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

TRIM50 Gene

protein-coding   GIFtS: 48
GCID: GC07M072726

tripartite motif containing 50

(Previous names: tripartite motif-containing 50A, tripartite motif-containing...)
(Previous symbol: TRIM50A)
 Explore 1 disease affiliated with
TRIM50 via our new
 Human Malady Compendium 
Biological research products
for TRIM50
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Tripartite Motif Containing 501 2     E3 Ubiquitin Ligase2
TRIM50A1 2 3 5     E3 Ubiquitin-Protein Ligase TRIM502
Tripartite Motif-Containing 501 2     Tripartite Motif Protein 502
Tripartite Motif-Containing 50A1 2     EC 6.3.2.-3
Tripartite Motif-Containing Protein 502 3     EC 6.3.28
FLJ328041     

External Ids:    HGNC: 190171   Entrez Gene: 1358922   Ensembl: ENSG000001467557   OMIM: 6125485   UniProtKB: Q86XT43   

Export aliases for TRIM50 gene to outside databases

Previous GC identifers: GC07M072124 GC07M072364 GC07M068608


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

UniProtKB/Swiss-Prot: TRI50_HUMAN, Q86XT4
Function: E3 ubiquitin-protein ligase




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000007.13  NC_018918.1  NT_007933.15  NT_079593.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the TRIM50 gene promoter:
         STAT1   STAT4   STAT1beta   STAT6   STAT5A   Tal-1beta   STAT1alpha   STAT2   STAT3   ITF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): TRIM50 promoter sequence
   Search SABiosciences Chromatin IP Primers for TRIM50

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat TRIM50


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

Entrez Gene cytogenetic band: 7q11.23   Ensembl cytogenetic band:  7q11.23   HGNC cytogenetic band: 7q11.23

TRIM50 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRIM50 gene location

GeneLoc information about chromosome 7         GeneLoc Exon Structure

GeneLoc location for GC07M072726:  view genomic region     (about GC identifiers)

Start:
72,726,535 bp from pter      End:
72,742,085 bp from pter
Size:
15,551 bases      Orientation:
minus strand

1 alternative location:
Chr7-,CRA_TCAG 72,059,607-72,075,157     

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: TRI50_HUMAN, Q86XT4 (See protein sequence)
Recommended Name: E3 ubiquitin-protein ligase TRIM50  
Size: 487 amino acids; 54774 Da
Subunit: Can form dimers and trimers. Interacts with several E2 ubiquitin-conjugating enzymes, including UBE2L6,
UBE2E1, UBE2E3. No interaction with UBE2H
Subcellular location: Cytoplasm
Secondary accessions: Q86XT3
Alternative splicing: 2 isoforms:  Q86XT4-1   Q86XT4-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for TRIM50: NX_Q86XT4

Post-translational modifications:

  • Auto-ubiquitinated1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q86XT4

  • 2 DME Specific Peptides for TRIM50 (Q86XT4)
     YLHYEQGELTFFDADRPDDLR  LYTFQADFQGKLYPILDTCWHERGSNSLPMVLP 

    TRIM50 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_835226.1  
    ENSEMBL proteins: 
     ENSP00000327994   ENSP00000413875  

    Human Recombinant Protein Products: 
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    Uscn Proteins for TRIM50

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IEA--
    GO:0043231intracellular membrane-bounded organelle IDA--


    TRIM50 for ontologies           About GeneDecksing



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

    TRIM50 for domains           About GeneDecksing

    5/9 InterPro domains/families (see all 9):
     IPR006574 PRY
     IPR017907 Znf_RING_CS
     IPR001841 Znf_RING
     IPR001870 B30.2/SPRY
     IPR003877 SPRY_rcpt

    Graphical View of Domain Structure for InterPro Entry Q86XT4

    ProtoNet protein and cluster: Q86XT4

    4 Blocks protein families:
    IPB000315 B-box zinc finger signature
    IPB001841 Zn-finger
    IPB003879 Butyrophylin C-terminal DUF signature
    IPB006574 SPRY-associated domain


