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TRIM48 Gene

protein-coding   GIFtS: 37
GCID: GC11P055029

Tripartite Motif Containing 48

(Previous name: tripartite motif-containing 48)
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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 481 2
Tripartite Motif-Containing 481 2
RNF1012 3
RING Finger Protein 1012 3
Tripartite Motif-Containing Protein 482

External Ids:    HGNC: 190211   Entrez Gene: 790972   Ensembl: ENSG000001502447   UniProtKB: Q8IWZ43   

Export aliases for TRIM48 gene to outside databases

Previous GC identifers: GC11P056542 GC11P055278 GC11P054805 GC11P054786 GC11P051358


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TRIM48 Gene:
TRIM48 (tripartite motif containing 48) is a protein-coding gene. An important paralog of this gene is TRIM43.


(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_000011.9  NT_167190.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the TRIM48 gene promoter:
         NCX/Ncx   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidTRIM48 promoter sequence
   Search Chromatin IP Primers for TRIM48

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TRIM48


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

Entrez Gene cytogenetic band: 11q11   Ensembl cytogenetic band:  11q11   HGNC cytogenetic band: 11q12

TRIM48 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TRIM48 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P055029:  view genomic region     (about GC identifiers)

Start:
55,029,658 bp from pter      End:
55,038,595 bp from pter
Size:
8,938 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: TRI48_HUMAN, Q8IWZ4 (See protein sequence)
Recommended Name: Tripartite motif-containing protein 48  
Size: 208 amino acids; 24498 Da
Sequence caution: Sequence=AAO14946.1; Type=Erroneous termination; Positions=209; Note=Translated as stop;
Secondary accessions: Q9BUW4

Explore the universe of human proteins at neXtProt for TRIM48: NX_Q8IWZ4

Explore proteomics data for TRIM48 at MOPED


See TRIM48 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_077019.2  
ENSEMBL proteins: 
 ENSP00000402414  

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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

3 InterPro protein domains:
 IPR001841 Znf_RING
 IPR000315 Znf_B-box
 IPR013083 Znf_RING/FYVE/PHD

Graphical View of Domain Structure for InterPro Entry Q8IWZ4

ProtoNet protein and cluster: Q8IWZ4

3 Blocks protein domains:
IPB000315 B-box zinc finger signature
IPB001841 Zn-finger
IPB003879 Butyrophylin C-terminal DUF signature


UniProtKB/Swiss-Prot: TRI48_HUMAN, Q8IWZ4
Similarity: Belongs to the TRIM/RBCC family
Similarity: Contains 1 B box-type zinc finger
Similarity: Contains 1 RING-type zinc finger


Find genes that share domains with TRIM48           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): 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 TRIM48           About GenesLikeMe


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
extracellular2
nucleus2
cytosol1
mitochondrion1
plasma membrane1

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

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

Find genes that share ontologies with TRIM48           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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    Pathway & Disease-focused RT2 Profiler PCR Array including TRIM48: 
          Ubiquitin Ligases in human mouse rat

Interactions:

    Search GeneGlobe Interaction Network for TRIM48

(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 TRIM48 (TRI48)



(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 TRIM48 gene: 
NM_024114.3  

Unigene Cluster for TRIM48:

Tripartite motif containing 48
Hs.195715  [show with all ESTs]
Unigene Representative Sequence: AF521869
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000417545(uc010rid.2)
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Additional mRNA sequence: 

AF521869.1 BC001862.2 

1 DOTS entry:

DT.70101068 

14 AceView cDNA sequences:

M85802 BE389590 BU154755 BE893553 BE727349 NM_024114 BE275390 AF521869 
BC001862 BI093942 BF025698 BG335390 BG475587 BF125311 

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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TRIM48 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TAGAATTATT
TRIM48 Expression
About this image

TRIM48 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TRIM48 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.195715
    Pathway & Disease-focused RT2 Profiler PCR Array including TRIM48: 
          Ubiquitin Ligases in human mouse rat

Primer
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In Situ
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM48

