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TRIM60 Gene

protein-coding   GIFtS: 41
GCID: GC04P165953

Tripartite Motif Containing 60

(Previous names: ring finger protein 129, tripartite motif-containing 60)
(Previous symbols: RNF129, RNF33)
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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 601 2     Tripartite Motif-Containing 601 2
RING Finger Protein 1291 2 3     RING Finger Protein 332 3
RNF1291 2 3     Tripartite Motif-Containing Protein 602
RNF331 2 3     

External Ids:    HGNC: 211621   Entrez Gene: 1666552   Ensembl: ENSG000001769797   UniProtKB: Q495X73   

Export aliases for TRIM60 gene to outside databases

Previous GC identifers: GC04P166311 GC04P166172 GC04P161706


(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 TRIM60 Gene:
The protein encoded by this gene contains a RING finger domain, a motif present in a variety of functionally
distinct proteins and known to be involved in protein-protein and protein-DNA interactions. Pseudogenes of this
gene are located on more than six chromosomes including chromosome 4. Multiple alternatively spliced variants,
encoding the same protein, have been identified. (provided by RefSeq, Jan 2013)

GeneCards Summary for TRIM60 Gene:
TRIM60 (tripartite motif containing 60) is a protein-coding gene. An important paralog of this gene is TRIM7.




(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_000004.11  NC_018915.2  NT_016354.20  
Regulatory elements:
   Regulatory transcription factor binding sites in the TRIM60 gene promoter:
         GR   RFX1   AML1a   NCX/Ncx   Brachyury   RelA   Nkx2-5   Pax-3   ARP-1   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTRIM60 promoter sequence
   Search Chromatin IP Primers for TRIM60

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRIM60


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

Entrez Gene cytogenetic band: 4q32.3   Ensembl cytogenetic band:  4q32.3   HGNC cytogenetic band: 4q32.3

TRIM60 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRIM60 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P165953:  view genomic region     (about GC identifiers)

Start:
165,953,105 bp from pter      End:
165,962,896 bp from pter
Size:
9,792 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: TRI60_HUMAN, Q495X7 (See protein sequence)
Recommended Name: Tripartite motif-containing protein 60  
Size: 471 amino acids; 55114 Da
Secondary accessions: Q8NA35

Explore the universe of human proteins at neXtProt for TRIM60: NX_Q495X7

Explore proteomics data for TRIM60 at MOPED


See TRIM60 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001244954.1  NP_689833.1  

ENSEMBL proteins: 
 ENSP00000421142   ENSP00000421784   ENSP00000426496   ENSP00000343765  

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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:
TRIM: Tripartite motif containing / Tripartite motif containing
RNF: RING-type (C3HC4) zinc fingers

Selected InterPro protein domains (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 Q495X7

ProtoNet protein and cluster: Q495X7

3 Blocks protein domains:
IPB000315 B-box zinc finger signature
IPB003879 Butyrophylin C-terminal DUF signature
IPB006574 SPRY-associated domain


UniProtKB/Swiss-Prot: TRI60_HUMAN, Q495X7
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


Find genes that share domains with TRIM60           About GenesLikeMe


(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,
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): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
GO:0008270zinc ion binding IEA--
GO:0046872metal ion binding ----
     
Find genes that share ontologies with TRIM60           About GenesLikeMe


Phenotypes:
     3 GenomeRNAi human phenotypes for TRIM60:
 Decreased influenza A H1N1 (A/  Decreased influenza A H1N1 (A/  Decreased influenza A/WSN/33 r 

Animal Models:
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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
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 TRIM60           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 TRIM60
Interactions:

    Search GeneGlobe Interaction Network for TRIM60

(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 TRIM60 (TRI60)



(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 TRIM60 gene (2 alternative transcripts): 
NM_001258025.1  NM_152620.2  

Unigene Cluster for TRIM60:

Tripartite motif containing 60
Hs.368004  [show with all ESTs]
Unigene Representative Sequence: NM_001258025
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000512596(uc003iqy.1 uc010iqx.1) ENST00000507119 ENST00000508504
ENST00000341062
miRNA
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Additional mRNA sequence: 

AK093201.1 BC100983.1 BC100984.1 BC100985.1 BC100986.2 

1 DOTS entry:

DT.100017163 

6 AceView cDNA sequences:

BX114353 AA700389 NM_152620 AK093201 AX747987 AA908904 

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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TRIM60 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TCCAATAAAA
TRIM60 Expression
About this image

