 BU956053 BG403204 BQ877925 BU554024 

    GeneLoc Exon Structure

    5/15 Alternative Splicing Database (ASD) splice patterns (SP) for TRIM28 (see all 15)    About this scheme

    ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b · 7c · 7d ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^
    SP1:                          -                       -     -           -                       -                                                               
    SP2:                          -     -     -     -     -     -           -                       -                                                               
    SP3:                                                                                                                                                  -         
    SP4:                                                  -     -           -                       -                                                               
    SP5:                                                                                                                                                            

    ExUns: 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20a · 20b · 20c
    SP1:                                                                  
    SP2:                                                                  
    SP3:                                                                  
    SP4:                                                                  
    SP5:                                                                  


    ECgene alternative splicing isoforms for TRIM28

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    TRIM28 expression in normal human tissues (normalized intensities)      TRIM28 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCCAGCCCAG
    TRIM28 Expression
    About this image


    TRIM28 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/31 selected tissues (see all 31) fully expand
     
     Brain (Nervous System)    fully expand to see all 6 entries
             Cerebral Cortex
             brain/midbrain   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 3 entries
             colon ; peripheral nerve/ganglion   
     
     Lung (Respiratory System)    fully expand to see all 3 entries
             lung ; pneumocytes   

    See TRIM28 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TRIM28

    SOURCE GeneReport for Unigene cluster: Hs.467408

    UniProtKB/Swiss-Prot: TIF1B_HUMAN, Q13263
    Tissue specificity: Expressed in all tissues tested including spleen, thymus, prostate, testis, ovary, small
    intestine, colon and peripheral blood leukocytes

        SABiosciences Expression via Pathway-Focused PCR Array including TRIM28: 
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for TRIM28 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Trim281 , 5 tripartite motif-containing 281, 5 85.77(n)1
    94.21(a)1
      7 (7.73 cM)5
    218491  NM_011588.31  NP_035718.21 
     130241525 
    chicken
    (Gallus gallus)
    Aves TRIM281 tripartite motif containing 28 63.31(n)
    59.76(a)
      430538  XM_428095.3  XP_428095.3 
    lizard
    (Anolis carolinensis)
    Reptilia TRIM286
    Uncharacterized protein
    60(a)
    1 ↔ 1
    GL343253.1(90437-112852)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.188432 Xenopus laevis transcribed sequence with strong similarity more 85.6(n)    BI446721.1 
    zebrafish
    (Danio rerio)
    Actinopterygii trim33l6
    tripartite motif-containing 33-like
    12(a)
    1 ↔ 1
    16(30992261-31018660)
    fruit fly
    (Drosophila melanogaster)
    Insecta bon3 peripheral nervous system development
    transcription more
    28(a)     --


    ENSEMBL Gene Tree for TRIM28 (if available)
    TreeFam Gene Tree for TRIM28 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TRIM28 gene
    TRIM332  TRIM662  TRIM242  AIRE2  

    TRIM28 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for TRIM28
    PGOHUM00000235181


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/388 SNPs in TRIM28 are shown (see all 388)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs760402671,2
    C--59053848(+) ACCCTC/TTTTCC 1 -- us2k10--------
    rs1824996111,2
    --59053917(+) ACACAC/GACCCT 1 -- us2k10--------
    rs1860547221,2
    --59054115(+) ACGCTA/GCTTCC 1 -- us2k10--------
    rs1422385781,2
    --59054260(+) TCCCCA/CCATGG 1 -- us2k10--------
    rs730683121,2
    C--59054288(+) CTTGGG/AATTCC 1 -- us2k14Minor allele frequency- A:0.22WA NA EA 360
    rs105347871,2
    C--59054442(+) ATGTG-/TATATAT 1 -- us2k10--------
    rs2004394781,2
    C--59054455(+) TATAT-/ATATTTTT 1 -- us2k10--------
    rs74083261,2
    C--59054457(+) tatatA/TtTTTT 1 -- us2k11Minor allele frequency- T:0.00NA 2
    rs600835451,2
    C--59054457(+) TATAT-/A/A   
       T
    /ATA
    TTTTT
    2 -- us2k1 cds10--------
    rs1916134201,2
    --59054553(+) CTGACA/GTCGGG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TRIM28 (59055458 - 59062089 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for TRIM28:    About this table     
    Variant IDTypeSubtypePubMed ID
    dgv4032n71CNV Loss21882294
    nsv912546CNV Loss21882294
    nsv828657CNV Gain20364138
    nsv515731CNV Gain+Loss19592680

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 601742    OMIM disorders: --

    9 diseases for TRIM28:    About MalaCards
    parotitis    kaposi's sarcoma    peritonitis    sarcoma
    neuroblastoma    gastric cancer    hepatocellular carcinoma    breast cancer
    prostatitis


    TRIM28 for disorders           About GeneDecksing

    2 Novoseek inferred disease relationships for TRIM28 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    carcinoma embryonal 48.5 1 17381543 (1)
    tumors 3.6 1 16107876 (1)


    Export disorders for TRIM28 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for TRIM28 gene, integrated from 9 sources (see all 203):
    (articles sorted by number of sources associating them with TRIM28)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. (PubMed id 11226167)1, 2, 3, 9 Capili A.D.... Borden K.L. (2001)
    2. Doxorubicin down-regulates Kruppel-associated box domain-associated protein 1 sumoylation that relieves its transcription repression on p21WAF1/CIP1 in breast cancer MCF-7 cells. (PubMed id 17079232)1, 2, 9 Lee Y.K....Ann D.K. (2007)
    3. Two novel Kruppel-associated box-containing zinc-finger proteins, KRAZ1 and KRAZ2, repress transcription through functional interaction with the corepressor KAP-1 (TIF1beta/KRIP-1). (PubMed id 10347202)1, 2, 9 Agata Y.... Shimizu A. (1999)
    4. KAP-1 corepressor protein interacts and colocalizes with heterochromatic and euchromatic HP1 proteins: a potential role for Kruppel-associated box-zinc finger proteins in heterochromatin- mediated gene silencing. (PubMed id 10330177)1, 2, 9 Ryan R.F.... Rauscher F.J. III (1999)
    5. Regulation of E2F1 function by the nuclear corepressor KAP1. (PubMed id 17704056)1, 2, 9 Wang C....Chen J. (2007)
    6. MDM2 interaction with nuclear corepressor KAP1 contributes to p53 inactivation. (PubMed id 16107876)1, 2, 9 Wang C....Chen J. (2005)
    7. The KRAB-associated co-repressor KAP-1 is a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. (PubMed id 16792528)1, 2, 9 Delfino F.J....Smithgall T.E. (2006)
    8. A novel GDNF-inducible gene, BMZF3, encodes a transcriptional repressor associated with KAP-1. (PubMed id 18060868)1, 2, 9 Suzuki C.... Takahashi M. (2008)
    9. Transcriptional repression by RING finger protein TIF1 beta that interacts with the KRAB repressor domain of KOX1. (PubMed id 9016654)1, 2, 9 Moosmann P.R....Schaffner W. (1996)
    10. Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. (PubMed id 18488044)1, 2, 9 Zeng L....Zhou M.M. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 10155 HGNC: 16384 AceView: TRIM28 Ensembl:ENSG00000130726 euGenes: HUgn10155
    ECgene: TRIM28 H-InvDB: TRIM28

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for TRIM28 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for TRIM28 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for TRIM28 gene:
    Search GeneIP for patents involving TRIM28

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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    About This Section

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