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Aliases for TDRD3 Gene

Aliases for TDRD3 Gene

  • Tudor Domain Containing 3 2 3 5

External Ids for TDRD3 Gene

Previous GeneCards Identifiers for TDRD3 Gene

  • GC13P054966
  • GC13P059907
  • GC13P058768
  • GC13P058769
  • GC13P059868
  • GC13P060970
  • GC13P041662

Summaries for TDRD3 Gene

GeneCards Summary for TDRD3 Gene

TDRD3 (Tudor Domain Containing 3) is a Protein Coding gene. Diseases associated with TDRD3 include Fragile X Syndrome. Among its related pathways are Translational Control and Chromatin Regulation / Acetylation. GO annotations related to this gene include poly(A) RNA binding and chromatin binding. An important paralog of this gene is RMI1.

UniProtKB/Swiss-Prot for TDRD3 Gene

  • Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins.

Gene Wiki entry for TDRD3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TDRD3 Gene

Genomics for TDRD3 Gene

Regulatory Elements for TDRD3 Gene

Enhancers for TDRD3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH13G060395 1.1 ENCODE 33.6 +1.2 1246 4.2 PKNOX1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 ZNF207 TDRD3 DIAPH3 GC13M060411
GH13G060409 0.6 ENCODE 33.4 +13.6 13571 1.1 SOX13 ZNF766 ZNF133 IKZF1 CEBPG HNF4A TDRD3 GC13M060411
GH13G060426 0.6 ENCODE 32.8 +31.1 31060 1.3 MTA2 BHLHE40 TBX21 RELA CBX5 IKZF1 NBN RELB IKZF2 TDRD3 GC13M060411 GC13P060445
GH13G060161 1.3 Ensembl ENCODE 13.2 -232.6 -232584 5.0 PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 YY1 ZNF143 ZNF207 FOS SP3 TDRD3 DIAPH3 DIAPH3-AS2
GH13G060582 1.2 Ensembl ENCODE 11.4 +188.2 188169 3.8 PKNOX1 ETS1 ZNF766 ELK1 KLF13 CAVIN1 ZBTB11 HDAC8 ZNF592 POLR2H TDRD3 RNA5SP31 GC13P060445
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TDRD3 on UCSC Golden Path with GeneCards custom track

Promoters for TDRD3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000063294 643 3001 PKNOX1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 ZNF207

Genomic Location for TDRD3 Gene

Chromosome:
13
Start:
60,396,457 bp from pter
End:
60,573,879 bp from pter
Size:
177,423 bases
Orientation:
Plus strand

Genomic View for TDRD3 Gene

Genes around TDRD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TDRD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TDRD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TDRD3 Gene

Proteins for TDRD3 Gene

  • Protein details for TDRD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H7E2-TDRD3_HUMAN
    Recommended name:
    Tudor domain-containing protein 3
    Protein Accession:
    Q9H7E2
    Secondary Accessions:
    • B2MWP9
    • Q53XA6
    • Q6P992

    Protein attributes for TDRD3 Gene

    Size:
    651 amino acids
    Molecular mass:
    73185 Da
    Quaternary structure:
    • Component of mRNA stress granules. Interacts with FMR1, FXR1, FXR2, EWSR1, FUS, SERBP1, EEF1A1 and DDX3X or DDX3Y, and with the small nuclear ribonucleoprotein-associated proteins SNRPB and SNRPN. Interacts with Lys-48-linked tetra-ubiquitin, but not with monoubiquitin or Lys-63-linked ubiquitin chains. May interact with the exon junction complex (EJC) composed at least of CASC3, EIF4A3, MAGOH and RBM8A. Interacts with POLR2A (via the C-terminal domain (CTD)).

