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    Tdrd1 tudor domain containing 1 [ Mus musculus (house mouse) ]

    Gene ID: 83561, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Tdrd1provided by MGI
    Official Full Name
    tudor domain containing 1provided by MGI
    Primary source
    MGI:MGI:1933218
    See related
    Ensembl:ENSMUSG00000025081 AllianceGenome:MGI:1933218
    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
    MTR-1
    Summary
    Predicted to enable metal ion binding activity. Involved in germ cell development; regulatory ncRNA-mediated gene silencing; and spermatogenesis. Located in chromatoid body and pi-body. Part of ribonucleoprotein complex. Is active in synapse. Is expressed in several structures, including reproductive system. Orthologous to human TDRD1 (tudor domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis adult (RPKM 23.7) and limb E14.5 (RPKM 0.9) See more
    Orthologs
    human all
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    Genomic context

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    See Tdrd1 in Genome Data Viewer
    Location:
    19 D2; 19 52.0 cM
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (56814603..56858444)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (56826171..56870012)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 32718 Neighboring gene rp1 MIF pseudogene Neighboring gene coiled-coil domain containing 186 Neighboring gene STARR-positive B cell enhancer ABC_E5712 Neighboring gene von Willebrand factor A domain containing 2 Neighboring gene STARR-seq mESC enhancer starr_46534 Neighboring gene actin filament associated protein 1-like 2 Neighboring gene STARR-seq mESC enhancer starr_46535 Neighboring gene predicted gene, 38597

    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 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. The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors. Mathioudakis N, et al. RNA, 2012 Nov. PMID 22996915, Free PMC Article
    2. Tdrd1/Mtr-1, a tudor-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice. Chuma S, et al. Proc Natl Acad Sci U S A, 2006 Oct 24. PMID 17038506, Free PMC Article
    3. Associations between PIWI proteins and TDRD1/MTR-1 are critical for integrated subcellular localization in murine male germ cells. Kojima K, et al. Genes Cells, 2009 Oct. PMID 19735482
    4. Mouse Tudor Repeat-1 (MTR-1) is a novel component of chromatoid bodies/nuages in male germ cells and forms a complex with snRNPs. Chuma S, et al. Mech Dev, 2003 Sep. PMID 14550528
    5. Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Reuter M, et al. Nat Struct Mol Biol, 2009 Jun. PMID 19465913

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TDRD1 can accommodate different peptides from different proteins, and can therefore act as a scaffold protein for complex assembly in the piRNA pathway.
      Title: The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors.
    2. Data suggest that the formation of complexes between MILI, MIWI and TDRD1/MTR-1 is critical for the integrated subcellular localizations of these proteins, and is presumably essential for spermatogenesis.
      Title: Associations between PIWI proteins and TDRD1/MTR-1 are critical for integrated subcellular localization in murine male germ cells.
    3. Tdrd1 ensures the entry of correct transcripts into the normal piRNA pool.
      Title: Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile.
    4. Results suggest that Mili interacts with Tdrd1 in the nuage and chromatoid body, and that this interaction does not contribute to piRNA biogenesis but represents a regulatory mechanism that is critical for spermatogenesis.
      Title: Mili interacts with tudor domain-containing protein 1 in regulating spermatogenesis.
    5. targeted mutation in Tudor domain containing 1/mouse tudor repeat 1 (Tdrd1/Mtr-1), a tudor-related gene in mice, leads to male sterility because of postnatal spermatogenic defects
      Title: Tdrd1/Mtr-1, a tudor-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice.
    6. isolated Mouse tudor repeat-1 (Mtr-1) which encodes a MYND domain and four copies of the tudor domain. Mtr-1 is expressed in germ-line cells and is most abundant in fetal prospermatogonia and postnatal primary spermatocytes.
      Title: Mouse Tudor Repeat-1 (MTR-1) is a novel component of chromatoid bodies/nuages in male germ cells and forms a complex with snRNPs.
    7. Tudor-related proteins, which contain multiple repeats of the Tudor domain, constitute an evolutionarily conserved class of nuage components in the germ-line, and their localization or accumulation to nuage is likely conferred by a Tudor domain structure
      Title: Tudor-related proteins TDRD1/MTR-1, TDRD6 and TDRD7/TRAP: domain composition, intracellular localization, and function in male germ cells in mice.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    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 metal ion 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 germ cell development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in meiotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 retrotransposon silencing by piRNA-directed DNA methylation 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 P granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromatoid body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in pi-body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in synapse EXP
    Inferred from Experiment
    more info
    		 PubMed 
    is_active_in synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tudor domain-containing protein 1

