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

    Gene ID: 72634, updated on 9-Dec-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, Dec 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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