    UniProtKB/Swiss-Prot: TRI50_HUMAN, Q86XT4
    Similarity: Belongs to the TRIM/RBCC family
    Similarity: Contains 1 B box-type zinc finger
    Similarity: Contains 1 B30.2/SPRY domain
    Similarity: Contains 1 RING-type zinc finger


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: TRI50_HUMAN, Q86XT4
    Function: E3 ubiquitin-protein ligase

    Enzyme Numbers (IUBMB): EC 6.3.2.-1 EC 6.3.22

    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmidTRIM50 3' UTR sequence
    Inhib. RNA
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    Search LifeMap BioReagents cell lines for TRIM50

    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM50

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008270zinc ion binding IEA--
    GO:0016874ligase activity IEA--


    TRIM50 for ontologies           About GeneDecksing


    2 GenomeRNAi human phenotypes for TRIM50:
     G0/1 arrest  Increased S DNA content 

    Animal Models:
         Mouse knock-out Trim50tm1Hta for TRIM50
         2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Trim50):
     digestive/alimentary  no phenotypic analysis 

    TRIM50 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TRIM50

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    5/8 Interacting proteins for TRIM50 (ENSP000003279944) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBE2D1ENSP000003630194STRING: ENSP00000363019
    UBE2D2ENSP000003817174STRING: ENSP00000381717
    UBE2D3ENSP000003497224STRING: ENSP00000349722
    UBE2D4ENSP000002224024STRING: ENSP00000222402
    UBE2E1ENSP000003037094STRING: ENSP00000303709
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 TRIM50
    Search CenterWatch for drugs/clinical trials and news about TRIM50 / TRI50 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for TRIM50 gene: 
    NM_178125.2  

    Unigene Cluster for TRIM50:

    Tripartite motif containing 50
    Hs.647053  [show with all ESTs]
    Unigene Representative Sequence: AY081948
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000333149(uc010lbd.1 uc003txy.1 uc003txz.1) ENST00000453152
    ENST00000488217 ENST00000493498

    miRNA
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    OriGene 3'-UTR Clone: TRIM50
    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat TRIM50
    Search QIAGEN for miScript miRNA Assays for microRNAs that regulate TRIM50
    SwitchGear 3'UTR luciferase reporter plasmidTRIM50 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for TRIM50 (see all 7)
    OriGene shRNA RFP: TRIM50
    OriGene siRNA: TRIM50
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    Clone
    Products:
         
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    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for TRIM50
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    GenScript: all cDNA clones in your preferred vector: TRIM50 (NM_178125)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TRIM50 
    Primer
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat TRIM50
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat TRIM50

    Additional cDNA sequence: 

    AK057366.1 AK292074.1 AY081948.1 AY081949.1 BC112152.1 BC112154.1 BC143787.1 

    8 DOTS entries:

    DT.40233928  DT.443249  DT.92417013  DT.40131438  DT.75101643  DT.75115935  DT.100736906  DT.440570 

    24/31 AceView cDNA sequences (see all 31):

    AW614271 AI310113 BE466482 AY081948 AW058675 AI916523 AI928331 AI675279 
    AY081949 AI306456 NM_178125 AA621610 AI949449 AI763201 AA844922 AW299621 
    AI027904 AW296619 BX100375 AI208986 BG413566 AI768759 AW024178 BG413545 

    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

    TRIM50 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TATACCTTTT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    TRIM50 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Posterior foregut-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See TRIM50 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for TRIM50

    SOURCE GeneReport for Unigene cluster: Hs.647053
        SABiosciences Custom PCR Arrays for TRIM50
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM50

    (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 TRIM50 gene from 1/6 species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves TRIM501 tripartite motif containing 50 68.66(n)
    61.32(a)
      417461  XM_415709.2  XP_415709.2 