    Three dimensional structures from OCA and Proteopedia for TDRD3 Gene

    Alternative splice isoforms for TDRD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TDRD3 Gene

Post-translational modifications for TDRD3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TDRD3 Gene

Domains & Families for TDRD3 Gene

Gene Families for TDRD3 Gene

Protein Domains for TDRD3 Gene

Suggested Antigen Peptide Sequences for TDRD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H7E2

UniProtKB/Swiss-Prot:

TDRD3_HUMAN :
  • The Tudor domain specifically recognizes and binds asymmetric dimethylation of histone H3 Arg-17 (H3R17me2a) and histones H4 Arg-3, 2 tags for epigenetic transcriptional activation.
Domain:
  • The Tudor domain specifically recognizes and binds asymmetric dimethylation of histone H3 Arg-17 (H3R17me2a) and histones H4 Arg-3, 2 tags for epigenetic transcriptional activation.
genes like me logo Genes that share domains with TDRD3: view

Function for TDRD3 Gene

Molecular function for TDRD3 Gene

UniProtKB/Swiss-Prot Function:
Scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In nucleus, acts as a coactivator: recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In cytoplasm, may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins.

Gene Ontology (GO) - Molecular Function for TDRD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003682 chromatin binding IDA 21172665
GO:0003713 transcription coactivator activity IDA 21172665
GO:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 26700805
GO:0035064 methylated histone binding IDA 21172665
genes like me logo Genes that share ontologies with TDRD3: view
genes like me logo Genes that share phenotypes with TDRD3: view

Animal Model Products

miRNA for TDRD3 Gene

miRTarBase miRNAs that target TDRD3

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TDRD3 Gene

Localization for TDRD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TDRD3 Gene

Cytoplasm. Nucleus. Note=Predominantly cytoplasmic. Associated with actively translating polyribosomes and with mRNA stress granules. {ECO:0000269 PubMed:18632687, ECO:0000269 PubMed:18664458}.

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 TDRD3 gene
Compartment Confidence
nucleus 5
cytosol 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for TDRD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 21172665
GO:0005737 cytoplasm IEA --
GO:0035145 colocalizes_with exon-exon junction complex IDA 20930030
genes like me logo Genes that share ontologies with TDRD3: view

Pathways & Interactions for TDRD3 Gene

genes like me logo Genes that share pathways with TDRD3: view

Pathways by source for TDRD3 Gene

2 Cell Signaling Technology pathways for TDRD3 Gene

Gene Ontology (GO) - Biological Process for TDRD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016569 covalent chromatin modification IEA --
GO:1903506 regulation of nucleic acid-templated transcription IEA --
genes like me logo Genes that share ontologies with TDRD3: view

No data available for SIGNOR curated interactions for TDRD3 Gene

Drugs & Compounds for TDRD3 Gene

No Compound Related Data Available

Transcripts for TDRD3 Gene

Unigene Clusters for TDRD3 Gene

Tudor domain containing 3:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for TDRD3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18
SP1: - - - - - -
SP2: - - - -
SP3: - - - -
SP4:
SP5:
SP6:
SP7:
SP8: -

Relevant External Links for TDRD3 Gene

GeneLoc Exon Structure for
TDRD3
ECgene alternative splicing isoforms for
TDRD3

Expression for TDRD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TDRD3 Gene

Protein differential expression in normal tissues from HIPED for TDRD3 Gene

This gene is overexpressed in Fetal gut (28.0) and Fetal Liver (27.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TDRD3 Gene



Protein tissue co-expression partners for TDRD3 Gene

NURSA nuclear receptor signaling pathways regulating expression of TDRD3 Gene:

TDRD3

SOURCE GeneReport for Unigene cluster for TDRD3 Gene:

Hs.525061

mRNA Expression by UniProt/SwissProt for TDRD3 Gene:

Q9H7E2-TDRD3_HUMAN
Tissue specificity: Detected in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.
genes like me logo Genes that share expression patterns with TDRD3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for TDRD3 Gene

