Aliases for TDRD3 Gene

Aliases for TDRD3 Gene

  • Tudor Domain Containing 3 2 3 5
  • Tudor Domain-Containing Protein 3 3 4
  • FLJ21007 2
  • TDRD3 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 and Chromosome 22Q11.2 Deletion Syndrome, Distal. Among its related pathways are Translational Control and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include chromatin binding.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for TDRD3 Gene

Genomics for TDRD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TDRD3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J060395 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 283.5 +1.1 1144 4.8 BCLAF1 SP1 ZNF207 MYC NCOR1 IKZF1 ZNF600 JUND ZNF580 ZMYM3 TDRD3 HSALNG0097501-001 NONHSAG013650.2 lnc-DIAPH3-22 lnc-DIAPH3-23 DIAPH3
GH13J060409 Promoter/Enhancer 0.8 EPDnew ENCODE 283.4 +13.6 13570 1.1 HNF4A ZNF133 IKZF1 SOX13 CEBPG TDRD3 L13713-064 piR-38352-147 NONHSAG013650.2
GH13J060426 Enhancer 0.7 Ensembl ENCODE 44.8 +30.9 30944 2.4 BHLHE40 IKZF1 IKZF2 MTA2 NBN RUNX3 RELB TDRD3 piR-38352-147 piR-50437-151 NONHSAG013650.2 PCDH20
GH13J060161 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 13.2 -232.7 -232665 5.2 SP1 ZNF207 IKZF1 ZNF600 ZNF580 ATF2 POLR2A BRCA1 NFIC YY1 DIAPH3 HSALNG0097494-001 HSALNG0097494-002 LOC105370227 lnc-TDRD3-14 TDRD3 HSALNG0097493 lnc-DIAPH3-7
GH13J060582 Enhancer 0.8 ENCODE 24.1 +188.2 188169 3.8 ZNF592 POLR2A ETS1 SIN3A TAF9B ZNF316 NFE2 RELA IRF9 SPI1 HSALNG0097508 TDRD3 RNA5SP31 PCDH20
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TDRD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TDRD3

Top Transcription factor binding sites by QIAGEN in the TDRD3 gene promoter:
  • aMEF-2
  • AP-4
  • Evi-1
  • HFH-1
  • MEF-2A
  • NF-kappaB
  • NF-kappaB1
  • Sox5
  • SRY
  • TBP

Genomic Locations for TDRD3 Gene

Latest Assembly
chr13:60,396,457-60,573,879
(GRCh38/hg38)
Size:
177,423 bases
Orientation:
Plus strand

Previous Assembly
chr13:60,970,591-61,148,013
(GRCh37/hg19 by Entrez Gene)
Size:
177,423 bases
Orientation:
Plus strand

chr13:60,970,591-61,148,012
(GRCh37/hg19 by Ensembl)
Size:
177,422 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

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

Protein Domains for TDRD3 Gene

InterPro:
Blocks:
  • Maternal tudor protein

Suggested Antigen Peptide Sequences for TDRD3 Gene

GenScript: Design optimal peptide antigens:
  • Tudor domain-containing protein 3 (TDRD3_HUMAN)

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.

Phenotypes From GWAS Catalog for TDRD3 Gene

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 HDA 22658674
GO:0005515 protein binding IPI 23066109
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

miRNA for TDRD3 Gene

miRTarBase miRNAs that target TDRD3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TDRD3

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 4
golgi apparatus 4
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
  • Cytosol (3)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TDRD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 21172665
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005794 Golgi apparatus IDA --
GO:0005829 cytosol IDA --
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

SIGNOR curated interactions for TDRD3 Gene

Other effect:

Gene Ontology (GO) - Biological Process for TDRD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0045893 positive regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with TDRD3: view

Drugs & Compounds for TDRD3 Gene

No Compound Related Data Available

Transcripts for TDRD3 Gene

mRNA/cDNA for TDRD3 Gene

3 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
9 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 TDRD3

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

Expression for TDRD3 Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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, MaxQB, and MOPED for TDRD3 Gene



Protein tissue co-expression partners for TDRD3 Gene

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

Evidence on tissue expression from TISSUES for TDRD3 Gene

  • Nervous system(2.5)
genes like me logo Genes that share expression patterns with TDRD3: view

No data available for mRNA differential expression in normal 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 29 30
  • 99.6 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TDRD3 29 30
  • 91.51 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia TDRD3 29
  • 91.22 (n)
-- 30
  • 89 (a)
OneToMany
-- 30
  • 80 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Tdrd3 29
  • 86.53 (n)
Mouse
(Mus musculus)
Mammalia Tdrd3 29 16 30
  • 85.6 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia TDRD3 30
  • 72 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TDRD3 30
  • 67 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TDRD3 29 30
  • 77 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TDRD3 30
  • 73 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia tdrd3 29
  • 68.59 (n)
MGC76148 29
African clawed frog
(Xenopus laevis)
Amphibia Xl.8087 29
Zebrafish
(Danio rerio)
Actinopterygii tdrd3 29 30
  • 57.79 (n)
OneToOne
Dr.16828 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG13472 30
  • 23 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea Y50D4C.3 30
  • 22 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3026 30
  • 37 (a)
OneToOne
Species where no ortholog for TDRD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for TDRD3: view image
Alliance of Genome Resources:
Additional Orthologs for TDRD3

Paralogs for TDRD3 Gene

No data available for Paralogs for TDRD3 Gene

Variants for TDRD3 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TDRD3 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 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)

Additional Variant Information for TDRD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TDRD3
Leiden Open Variation Database (LOVD)
TDRD3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TDRD3 Gene

Disorders for TDRD3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for TDRD3 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
fragile x syndrome
  • fxs
chromosome 22q11.2 deletion syndrome, distal
  • distal chromosome 22q11.2 deletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search TDRD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for 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) Zhao DY … Greenblatt JF (Nature 2016) 3 4
  2. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. (PMID: 22267201) Stolk L … Lunetta KL (Nature genetics 2012) 3 40
  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 & development 2010) 3 4
  4. TDRD3 is an effector molecule for arginine-methylated histone marks. (PMID: 21172665) Yang Y … Bedford MT (Molecular cell 2010) 3 4
  5. Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP. (PMID: 18664458) Linder B … Fischer U (Human molecular genetics 2008) 3 4

Products for TDRD3 Gene

Sources for TDRD3 Gene