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Aliases for TDRKH Gene

Aliases for TDRKH Gene

  • Tudor And KH Domain Containing 2 3 5
  • Tudor Domain-Containing Protein 2 3 4
  • TDRD2 3 4
  • Tudor And KH Domain-Containing Protein 3
  • Putative RNA Binding Protein 3
  • Tudor Domain Containing 2 3

External Ids for TDRKH Gene

Previous GeneCards Identifiers for TDRKH Gene

  • GC01M149584
  • GC01M147526
  • GC01M148517
  • GC01M148960
  • GC01M148557
  • GC01M150010
  • GC01M151745
  • GC01M123120
  • GC01M151781
  • GC01M151784
  • GC01M151785
  • GC01M151787
  • GC01M151788

Summaries for TDRKH Gene

GeneCards Summary for TDRKH Gene

TDRKH (Tudor And KH Domain Containing) is a Protein Coding gene. Diseases associated with TDRKH include Ewing Sarcoma. Among its related pathways are Gene Expression and Mitotic Prophase. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is TDRD7.

UniProtKB/Swiss-Prot for TDRKH Gene

  • Participates in the primary piRNA biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Required for the final steps of primary piRNA biogenesis by participating in the processing of 31-37 nt intermediates into mature piRNAs. May act in pi-bodies and piP-bodies by transferring piRNA precursors or intermediates to or between these granules.

Gene Wiki entry for TDRKH Gene

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

Genomics for TDRKH Gene

Regulatory Elements for TDRKH Gene

Enhancers for TDRKH 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
GH01G151835 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11 -46.7 -46704 6.0 HDGF PKNOX1 WRNIP1 ARID4B SIN3A ZNF2 ZBTB7B ZNF143 ZNF207 FOS LYSMD1 GABPB2 TDRKH-AS1 TDRKH ENSG00000252840 CGN MRPL9 ENSG00000232937 OAZ3 C2CD4D
GH01G151739 0.9 ENCODE 19.5 +51.2 51177 0.9 HDAC1 PKNOX1 NFIB ZSCAN4 SIN3A RAD21 RCOR1 CEBPB ZHX2 ZNF217 TDRKH RIIAD1 OAZ3 MRPL9 ENSG00000232937 CELF3 RPS10P6 MIR554 TUFT1 ENSG00000252840
GH01G151818 1.4 FANTOM5 ENCODE dbSUPER 11.7 -28.7 -28713 2.7 NFIB YY1 ZNF335 ZNF121 GLIS2 ELK1 SCRT2 CEBPB ZHX2 REST TDRKH TDRKH-AS1 ENSG00000201134 C2CD4D THEM5 ENSG00000232937 MRPL9 OAZ3 RPS10P6 TUFT1
GH01G151817 1.3 Ensembl dbSUPER 11.6 -26.2 -26185 0.4 HDGF PKNOX1 SIN3A GLI4 ZNF48 ZNF2 SLC30A9 ZNF121 GLIS2 CBX5 GABPB2 SETDB1 MRPL9 LYSMD1 TDRKH-AS1 TDRKH THEM5 ENSG00000252840 CGN GC01P151821
GH01G151773 0.8 ENCODE 15.4 +17.4 17438 1.3 HDAC1 TBL1XR1 TCF12 GATA2 CREM NCOA1 ZEB2 ZNF592 MBD2 SMARCA4 TDRKH RORC LINGO4 CELF3 ENSG00000252840 CGN TUFT1 ENSG00000232536 RNU6-1062P SELENBP1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TDRKH on UCSC Golden Path with GeneCards custom track

Promoters for TDRKH Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000013668 616 2001 CREB3L1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC TBX21 ZNF610

Genomic Location for TDRKH Gene

Chromosome:
1
Start:
151,770,107 bp from pter
End:
151,791,416 bp from pter
Size:
21,310 bases
Orientation:
Minus strand

Genomic View for TDRKH Gene

Genes around TDRKH on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for TDRKH Gene

Proteins for TDRKH Gene

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

    Protein Symbol:
    Q9Y2W6-TDRKH_HUMAN
    Recommended name:
    Tudor and KH domain-containing protein
    Protein Accession:
    Q9Y2W6
    Secondary Accessions:
    • D3DV24
    • Q5SZR3
    • Q5SZR5
    • Q8N582
    • Q9NYV5

