Aliases for TDRKH Gene

Aliases for TDRKH Gene

  • Tudor And KH Domain Containing 2 3 5
  • Tudor And KH Domain-Containing Protein 3 4
  • Tudor Domain-Containing Protein 2 3 4
  • TDRD2 3 4
  • 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
  • GC01M151794
  • GC01M151795
  • GC01M151785
  • GC01M151787
  • GC01M151788
  • GC01M151789
  • GC01M151790
  • GC01M151791
  • GC01M151792
  • GC01M151793

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 PIWI-interacting RNA (piRNA) biogenesis. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is TDRD6.

UniProtKB/Swiss-Prot Summary 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

Additional gene information for TDRKH Gene

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

Genomics for TDRKH Gene

GeneHancer (GH) Regulatory Elements for TDRKH Gene

Promoters and enhancers for TDRKH 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
GH01J151789 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 762.8 +0.6 615 2.8 SIN3A SP1 CTCF SREBF1 ZBTB6 SMARCE1 CEBPZ CTBP1 ATF1 FOS TDRKH TDRKH-AS1 lnc-LINGO4-2 SETDB1 PIP5K1A MRPL9 PI4KB GABPB2 ARNT UBE2D3P3
GH01J151054 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 11.8 +732.3 732282 10.1 SIN3A ZBTB40 CTCF SMARCE1 RBPJ POLR2A CTBP1 ZNF217 ZNF362 MYC CDC42SE1 MLLT11 RF00017-343 SETDB1 PIP5K1A PRPF3 ARNT GABPB2 PI4KB UBE2D3P3
GH01J151398 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11.8 +391.3 391315 3 E2F8 SIN3A ZNF24 ZBTB40 CTCF SIX5 FOXA1 RBPJ POLR2A ATF1 PSMB4 SELENBP1 POGZ LYSMD1 SETDB1 ARNT CTSK ADAMTSL4-AS1 MRPL9 PI4KB
GH01J151254 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11.8 +536.2 536215 2.8 ZNF785 SIN3A SP1 ZBTB40 SIX5 SMARCE1 POLR2A USF2 ATF1 FOS PSMD4 SETDB1 PRPF3 PIP5K1A POGZ PI4KB UBE2D3P3 ZNF687 ARNT MRPL9
GH01J151835 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11 -46.7 -46704 6 E2F8 ZNF24 CTCF RBPJ MYC CC2D1A MAX RAD21 MNT MTA3 C2CD4D-AS1 SETDB1 PIP5K1A MRPL9 ARNT PI4KB GABPB2 ZNF687 POGZ LYSMD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TDRKH on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the TDRKH gene promoter:
  • AP-1
  • AP-4
  • AREB6
  • c-Rel
  • CBF(2)
  • Elk-1
  • HOXA5
  • NF-Y
  • p53
  • Pax-4a

Genomic Locations for TDRKH Gene

Genomic Locations for TDRKH Gene
chr1:151,770,107-151,791,416
(GRCh38/hg38)
Size:
21,310 bases
Orientation:
Minus strand
chr1:151,742,583-151,763,892
(GRCh37/hg19)
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 PRKN during mitophagy, leading to its degradation and enhancement of mitophagy. Deubiquitinated by USP30.
  • Ubiquitination at Lys65, Lys76, Lys110, Lys112, Lys175, Lys181, Lys187, Lys193, Lys152, Lys256, Lys267, Lys479, Lys510, and Lys529
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TDRKH Gene

Domains & Families for TDRKH Gene

Gene Families for TDRKH Gene

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

Suggested Antigen Peptide Sequences for TDRKH Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ54003, highly similar to Tudor and KH domain-containing protein (B4DJ68_HUMAN)
  • cDNA, FLJ79178, highly similar to Tudor and KH domain-containing protein (B7ZAG4_HUMAN)
  • Tudor and KH domain containing, isoform CRA_c (Q5SZR5_HUMAN)
  • Tudor domain-containing protein 2 (TDRKH_HUMAN)

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.

Phenotypes From GWAS Catalog for TDRKH Gene

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

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

Clone Products

  • Addgene plasmids for TDRKH

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 4
cytosol 3
plasma membrane 2
cytoskeleton 2
nucleus 2
extracellular 1
endoplasmic reticulum 1
peroxisome 0
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (2)
  • Cytosol (2)
See all subcellular structures

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

Gene Ontology (GO) - Biological Process for TDRKH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007140 male meiotic nuclear division 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

CRISPR Products

Inhibitory RNA Products

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

Clone Products

  • Addgene plasmids for TDRKH

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, 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

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 33 32
  • 99.58 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TDRKH 33 32
  • 90.6 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Tdrkh 17 33 32
  • 89.82 (n)
rat
(Rattus norvegicus)
Mammalia Tdrkh 32
  • 89.76 (n)
cow
(Bos Taurus)
Mammalia TDRKH 33 32
  • 89.12 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TDRKH 33
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia TDRKH 33
  • 48 (a)
OneToOne
chicken
(Gallus gallus)
Aves TDRKH 33 32
  • 62.09 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TDRKH 33
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tdrkh 32
  • 53.85 (n)
Str.6287 32
zebrafish
(Danio rerio)
Actinopterygii tdrkh 33 32
  • 52.87 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta papi 33
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for TDRKH: view image

Paralogs for TDRKH Gene

Paralogs for TDRKH Gene

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

  • TDRKH_HUMAN
  • B4DJ68_HUMAN
  • B7ZAG4_HUMAN
  • E9PKN8_HUMAN
  • E9PQX4_HUMAN
  • Q5SZR4_HUMAN
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 Variation AA Info Type
rs375454176 likely-pathogenic, Distal spinal muscular atrophy 151,776,497(-) C/T coding_sequence_variant, missense_variant
rs1000020886 -- 151,782,258(-) C/A intron_variant
rs1000077895 -- 151,771,494(-) T/C/G downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000129915 -- 151,771,939(-) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs1000205346 -- 151,785,093(-) G/A intron_variant

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)

Additional Variant Information for TDRKH Gene

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

SNP Genotyping and Copy Number Assay Products

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
  • es
- elite association - COSMIC cancer census association via MalaCards
Search TDRKH in MalaCards View complete list of genes associated with diseases

Additional Disease Information for TDRKH

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 FS … Schutte BC (Gene 2000) 2 3 4 56
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 43 56
  3. 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 56
  4. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells. (PMID: 29509190) Giurato G … Tarallo R (Scientific data 2018) 3 56
  5. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. (PMID: 29568061) Liu X … Varjosalo M (Nature communications 2018) 3 56

Products for TDRKH Gene

Sources for TDRKH Gene