TRIM47 Gene (Protein Coding)

Tripartite Motif Containing 47

GC17M075874
GIFtS:
35
See more...

Aliases for TRIM47 Gene

Aliases for TRIM47 Gene

  • Tripartite Motif Containing 47 2 3 5
  • RNF100 2 3 4
  • GOA 2 3 4
  • Gene Overexpressed In Astrocytoma Protein 3 4
  • Tripartite Motif-Containing Protein 47 3 4
  • E3 Ubiquitin-Protein Ligase TRIM47 3 4
  • RING Finger Protein 100 3 4
  • Tripartite Motif-Containing 47 2
  • EC 2.3.2.27 4
  • TRIM47 5

External Ids for TRIM47 Gene

Previous GeneCards Identifiers for TRIM47 Gene

  • GC17M076896
  • GC17M074334
  • GC17M074468
  • GC17M074469
  • GC17M071381
  • GC17M073870
  • GC17M069295

Summaries for TRIM47 Gene

GeneCards Summary for TRIM47 Gene

TRIM47 (Tripartite Motif Containing 47) is a Protein Coding gene. Diseases associated with TRIM47 include Miller-Dieker Lissencephaly Syndrome. An important paralog of this gene is TRIM9.

UniProtKB/Swiss-Prot Summary for TRIM47 Gene

  • E3 ubiquitin-protein ligase that mediates the ubiquitination and proteasomal degradation of CYLD.

Additional gene information for TRIM47 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRIM47 Gene

Genomics for TRIM47 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for TRIM47 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRIM47 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRIM47

Top Transcription factor binding sites by QIAGEN in the TRIM47 gene promoter:
  • CUTL1
  • ER-alpha
  • p53
  • Pax-2
  • Pax-2a
  • Pax-5
  • SEF-1 (1)
  • Sp1

Genomic Locations for TRIM47 Gene

Latest Assembly
chr17:75,874,164-75,878,599
(GRCh38/hg38)
Size:
4,436 bases
Orientation:
Minus strand

Previous Assembly
chr17:73,870,245-73,874,662
(GRCh37/hg19 by Entrez Gene)
Size:
4,418 bases
Orientation:
Minus strand

chr17:73,870,242-73,874,656
(GRCh37/hg19 by Ensembl)
Size:
4,415 bases
Orientation:
Minus strand

Genomic View for TRIM47 Gene

Genes around TRIM47 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRIM47 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRIM47 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for TRIM47 Gene

Proteins for TRIM47 Gene

Products:

  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • Protein details for TRIM47 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96LD4-TRI47_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase TRIM47
    Protein Accession:
    Q96LD4
    Secondary Accessions:
    • Q96AD0
    • Q96GU5
    • Q9BRN7

    Protein attributes for TRIM47 Gene

    Size:
    638 amino acids
    Molecular mass:
    69532 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for TRIM47 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRIM47 Gene

Protein Expression for TRIM47 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for TRIM47 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TRIM47 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for TRIM47

No data available for DME Specific Peptides for TRIM47 Gene

Domains & Families for TRIM47 Gene

Gene Families for TRIM47 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for TRIM47 Gene

InterPro:
Blocks:
  • Zn-finger, RING
  • SPRY-associated domain
  • B-box zinc finger signature
ProtoNet:

Suggested Antigen Peptide Sequences for TRIM47 Gene

GenScript: Design optimal peptide antigens:
  • Tripartite motif-containing 47, isoform CRA_c (Q96AD0_HUMAN)
  • RING finger protein 100 (TRI47_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96LD4

UniProtKB/Swiss-Prot:

TRI47_HUMAN :
  • Belongs to the TRIM/RBCC family.
Family:
  • Belongs to the TRIM/RBCC family.
genes like me logo Genes that share domains with TRIM47: view

Function for TRIM47 Gene

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  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for TRIM47 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase that mediates the ubiquitination and proteasomal degradation of CYLD.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27; Evidence={ECO:0000269|PubMed:29291351};.

