Mouse Gene Tdrkh (ENSMUST00000166032.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Interacts with PIWIL1 and PIWIL4. (from UniProt Q80VL1)
Gencode Transcript: ENSMUST00000166032.7
Gencode Gene: ENSMUSG00000041912.12
Transcript (Including UTRs)
   Position: mm10 chr3:94,413,273-94,434,668 Size: 21,396 Total Exon Count: 14 Strand: +
Coding Region
   Position: mm10 chr3:94,422,828-94,430,609 Size: 7,782 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:94,413,273-94,434,668)mRNA (may differ from genome)Protein (560 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsMGIPubMed
ReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: TDRKH_MOUSE
DESCRIPTION: RecName: Full=Tudor and KH domain-containing protein;
SUBUNIT: Interacts with PIWIL1 and PIWIL4.
SIMILARITY: Contains 2 KH domains.
SIMILARITY: Contains 1 Tudor domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • D013749 Tetrachlorodibenzodioxin
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • D001564 Benzo(a)pyrene
  • D002117 Calcitriol
  • D010795 Phthalic Acids

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -42.50116-0.366 Picture PostScript Text
3' UTR -1110.503893-0.285 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004087 - KH_dom
IPR004088 - KH_dom_type_1
IPR002999 - Tudor

Pfam Domains:
PF00013 - KH domain
PF00567 - Tudor domain

SCOP Domains:
50044 - SH3-domain
63748 - Tudor/PWWP/MBT
54791 - Eukaryotic type KH-domain (KH-domain type I)
54814 - Prokaryotic type KH domain (KH-domain type II)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WE8 - NMR


ModBase Predicted Comparative 3D Structure on Q80VL1
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0007140 male meiosis
GO:0007283 spermatogenesis
GO:0009566 fertilization
GO:0030154 cell differentiation
GO:0031047 gene silencing by RNA
GO:0034587 piRNA metabolic process
GO:0043046 DNA methylation involved in gamete generation

Cellular Component:
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0071546 pi-body
GO:0071547 piP-body


-  Descriptions from all associated GenBank mRNAs
  AK012596 - Mus musculus 11 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2700091C21 product:similar to PUTATIVE RNA BINDING PROTEIN [Homo sapiens], full insert sequence.
BC057030 - Mus musculus tudor and KH domain containing protein, mRNA (cDNA clone MGC:67203 IMAGE:6833743), complete cds.
BC031886 - Mus musculus tudor and KH domain containing protein, mRNA (cDNA clone IMAGE:5365523), with apparent retained intron.
BC049363 - Mus musculus tudor and KH domain containing protein, mRNA (cDNA clone MGC:57093 IMAGE:6490411), complete cds.
AK018134 - Mus musculus adult male medulla oblongata cDNA, RIKEN full-length enriched library, clone:6330407D06 product:unclassifiable, full insert sequence.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q80VL1 (Reactome details) participates in the following event(s):

R-MMU-5615685 Complexed Piwil1 binds pre-piRNA
R-MMU-5629239 Henmt1 methylates 2' hydroxyl at 3' end of piRNA in 4xMeR-Piwil1:piRNA:Tdrd6:Tdrkh
R-MMU-5629230 Henmt1 methylates 2' hydroxyl at 3' end of piRNA in MeR-Piwil4:piRNA:Tdrd9:Mael:Tdrkh

-  Other Names for This Gene
  Alternate Gene Symbols: BC057030, Q80VL1, TDRKH_MOUSE, uc008qge.1, uc008qge.2
UCSC ID: uc008qge.2
RefSeq Accession: NM_001357711
Protein: Q80VL1 (aka TDRKH_MOUSE or TDRH_MOUSE)
CCDS: CCDS38534.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.