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TRIM42 Gene

protein-coding   GIFtS: 45
GCID: GC03P140396

Tripartite Motif Containing 42

(Previous name: tripartite motif-containing 42)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Tripartite Motif Containing 421 2     PPP1R402
Tripartite Motif-Containing 421 2     Protein Phosphatase 1, Regulatory Subunit 402
Protein Phosphatase 11     Tripartite Motif-Containing Protein 422
Regulatory Subunit 401     

External Ids:    HGNC: 190141   Entrez Gene: 2870152   Ensembl: ENSG000001558907   UniProtKB: Q8IWZ53   

Export aliases for TRIM42 gene to outside databases

Previous GC identifers: GC03M141225 GC03P141678 GC03P141717 GC03P141879 GC03P137770


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for TRIM42 Gene:
This gene encodes a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding
domains, namely 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 TRIM42 Gene:
TRIM42 (tripartite motif containing 42) is a protein-coding 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000003.11  NT_005612.17  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TRIM42 gene promoter:
         Max1   AML1a   GCNF   GCNF-1   GCNF-2   c-Myc   Arnt   YY1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTRIM42 promoter sequence
   Search Chromatin IP Primers for TRIM42

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRIM42


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

Entrez Gene cytogenetic band: 3q23   Ensembl cytogenetic band:  3q23   HGNC cytogenetic band: 3q23

TRIM42 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRIM42 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P140396:  view genomic region     (about GC identifiers)

Start:
140,396,866 bp from pter      End:
140,419,992 bp from pter
Size:
23,127 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: TRI42_HUMAN, Q8IWZ5 (See protein sequence)
Recommended Name: Tripartite motif-containing protein 42  
Size: 723 amino acids; 82745 Da
Sequence caution: Sequence=BAC05042.1; Type=Erroneous termination; Positions=709; Note=Translated as Trp;
Secondary accessions: A1L4B4 Q8N832 Q8NDL3
Alternative splicing: 2 isoforms:  Q8IWZ5-1   Q8IWZ5-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TRIM42: NX_Q8IWZ5

Explore proteomics data for TRIM42 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See TRIM42 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689829.3  
    ENSEMBL proteins: 
     ENSP00000286349  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    FN3: Fibronectin type III domain containing
    TRIM: Tripartite motif containing / Tripartite motif containing
    PPP1R: Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits
    RNF: RING-type (C3HC4) zinc fingers

    Selected InterPro protein domains (see all 6):
     IPR017907 Znf_RING_CS
     IPR001841 Znf_RING
     IPR017903 COS_domain
     IPR003961 Fibronectin_type3
     IPR000315 Znf_B-box

    Graphical View of Domain Structure for InterPro Entry Q8IWZ5

    ProtoNet protein and cluster: Q8IWZ5

    2 Blocks protein domains:
    IPB000315 B-box zinc finger signature
    IPB001841 Zn-finger


    UniProtKB/Swiss-Prot: TRI42_HUMAN, Q8IWZ5
    Similarity: Belongs to the TRIM/RBCC family
    Similarity: Contains 2 B box-type zinc fingers
    Similarity: Contains 1 COS domain
    Similarity: Contains 1 fibronectin type-III domain
    Similarity: Contains 1 RING-type zinc finger


    Find genes that share domains with TRIM42           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
         
    Find genes that share ontologies with TRIM42           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for TRIM42

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    mitochondrion1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular IEA--

    Find genes that share ontologies with TRIM42           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for TRIM42
    Interactions:

        Search GeneGlobe Interaction Network for TRIM42

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for TRIM42 (ENSP000002863494) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPP1CAENSP000003260314STRING: ENSP00000326031
    HAT1ENSP000002641084STRING: ENSP00000264108
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for TRIM42 (TRI42)



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for TRIM42 gene: 
    NM_152616.4  

    Unigene Cluster for TRIM42:

    Tripartite motif containing 42
    Hs.343487  [show with all ESTs]
    Unigene Representative Sequence: NM_152616
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000286349(uc003eto.2)
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate TRIM42:
    hsa-miR-539
    SwitchGear 3'UTR luciferase reporter plasmidTRIM42 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiFast Probe-based Assays in human, mouse, rat TRIM42

    Additional mRNA sequence: 

    AF521868.1 AK097416.1 AK310536.1 AL833848.1 BC130472.1 BC130474.1 

    1 DOTS entry:

    DT.91650839 

    11 AceView cDNA sequences:

    NM_152616 AF521868 BX093220 AA931321 AI240184 AL833848 BI830098 AK097416 
    BG193918 BG192318 BG193917 

    GeneLoc Exon Structure


    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    TRIM42 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGAATCCAAA
    TRIM42 Expression
    About this image

    TRIM42 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    TRIM42 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.343487
        Custom PCR Arrays for TRIM42
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM42

    (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)
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    This gene was present in the common ancestor of chordates.