TRIM60 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TRIM60 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.368004
    Custom PCR Arrays for TRIM60
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM60

(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 TRIM60 gene from Selected species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Trim601 , 5 tripartite motif-containing 601, 5 67.84(n)1
53.96(a)1
  8 (32.51 cM)5
2343291  NM_153097.21  NP_694737.11 
 649984575 
chicken
(Gallus gallus)
Aves TRIM7.26
Gallus gallus tripartite motif containing 27 (TRIM...
28(a)
many ↔ many
16(209966-214262)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
29(a)
many ↔ many
4(91149661-91159458)


ENSEMBL Gene Tree for TRIM60 (if available)
TreeFam Gene Tree for TRIM60 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TRIM60 gene
TRIM72  TRIM42  TRIM392  TRIM342  TRIML12  TRIM272  TRIM582  TRIM682  
TRIM222  TRIM172  TRIM52  TRIM62  TRIM6-TRIM342  TRIM212  TRIM382  TRIM112  
TRIM39-RPP212  
Selected SIMAP similar genes for TRIM60 using alignment to 2 protein entries:     TRI60_HUMAN (see all proteins) (see all similar genes):
TRIM61    TRIM73    TRIM39    TRIM75    TRIM39R    TRIM5
TRIM41    TRIM26    RNF170    TRIM68    BFAR    PCGF3
TRAF5    TRIM17    CHFR    RNF138    TRAF4    TRIM67

Find genes that share paralogs with TRIM60           About GenesLikeMe


Selected Pseudogenes.org Pseudogenes for TRIM60 (see all 31)
PGOHUM00000251273 PGOHUM00000256696 PGOHUM00000248457 PGOHUM00000256732 PGOHUM00000244400


(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 TRIM60 (see all 293)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 4 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1403012391,2
C--165951334(+) CAATAC/TAATCC 2 -- us2k10--------
rs1863807371,2
--165951415(+) GCAATA/CCTCTC 2 -- us2k10--------
rs802180081,2
C,F--165951463(+) GCCACC/TCGCCC 2 -- us2k12Minor allele frequency- T:0.05WA NA 238
rs1503407661,2
--165951544(+) CATCCC/TATTGG 2 -- us2k10--------
rs1891795491,2
--165951594(+) TCATCC/TTCTCT 2 -- us2k10--------
rs794309281,2
C,F--165951660(+) TGTTCC/TTACTT 2 -- us2k11Minor allele frequency- T:0.02WA 118
rs1164740241,2
C--165951680(+) CCATCA/CAATCT 2 -- us2k10--------
rs1381459661,2
--165951695(+) CTTCAC/TCACAA 2 -- us2k10--------
rs125052131,2
C,F,A,H--165951703(+) CAAGAG/AGGTAT 2 -- us2k115Minor allele frequency- A:0.18NS EA WA NA 2336
rs1411429961,2
--165951928(+) TTTTTA/GGAGAG 2 -- us2k10--------

HapMap Linkage Disequilibrium report for TRIM60 (165953105 - 165962896 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for TRIM60:    About this table    
Variant IDTypeSubtypePubMed ID
esv2728685CNV Deletion23290073
nsv830140CNV Loss17160897
nsv880382CNV Gain21882294
dgv1711e1CNV Complex17122850

Site Specific Mutation Identification with PCR Assays
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(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 TRIM60           About GenesLikeMe

Genetic Association Database (GAD): TRIM60
Human Genome Epidemiology (HuGE) Navigator: TRIM60 (1 document)

Export disorders for TRIM60 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 TRIM60 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TRIM60)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PubMed id 19240061)1, 4 Trynka G....Wijmenga C. (Gut 2009)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  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. 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)
  5. Does this have a familiar RING? (PubMed id 8744354)1 Saurin A.J....Freemont P.S. (Trends Biochem. Sci. 1996)

(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: 166655 HGNC: 21162 AceView: RNF129 Ensembl:ENSG00000176979 euGenes: HUgn166655
ECgene: TRIM60 H-InvDB: TRIM60

(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 TRIM60 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 TRIM60 gene:
Search GeneIP for patents involving TRIM60

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, LSBio, eBioscience, 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 inGenious Targeting Laboratory, genOway)
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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

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