    ENSEMBL Gene Tree for TRIM50 (if available)
    TreeFam Gene Tree for TRIM50 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for TRIM50 gene
    TRIM312  TRIM352  TRIM732  TRIM522  TRIM692  TRIM742  TRIM622  TRIM412  
    TRIM722  
    13 SIMAP similar genes for TRIM50 using alignment to 3 protein entries:     TRI50_HUMAN (see all proteins):
    TRIM73    TRIM74    MEFV    BRCA1    TRIM5    TRIM39
    TRIM72    BT3.3    BTNL9    TRIM61    TRIM62    TRIM27
    TRIM69

    TRIM50 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/261 NCBI SNPs in TRIM50 are shown (see all 261    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 7 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1491498271,2
    --72726061(+) CTCAGA/GAGGCT 1 -- ds50010--------
    rs1855337321,2
    --72726143(+) CCTGGC/GTGACA 1 -- ds50010--------
    rs1432832771,2
    --72726200(+) GCTCAC/TGCCTG 1 -- ds50010--------
    rs1904049561,2
    --72726283(+) CACAGC/TGAAAC 1 -- ds50010--------
    rs1931544781,2
    --72726386(+) GAATCC/TGGGAG 1 -- ds50010--------
    rs356219391,2
    C--72726465(+) AAAAA-/AGACTC 1 -- ds50011Minor allele frequency- A:0.00NA 2
    rs1483327021,2
    --72726732(+) AAATAC/TACCCT 1 -- ut310--------
    rs1475155961,2
    C--72727111(+) GAGTTC/AGCCCT 2 /E /* stg11Minor allele frequency- A:0.00NA 3518
    rs1112791101,2
    C,F--72727156(+) GTGGCC/TGGCCA 2 S G mis11Minor allele frequency- T:0.00NA 2910
    rs2002207851,2
    --72727157(+) TGGCCA/GGCCAC 2 A syn10--------

    HapMap Linkage Disequilibrium report for TRIM50 (72726535 - 72742085 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for TRIM50
         3 CNVs: 2699 3685 8567

    SABiosciences Cancer Mutation PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing TRIM50
    DNA2.0 Custom Variant and Variant Library Synthesis for TRIM50

    (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.)
    About This Section

    TRIM50 for disorders           About GeneDecksing

    OMIM gene information: 612548    OMIM disorders: --

    1 disease for TRIM50:    About MalaCards
    williams-beuren syndrome

    1 disease from the University of Copenhagen DISEASES database for TRIM50:
    Williams-Beuren syndrome

    Export disorders for TRIM50 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 TRIM50 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with TRIM50)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Williams-Beuren syndrome TRIM50 encodes an E3 ubiquitin ligase. (PubMed id 18398435)1, 2 Micale L....Reymond A. (2008)
    2. The DNA sequence of human chromosome 7. (PubMed id 12853948)1, 2 Hillier L.W.... Wilson R.K. (2003)
    3. Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. (PubMed id 22610502)1 Kennedy R.B....Poland G.A. (2012)
    4. The E3-ubiquitin ligase TRIM50 interacts with HDAC6 an d p62, and promotes the sequestration and clearance of ubiquitinated proteins in to the aggresome. (PubMed id 22792322)1 Fusco C....Merla G. (2012)
    5. Functional interactions between ubiquitin E2 enzymes a nd TRIM proteins. (PubMed id 21143188)1 Napolitano L.M....Meroni G. (2011)
    6. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    7. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
    8. 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)

    (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: 135892 HGNC: 19017 AceView: TRIM50A Ensembl:ENSG00000146755 euGenes: HUgn135892
    ECgene: TRIM50 H-InvDB: TRIM50

    (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 TRIM50 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 TRIM50 gene:
    Search GeneIP for patents involving TRIM50

    GeneCards and IP:
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    (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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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),
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     TRIM50 Proteins, Antibodies, CLIAs, and ELISAs
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     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TRIM50
           
    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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