    Protein attributes for TDRKH Gene

    Size:
    561 amino acids
    Molecular mass:
    62046 Da
    Quaternary structure:
    • Interacts with (symmetrically methylated) PIWIL1, PIWIL2 and PIWIL4.
    SequenceCaution:
    • Sequence=AAD30971.1; Type=Erroneous termination; Positions=562; Note=Translated as stop.; Evidence={ECO:0000305}; Sequence=BC022467; Type=Erroneous termination; Positions=175; Note=Translated as Lys.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for TDRKH Gene

    Alternative splice isoforms for TDRKH Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TDRKH Gene

Post-translational modifications for TDRKH Gene

  • Ubiquitinated by PARK2 during mitophagy, leading to its degradation and enhancement of mitophagy. Deubiquitinated by USP30.
  • Ubiquitination at Lys65, posLast=7676, posLast=110110, isoforms=112, isoforms=152, Lys175, Lys181, posLast=187187, Lys193, Lys256, isoforms=3267, Lys479, Lys510, and isoforms=3529
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TDRKH Gene

Domains & Families for TDRKH Gene

Gene Families for TDRKH Gene

Graphical View of Domain Structure for InterPro Entry

Q9Y2W6

UniProtKB/Swiss-Prot:

TDRKH_HUMAN :
  • Belongs to the Tdrkh family.
Family:
  • Belongs to the Tdrkh family.
genes like me logo Genes that share domains with TDRKH: view

Function for TDRKH Gene

Molecular function for TDRKH Gene

UniProtKB/Swiss-Prot Function:
Participates in the primary piRNA biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for the germline integrity. The piRNA metabolic process mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and govern the methylation and subsequent repression of transposons. Required for the final steps of primary piRNA biogenesis by participating in the processing of 31-37 nt intermediates into mature piRNAs. May act in pi-bodies and piP-bodies by transferring piRNA precursors or intermediates to or between these granules.

Gene Ontology (GO) - Molecular Function for TDRKH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
genes like me logo Genes that share ontologies with TDRKH: view
genes like me logo Genes that share phenotypes with TDRKH: view

Animal Models for TDRKH Gene

MGI Knock Outs for TDRKH:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

Localization for TDRKH Gene

Subcellular locations from UniProtKB/Swiss-Prot for TDRKH Gene

Cytoplasm. Mitochondrion. Note=Probable component of the meiotic nuage, also named P granule, a germ-cell-specific organelle required to repress transposon activity during meiosis. Colocalizes with pi- and piP-bodies, a subset of the nuage which contains secondary piRNAs. Associated with mitochondria in the germline. {ECO:0000250 UniProtKB:Q80VL1}.

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 TDRKH gene
Compartment Confidence
mitochondrion 5
cytosol 3
plasma membrane 2
cytoskeleton 2
nucleus 2
extracellular 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for TDRKH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0071546 pi-body ISS --
genes like me logo Genes that share ontologies with TDRKH: view

Pathways & Interactions for TDRKH Gene

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

Pathways by source for TDRKH Gene

Interacting Proteins for TDRKH Gene

Gene Ontology (GO) - Biological Process for TDRKH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007140 male meiosis ISS --
GO:0007283 spermatogenesis ISS --
GO:0009566 fertilization ISS --
GO:0030154 cell differentiation IEA --
GO:0031047 gene silencing by RNA IEA --
genes like me logo Genes that share ontologies with TDRKH: view

No data available for SIGNOR curated interactions for TDRKH Gene

Drugs & Compounds for TDRKH Gene

No Compound Related Data Available

Transcripts for TDRKH Gene

Unigene Clusters for TDRKH Gene

Tudor and KH domain containing:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c · 5d · 5e ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^
SP1: - - -
SP2: - - -
SP3: - - - - -
SP4: - - - -
SP5: - - - - -
SP6: - - - -
SP7:
SP8: - -
SP9: -
SP10:

ExUns: 13 ^ 14 ^ 15a · 15b · 15c ^ 16
SP1: - - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for TDRKH Gene

GeneLoc Exon Structure for
TDRKH
ECgene alternative splicing isoforms for
TDRKH

Expression for TDRKH Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for TDRKH Gene

This gene is overexpressed in Testis (x4.2).

