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Tdrkh tudor and KH domain containing protein [ Mus musculus (house mouse) ]

Gene ID: 72634, updated on 27-Nov-2024

Summary

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Official Symbol
Tdrkhprovided by MGI
Official Full Name
tudor and KH domain containing proteinprovided by MGI
Primary source
MGI:MGI:1919884
See related
Ensembl:ENSMUSG00000041912 AllianceGenome:MGI:1919884
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Tdrd2; 2700091C21Rik
Summary
Predicted to enable RNA binding activity. Involved in several processes, including male meiotic nuclear division; piRNA processing; and spermatogenesis. Located in mitochondrion; pi-body; and piP-body. Is expressed in central nervous system; reproductive system; sensory organ; and urinary system. Orthologous to human TDRKH (tudor and KH domain containing). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in testis adult (RPKM 43.0), CNS E18 (RPKM 3.9) and 5 other tissues See more
Orthologs
human all
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Genomic context

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See Tdrkh in Genome Data Viewer
Location:
3 F2.1; 3 40.62 cM
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (94320551..94342161)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (94413243..94434854)

Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene leucine rich repeat and Ig domain containing 4 Neighboring gene RIKEN cDNA 1700040D17 gene Neighboring gene STARR-positive B cell enhancer mm9_chr3:94216846-94217147 Neighboring gene ornithine decarboxylase antizyme 3 Neighboring gene mitochondrial ribosomal protein L9 Neighboring gene 40S ribosomal protein S2-like

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. PNLDC1 is essential for piRNA 3' end trimming and transposon silencing during spermatogenesis in mice. Ding D, et al. Nat Commun, 2017 Oct 10. PMID 29018194, Free PMC Article
  2. Tudor domains bind symmetrical dimethylated arginines. Côté J, et al. J Biol Chem, 2005 Aug 5. PMID 15955813
  3. Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Chen C, et al. Proc Natl Acad Sci U S A, 2009 Dec 1. PMID 19918066, Free PMC Article
  4. Mitochondrial membrane-based initial separation of MIWI and MILI functions during pachytene piRNA biogenesis. Ding D, et al. Nucleic Acids Res, 2019 Mar 18. PMID 30590800, Free PMC Article
  5. Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2. Zhang H, et al. Proc Natl Acad Sci U S A, 2017 Nov 21. PMID 29118143, Free PMC Article

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. we show that mitochondria-anchored TDRKH controls multiple steps of pachytene piRNA biogenesis in mice. TDRKH specifically recruits MIWI, but not MILI, to engage the piRNA pathway. It is required for the production of the entire MIWI-bound piRNA population and enables trimming of MILI-bound piRNAs.
    Title: Mitochondrial membrane-based initial separation of MIWI and MILI functions during pachytene piRNA biogenesis.
  2. Unlike most other Tudor domains TDRD2 preferentially recognizes an unmethylated arginine-rich sequence from PIWIL1.
    Title: Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2.
  3. Loss of Tdrkh is associated with impaired spermatogenesis.
    Title: Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 
  • Targeted (5)  1 citation

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in P granule organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in fertilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in male meiotic nuclear division IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in piRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in piRNA processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in spermatogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spermatogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in P granule IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in mitochondrion HDA PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in pi-body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in piP-body IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
tudor and KH domain-containing protein
Names
tudor domain-containing protein 2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001357711.1 → NP_001344640.1  tudor and KH domain-containing protein isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC122808, BC057030
    Consensus CDS
    CCDS38534.1
    UniProtKB/Swiss-Prot
    Q80VL1
    UniProtKB/TrEMBL
    Q6PGG8
    Related
    ENSMUSP00000129635.2, ENSMUST00000166032.8
    Conserved Domains (2) summary
    pfam00013
    Location:54 → 117
    KH_1; KH domain
    pfam00567
    Location:303 → 422
    TUDOR; Tudor domain

  2. NM_001357712.1 → NP_001344641.1  tudor and KH domain-containing protein isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC122808
    Consensus CDS
    CCDS38534.1
    UniProtKB/Swiss-Prot
    Q80VL1
    UniProtKB/TrEMBL
    Q6PGG8
    Related
    ENSMUSP00000142561.2, ENSMUST00000197901.5
    Conserved Domains (2) summary
    pfam00013
    Location:54 → 117
    KH_1; KH domain
    pfam00567
    Location:303 → 422
    TUDOR; Tudor domain

  3. NM_001357713.1 → NP_001344642.1  tudor and KH domain-containing protein isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC122808
    Consensus CDS
    CCDS89664.1
    UniProtKB/TrEMBL
    A0A0G2JE08
    Related
    ENSMUSP00000142584.2, ENSMUST00000200486.5
    Conserved Domains (1) summary
    pfam00013
    Location:54 → 117
    KH_1; KH domain

  4. NM_001357714.1 → NP_001344643.1  tudor and KH domain-containing protein isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC122808
    Consensus CDS
    CCDS89663.1
    UniProtKB/TrEMBL
    A0A0G2JFP5
    Related
    ENSMUSP00000143256.2, ENSMUST00000196386.5
    Conserved Domains (1) summary
    pfam00013
    Location:54 → 117
    KH_1; KH domain

  5. NM_028307.2 → NP_082583.1  tudor and KH domain-containing protein isoform 1

    See identical proteins and their annotated locations for NP_082583.1

    Status: VALIDATED

    Source sequence(s)
    AC122808, BC049363, BE945944
    Consensus CDS
    CCDS38534.1
    UniProtKB/Swiss-Prot
    Q80VL1
    UniProtKB/TrEMBL
    Q6PGG8
    Related
    ENSMUSP00000041002.6, ENSMUST00000045245.10
    Conserved Domains (2) summary
    pfam00013
    Location:54 → 117
    KH_1; KH domain
    pfam00567
    Location:303 → 422
    TUDOR; Tudor domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000069.7 Reference GRCm39 C57BL/6J

    Range
    94320551..94342161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030252843.2 → XP_030108703.1  tudor and KH domain-containing protein isoform X1

    Conserved Domains (1) summary
    pfam00567
    Location:66 → 179
    TUDOR; Tudor domain

RNA

  1. XR_003954404.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q80VL1.1 GenPept UniProtKB/Swiss-Prot:Q80VL1

Gene LinkOut

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