Orthologs for TDRD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for TDRD3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TDRD3 34 35
  • 99.6 (n)
cow
(Bos Taurus)
Mammalia TDRD3 34 35
  • 91.51 (n)
dog
(Canis familiaris)
Mammalia TDRD3 34
  • 91.22 (n)
-- 35
  • 89 (a)
OneToMany
-- 35
  • 80 (a)
OneToMany
rat
(Rattus norvegicus)
Mammalia Tdrd3 34
  • 86.53 (n)
mouse
(Mus musculus)
Mammalia Tdrd3 34 16 35
  • 85.6 (n)
oppossum
(Monodelphis domestica)
Mammalia TDRD3 35
  • 72 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TDRD3 35
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves TDRD3 34 35
  • 77 (n)
lizard
(Anolis carolinensis)
Reptilia TDRD3 35
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tdrd3 34
  • 68.59 (n)
MGC76148 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.8087 34
zebrafish
(Danio rerio)
Actinopterygii tdrd3 34 35
  • 57.79 (n)
Dr.16828 34
fruit fly
(Drosophila melanogaster)
Insecta CG13472 35
  • 23 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y50D4C.3 35
  • 22 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3026 35
  • 37 (a)
OneToOne
Species where no ortholog for TDRD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 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)
  • wheat (Triticum aestivum)

Evolution for TDRD3 Gene

ENSEMBL:
Gene Tree for TDRD3 (if available)
TreeFam:
Gene Tree for TDRD3 (if available)

Paralogs for TDRD3 Gene

Paralogs for TDRD3 Gene

genes like me logo Genes that share paralogs with TDRD3: view

Variants for TDRD3 Gene

Sequence variations from dbSNP and Humsavar for TDRD3 Gene

SNP ID Clin Chr 13 pos Sequence Context AA Info Type
rs1000013214 -- 60,414,576(+) CAGAA(G/T)TTGTC intron-variant
rs1000038966 -- 60,569,628(+) CCTGA(A/G)CATAA intron-variant
rs1000069730 -- 60,510,902(+) TGTTT(C/G/T)TTTAT intron-variant
rs1000127480 -- 60,516,269(+) TTATG(G/T)CATAT intron-variant
rs1000135090 -- 60,504,832(+) GCACA(A/G)GGGGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TDRD3 Gene

Variant ID Type Subtype PubMed ID
dgv3184n54 CNV loss 21841781
esv29450 CNV gain 19812545
esv3331016 CNV insertion 20981092
esv3580686 CNV loss 25503493
esv3580687 CNV loss 25503493
nsv1070590 CNV deletion 25765185
nsv1144680 CNV deletion 24896259
nsv455903 CNV loss 19166990
nsv523359 CNV loss 19592680

Variation tolerance for TDRD3 Gene

Residual Variation Intolerance Score: 35.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.15; 75.73% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TDRD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TDRD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TDRD3 Gene

Disorders for TDRD3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TDRD3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
fragile x syndrome
  • fragile x mental retardation syndrome
- elite association - COSMIC cancer census association via MalaCards
Search TDRD3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for TDRD3

Genetic Association Database (GAD)
TDRD3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TDRD3
genes like me logo Genes that share disorders with TDRD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TDRD3 Gene

Publications for TDRD3 Gene

  1. SMN and symmetric arginine dimethylation of RNA polymerase II C- terminal domain control termination. (PMID: 26700805) Yanling Zhao D. … Greenblatt J.F. (Nature 2015) 3 4 64
  2. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. (PMID: 22267201) Stolk L. … Lunetta K.L. (Nat. Genet. 2012) 3 46 64
  3. SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay. (PMID: 20930030) Kashima I. … Izaurralde E. (Genes Dev. 2010) 3 4 64
  4. TDRD3 is an effector molecule for arginine-methylated histone marks. (PMID: 21172665) Yang Y. … Bedford M.T. (Mol. Cell 2010) 3 4 64
  5. TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. (PMID: 18632687) Goulet I. … Cote J. (Hum. Mol. Genet. 2008) 3 4 64

Products for TDRD3 Gene

  • Addgene plasmids for TDRD3

Sources for TDRD3 Gene

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