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

TRIM42 Gene

protein-coding   GIFtS: 44
GCID: GC03P140396

Tripartite Motif Containing 42

(Previous name: tripartite motif-containing 42)
  Search for TRIM42
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 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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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. GO annotations related to this gene include zinc ion binding.




(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_000003.11  NT_005612.16  NC_018914.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for TRIM42

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 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: 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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q8IWZ5

  • TRIM42 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    TRIM42 Protein Expression
    REFSEQ proteins: NP_689829.3  
    ENSEMBL proteins: 
     ENSP00000286349  

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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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

    TRIM42 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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

    5/6 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


    TRIM42 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

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
         
    TRIM42 for ontologies           About GeneDecksing


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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



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TRIM42

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

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

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

    Browse Tocris compounds for TRIM42 (TRI42)

    Search CenterWatch for drugs/clinical trials and news about 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,
    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 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 QIAGEN miScript miRNA Assays for microRNA that regulate TRIM42:
    hsa-miR-539
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    Inhib. RNA
    Products:
         
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    Clone
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    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat TRIM42
      QIAGEN 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:

    BX093220 NM_152616 AF521868 AK097416 BI830098 AA931321 AL833848 AI240184 
    BG193918 BG193917 BG192318 

    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™, 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

    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


    See TRIM42 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TRIM42

    SOURCE GeneReport for Unigene cluster: Hs.343487
        SABiosciences Custom PCR Arrays for TRIM42
    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat TRIM42
    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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for TRIM42 gene from 3/9 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 55.92(n)
    47.25(a)
      424818  XM_422632.3  XP_422632.3 
    lizard
    (Anolis carolinensis)
    Reptilia TRIM426
    Uncharacterized protein
    45(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)
    About This Section
      --

    (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

    10/593 SNPs in TRIM42 are shown (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

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

    TRIM42 for disorders           About MalaCards

    TRIM42 for disorders           About GeneDecksing

    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)
    About This Section

    PubMed articles for TRIM42 gene, integrated from 9 sources (see all 11):
    (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. (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. (2008)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Docking motif-guided mapping of the interactome of protein phosphatase-1. (PubMed id 19389623)1 Hendrickx A.... Bollen M. (2009)
    5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    6. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    7. The DNA sequence, annotation and analysis of human chromosome 3. (PubMed id 16641997)2 Muzny D.M....Gibbs R.A. (2006)
    8. 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. (2004)
    9. 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. (2002)
    10. The tripartite motif family identifies cell compartments. (PubMed id 11331580)1 Reymond A.... Ballabio A. (2001)

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

    (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 TRIM42 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    (GIFtS: 73)
    transforming growth factor, beta 1
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