    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_001002238.2 → NP_001002238.1  tudor domain-containing protein 1

      See identical proteins and their annotated locations for NP_001002238.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 3. All four variants encode the same protein.
      Source sequence(s)
      AC125150, AC158549
      Consensus CDS
      CCDS29922.1
      UniProtKB/Swiss-Prot
      A2VDG6, Q6F3G0, Q8CDN7, Q8K1G3, Q99MV1
      Related
      ENSMUSP00000107233.2, ENSMUST00000111606.8
      Conserved Domains (3) summary
      cd04508
      Location:760 → 805
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      pfam00567
      Location:487 → 606
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    2. NM_001002240.2 → NP_001002240.1  tudor domain-containing protein 1

      See identical proteins and their annotated locations for NP_001002240.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 3. All four variants encode the same protein.
      Source sequence(s)
      AC125150, AC158549
      Consensus CDS
      CCDS29922.1
      UniProtKB/Swiss-Prot
      A2VDG6, Q6F3G0, Q8CDN7, Q8K1G3, Q99MV1
      Related
      ENSMUSP00000077785.5, ENSMUST00000078723.11
      Conserved Domains (3) summary
      cd04508
      Location:760 → 805
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      pfam00567
      Location:487 → 606
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    3. NM_001002241.2 → NP_001002241.1  tudor domain-containing protein 1

      See identical proteins and their annotated locations for NP_001002241.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents the longest transcript. All four variants encode the same protein.
      Source sequence(s)
      AC125150, AC158549
      Consensus CDS
      CCDS29922.1
      UniProtKB/Swiss-Prot
      A2VDG6, Q6F3G0, Q8CDN7, Q8K1G3, Q99MV1
      Related
      ENSMUSP00000107231.2, ENSMUST00000111604.2
      Conserved Domains (3) summary
      cd04508
      Location:760 → 805
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      pfam00567
      Location:487 → 606
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    4. NM_031387.3 → NP_113564.2  tudor domain-containing protein 1

      See identical proteins and their annotated locations for NP_113564.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 3. All four variants encode the same protein.
      Source sequence(s)
      AC125150, AK029806
      Consensus CDS
      CCDS29922.1
      UniProtKB/Swiss-Prot
      A2VDG6, Q6F3G0, Q8CDN7, Q8K1G3, Q99MV1
      Related
      ENSMUSP00000112786.2, ENSMUST00000121249.8
      Conserved Domains (3) summary
      cd04508
      Location:760 → 805
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...
      pfam00567
      Location:487 → 606
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    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_000085.7 Reference GRCm39 C57BL/6J

      Range
      56814603..56858444
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006527473.1 → XP_006527536.1  tudor domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006527536.1

      Conserved Domains (2) summary
      pfam00567
      Location:718 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    2. XM_006527478.1 → XP_006527541.1  tudor domain-containing protein 1 isoform X2

      Conserved Domains (2) summary
      pfam00567
      Location:718 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    3. XM_006527475.4 → XP_006527538.1  tudor domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006527538.1

      Conserved Domains (2) summary
      pfam00567
      Location:718 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    4. XM_006527474.1 → XP_006527537.1  tudor domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006527537.1

      Conserved Domains (2) summary
      pfam00567
      Location:718 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    5. XM_006527476.2 → XP_006527539.1  tudor domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006527539.1

      Conserved Domains (2) summary
      pfam00567
      Location:718 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    6. XM_006527477.4 → XP_006527540.1  tudor domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006527540.1

      Conserved Domains (2) summary
      pfam00567
      Location:718 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:163 → 199
      zf-MYND; MYND finger

    7. XM_006527479.3 → XP_006527542.1  tudor domain-containing protein 1 isoform X3

      Conserved Domains (2) summary
      pfam00567
      Location:613 → 720
      TUDOR; Tudor domain
      pfam01753
      Location:58 → 94
      zf-MYND; MYND finger
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99MV1.2 GenPept UniProtKB/Swiss-Prot:Q99MV1

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

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