Enzyme Numbers (IUBMB) for TRIM47 Gene

Phenotypes From GWAS Catalog for TRIM47 Gene

Gene Ontology (GO) - Molecular Function for TRIM47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IEA,IDA 29291351
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with TRIM47: view
genes like me logo Genes that share phenotypes with TRIM47: view

Animal Models for research

miRNA for TRIM47 Gene

miRTarBase miRNAs that target TRIM47

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM47

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TRIM47 Gene

Localization for TRIM47 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRIM47 Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRIM47 gene
Compartment Confidence
cytosol 5
nucleus 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRIM47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with TRIM47: view

Pathways & Interactions for TRIM47 Gene

PathCards logo

SuperPathways for TRIM47 Gene

No Data Available

UniProtKB/Swiss-Prot Q96LD4-TRI47_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for TRIM47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with TRIM47: view

No data available for Pathways by source and SIGNOR curated interactions for TRIM47 Gene

Drugs & Compounds for TRIM47 Gene

Products:

  1. Drug products for research
No Compound Related Data Available

Transcripts for TRIM47 Gene

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  2. miRNA products for research
  3. Inhibitory RNAs for research
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mRNA/cDNA for TRIM47 Gene

1 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRIM47

Alternative Splicing Database (ASD) splice patterns (SP) for TRIM47 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b
SP1: - -
SP2: -
SP3:

Relevant External Links for TRIM47 Gene

GeneLoc Exon Structure for
TRIM47

Expression for TRIM47 Gene

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  1. Primer products for research
  2. Gene Expression Assays for research

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRIM47 Gene

mRNA expression in normal human tissues for TRIM47 Gene
mRNA expression by GTEx for TRIM47 GenemRNA expression by BioGPS for TRIM47 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TRIM47 Gene

This gene is overexpressed in Breast (25.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRIM47 Gene



Protein tissue co-expression partners for TRIM47 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRIM47

SOURCE GeneReport for Unigene cluster for TRIM47 Gene:

Hs.293660

mRNA Expression by UniProt/SwissProt for TRIM47 Gene:

Q96LD4-TRI47_HUMAN
Tissue specificity: Low expression in most tissues. Higher expression in kidney tubular cells. Overexpressed in astrocytoma tumor cells.

Evidence on tissue expression from TISSUES for TRIM47 Gene

  • Lung(4.3)
  • Pancreas(4.2)
  • Liver(4.2)
  • Nervous system(2.8)
  • Skin(2.2)
genes like me logo Genes that share expression patterns with TRIM47: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRIM47 Gene

Orthologs for TRIM47 Gene

This gene was present in the common ancestor of chordates.

Orthologs for TRIM47 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia TRIM47 30 31
  • 99.01 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia TRIM47 30 31
  • 88.23 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia TRIM47 30 31
  • 87.77 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Trim47 30
  • 85.79 (n)
Mouse
(Mus musculus)
 Mammalia Trim47 30 17 31
  • 83.7 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia TRIM47 31
  • 77 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia TRIM47 31
  • 59 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves TRIM47 30 31
  • 65.16 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia TRIM47 31
  • 55 (a)
 OneToOne
Zebrafish
(Danio rerio)
 Actinopterygii zgc:153258 31
  • 23 (a)
 ManyToMany
Species where no ortholog for TRIM47 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for TRIM47 Gene

ENSEMBL:
Gene Tree for TRIM47 (if available)
TreeFam:
Gene Tree for TRIM47 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRIM47: view image

Paralogs for TRIM47 Gene

Paralogs for TRIM47 Gene

genes like me logo Genes that share paralogs with TRIM47: view

Variants for TRIM47 Gene

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  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRIM47 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
rs1047043 - p.Glu500Ala

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRIM47 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TRIM47 Gene

Variant ID Type Subtype PubMed ID
nsv510728 CNV deletion 20534489
nsv833545 CNV gain 17160897

Variation tolerance for TRIM47 Gene

Residual Variation Intolerance Score: 43.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.10; 84.52% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRIM47 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM47

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRIM47 Gene

Disorders for TRIM47 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TRIM47 Gene - From: COP

Disorder Aliases PubMed IDs
miller-dieker lissencephaly syndrome
  • mdls
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for TRIM47

Genetic Association Database
(GAD)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with TRIM47: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TRIM47 Gene

Publications for TRIM47 Gene

  1. The deubiquitinating enzyme cylindromatosis mitigates nonalcoholic steatohepatitis. (PMID: 29291351) Ji YX … Li H (Nature medicine 2018) 3 4
  2. Genome-wide association studies of cerebral white matter lesion burden: the CHARGE consortium. (PMID: 21681796) Fornage M … Launer LJ (Annals of neurology 2011) 3 41
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4
  4. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PMID: 16964243) Beausoleil SA … Gygi SP (Nature biotechnology 2006) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

ExternalLinks

View latest publications for TRIM47 gene in Mastermind

Products for TRIM47 Gene

Sources for TRIM47 Gene