    Orthologs for TRIM42 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Trim421 , 5 tripartite motif-containing 421, 5 85.62(n)1
    87(a)1
      9 (51.06 cM)5
    789111  NM_030219.21  NP_084495.21 
     973495625 
    chicken
    (Gallus gallus)
    Aves TRIM421 tripartite motif containing 42 55.9(n)
    46.72(a)
      424818  XM_422632.4  XP_422632.4 
    lizard
    (Anolis carolinensis)
    Reptilia TRIM426
    tripartite motif containing 42
    47(a)
    1 ↔ 1
    3(26530093-26540886)


    ENSEMBL Gene Tree for TRIM42 (if available)
    TreeFam Gene Tree for TRIM42 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for TRIM42 (see all 593)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2009312451,2
    Cuntested1140406642(+) AAAGCA/GAAAAG 2 Q R mis10--------
    rs1167826501,2
    C,F--140394979(+) AATCAG/AAAGAA 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs1826001351,2
    --140395009(+) GAAAAC/TGATGT 1 -- us2k10--------
    rs1871977491,2
    --140395187(+) ACACAA/CAAAAA 1 -- us2k10--------
    rs1881368111,2
    --140395315(+) CAGCCA/TTAAAA 1 -- us2k10--------
    rs593625421,2
    C,F--140395429(+) CTCCAG/CAATAG 1 -- us2k12Minor allele frequency- C:0.16WA 120
    rs557383111,2
    C,F--140395458(+) AAAAGT/CAGAGT 1 -- us2k12Minor allele frequency- C:0.06WA 120
    rs1413687011,2
    C--140395495(+) GAACAA/GGGAGA 1 -- us2k10--------
    rs1809212191,2
    --140395522(+) TTTACA/GGGGGT 1 -- us2k10--------
    rs1855807491,2
    --140395771(+) GCAAAC/TGTGAG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for TRIM42 (140396866 - 140419992 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for TRIM42:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv829743CNV Loss17160897
    nsv818170CNV Gain17921354
    nsv527831CNV Gain19592680
    nsv460869CNV Gain19166990
    nsv877546CNV Gain21882294
    nsv877547CNV Gain21882294
    esv34489CNV Gain17911159
    dgv1513e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for TRIM42

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    Find genes that share disorders with TRIM42           About GenesLikeMe

    Genetic Association Database (GAD): TRIM42
    Human Genome Epidemiology (HuGE) Navigator: TRIM42 (1 document)

    Export disorders for TRIM42 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)
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    PubMed articles for TRIM42 gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with TRIM42)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    2. Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. (PubMed id 19010793)1, 4 Baranzini S.E....Oksenberg J.R. (Hum. Mol. Genet. 2009)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Docking motif-guided mapping of the interactome of protein phosphatase-1. (PubMed id 19389623)1 Hendrickx A.... Bollen M. (Chem. Biol. 2009)
    5. Genome-scale RNAi screen for host factors required for HIV replication. (PubMed id 18976975)1 Zhou H....Espeseth A.S. (amp 2008)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    7. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    8. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (Nature 2006)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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)
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    Entrez Gene: 287015 HGNC: 19014 AceView: TRIM42 Ensembl:ENSG00000155890 euGenes: HUgn287015
    ECgene: TRIM42 H-InvDB: TRIM42

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for TRIM42 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for TRIM42 gene:
    Search GeneIP for patents involving TRIM42

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from genOway)
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     Block miRNA regulation of human, mouse, rat TRIM42 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing TRIM42
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     Custom PCR Arrays for TRIM42 Search Chromatin IP Primers for TRIM42
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     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

     Novus Tissue Slides
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     Browse compounds at ApexBio
     Search Addgene for plasmids for TRIM42
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     genOway: Develop your customized and physiologically relevant rodent model for TRIM42
     antibodies-online antibodies for TRIM42 (11 products)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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