(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 TRIM48 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
dog
(Canis familiaris)
Mammalia --
Uncharacterized protein
24(a)
many ↔ many
21(10273971-10281545)
lizard
(Anolis carolinensis)
Reptilia --
--
(see all 10)
Uncharacterized protein
(see all 10)
30(a)
28(a)
(see all 10)
many ↔ many
many ↔ many
(see all 10)
2(193472385-193473600)
GL343438.1(452464-452939)
zebrafish
(Danio rerio)
Actinopterygii trim1096
tripartite motif containing 109
10(a)
many ↔ many
16(15829385-15839582) ENSDARG00000062429


ENSEMBL Gene Tree for TRIM48 (if available)
TreeFam Gene Tree for TRIM48 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for TRIM48 gene
TRIM432  TRIM772  TRIM612  TRIM492  TRIM64B2  TRIM49B2  TRIM64C2  TRIM49C2  
TRIM512  TRIM49D12  
Selected SIMAP similar genes for TRIM48 using alignment to 1 protein entry:     TRI48_HUMAN(see all similar genes):
TRIM51    TRIM49    TRIM49C    TRIM49D1    TRIM49D2P    TRIM64B
TRIM64    TRIM64C    TRIM49B    TRIM77    TRIM22    TRIM21
TRIM26    TRIM75    TRIM34    TRIM60    TRIM61    TRIM39

Find genes that share paralogs with TRIM48           About GenesLikeMe


5 Pseudogenes.org Pseudogenes for TRIM48
PGOHUM00000257810 PGOHUM00000257817 PGOHUM00000240217 PGOHUM00000258143 PGOHUM00000259791


(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 TRIM48 (see all 497)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs352289331,2
C,F,H--55027673(+) GGCAGG/AGGGTC 1 -- us2k115Minor allele frequency- A:0.06NS EA WA NA 2332
rs1825327361,2
C--55027675(+) CAGGGG/TGTCAA 1 -- us2k10--------
rs1481259121,2
C--55027712(+) GGAATC/TTCCCT 1 -- us2k10--------
rs1419376671,2
--55027730(+) TATTTC/TGACCC 1 -- us2k10--------
rs1868149531,2
--55027749(+) GCTCTG/TGTTCC 1 -- us2k10--------
rs1907055061,2
--55027803(+) TATCCC/TCTCTC 1 -- us2k10--------
rs1122939761,2
F--55027835(+) CTGCTG/ACAGCC 1 -- us2k11Minor allele frequency- A:0.50CSA 2
rs1832742391,2
--55027845(+) CAACTA/GTCTGG 1 -- us2k10--------
rs71036051,2
C--55027908(+) catggC/Tactgg 1 -- us2k10--------
rs618984121,2
F--55027955(+) GAGAAC/TCCAGA 1 -- us2k11Minor allele frequency- T:0.50NA 2

HapMap Linkage Disequilibrium report for TRIM48 (55029658 - 55038595 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for TRIM48 (see all 12):    About this table    
Variant IDTypeSubtypePubMed ID
esv2664161CNV Deletion23128226
esv2421639CNV Deletion20811451
nsv512228CNV Loss21212237
nsv508631CNV Loss20534489
nsv498756CNV Loss21111241
esv8902CNV Loss19470904
nsv321CNV Loss18451855
esv2751030CNV Gain17911159
nsv524091CNV Gain19592680
esv27386CNV Gain+Loss19812545

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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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  --

(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 TRIM48 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TRIM48)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
  3. 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)
  4. (PubMed id )2 

(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: 79097 HGNC: 19021 AceView: TRIM48 Ensembl:ENSG00000150244 euGenes: HUgn79097
ECgene: TRIM48 H-InvDB: TRIM48

(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 TRIM48 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 TRIM48 gene:
Search GeneIP for patents involving TRIM48

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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 Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for TRIM48
 SwitchGear 3'UTR luciferase reporter plasmids for TRIM48
 SwitchGear Promoter luciferase reporter plasmids for TRIM48
 Search ThermoFisher Antibodies for TRIM48
 Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat TRIM48
 Browse compounds at ApexBio
 Search Addgene for plasmids for TRIM48
  Search eBioscience for proteins for TRIM48
  Search eBioscience for elisas for TRIM48
  eBioscience FlowRNA Probe Sets
 genOway: Develop your customized and physiologically relevant rodent model for TRIM48
 antibodies-online antibodies for TRIM48 (14 products)
 antibodies-online kits for TRIM48 (2 products)
 antibodies-online peptides for TRIM48
 antibodies-online proteins for TRIM48 (3 products)
       
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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