Protein differential expression in normal tissues from HIPED for TDRKH Gene

This gene is overexpressed in Testis (26.7), Peripheral blood mononuclear cells (8.7), Fetal ovary (8.2), and Lung (6.9).

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



Protein tissue co-expression partners for TDRKH Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TDRKH Gene:

TDRKH

SOURCE GeneReport for Unigene cluster for TDRKH Gene:

Hs.144439

Evidence on tissue expression from TISSUES for TDRKH Gene

  • Nervous system(4.6)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with TDRKH: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TDRKH Gene

Orthologs for TDRKH Gene

This gene was present in the common ancestor of animals.

Orthologs for TDRKH Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TDRKH 34 35
  • 99.58 (n)
dog
(Canis familiaris)
Mammalia TDRKH 34 35
  • 90.6 (n)
mouse
(Mus musculus)
Mammalia Tdrkh 34 16 35
  • 89.82 (n)
rat
(Rattus norvegicus)
Mammalia Tdrkh 34
  • 89.76 (n)
cow
(Bos Taurus)
Mammalia TDRKH 34 35
  • 89.12 (n)
oppossum
(Monodelphis domestica)
Mammalia TDRKH 35
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TDRKH 35
  • 48 (a)
OneToOne
chicken
(Gallus gallus)
Aves TDRKH 34 35
  • 62.09 (n)
lizard
(Anolis carolinensis)
Reptilia TDRKH 35
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tdrkh 34
  • 53.85 (n)
Str.6287 34
zebrafish
(Danio rerio)
Actinopterygii tdrkh 35 34
  • 52.87 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta papi 35
  • 23 (a)
OneToMany
Species where no ortholog for TDRKH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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 squirt (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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for TDRKH Gene

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

Paralogs for TDRKH Gene

Paralogs for TDRKH Gene

(1) SIMAP similar genes for TDRKH Gene using alignment to 6 proteins:

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

Variants for TDRKH Gene

Sequence variations from dbSNP and Humsavar for TDRKH Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000020886 -- 151,782,258(+) AGCCA(A/C)CCTGG intron-variant
rs1000077895 -- 151,771,494(+) CAAAC(C/T)ATTTC intron-variant, downstream-variant-500B
rs1000129915 -- 151,771,939(+) TAGCA(C/T)CAGTT intron-variant, utr-variant-3-prime
rs1000205346 -- 151,785,093(+) TGCCC(A/G)GCTAA intron-variant
rs1000257055 -- 151,792,355(+) CAGCA(A/G)TGTAT upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
esv2371131 CNV deletion 18987734
esv2717884 CNV deletion 23290073
esv2717895 CNV deletion 23290073
nsv1010398 CNV gain 25217958

Variation tolerance for TDRKH Gene

Residual Variation Intolerance Score: 59.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.08; 50.78% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TDRKH Gene

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

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

Disorders for TDRKH Gene

MalaCards: The human disease database

(1) MalaCards diseases for TDRKH Gene - From: Novoseek and GeneCards

Disorder Aliases PubMed IDs
ewing sarcoma
  • neuroepithelioma
- elite association - COSMIC cancer census association via MalaCards
Search TDRKH in MalaCards View complete list of genes associated with diseases

Relevant External Links for TDRKH

Genetic Association Database (GAD)
TDRKH
Human Genome Epidemiology (HuGE) Navigator
TDRKH
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TDRKH
genes like me logo Genes that share disorders with TDRKH: view

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

Publications for TDRKH Gene

  1. Complex RNA processing of TDRKH, a novel gene encoding the putative RNA-binding tudor and KH domains. (PMID: 10767542) Lamb F.S. … Schutte B.C. (Gene 2000) 2 3 4 64
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. N-terminome analysis of the human mitochondrial proteome. (PMID: 25944712) Vaca Jacome A.S. … Carapito C. (Proteomics 2015) 4 64
  5. USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria. (PMID: 25621951) Cunningham C.N. … Corn J.E. (Nat. Cell Biol. 2015) 4 64

Products for TDRKH Gene

  • Addgene plasmids for TDRKH

Sources for TDRKH Gene

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