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    Tdrd1 tudor domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 292129, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Tdrd1provided by RGD
    Official Full Name
    tudor domain containing 1provided by RGD
    Primary source
    RGD:1306140
    See related
    EnsemblRapid:ENSRNOG00000017064 AllianceGenome:RGD:1306140
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable metal ion binding activity. Predicted to be involved in P granule organization; regulatory ncRNA-mediated gene silencing; and spermatogenesis. Predicted to be located in chromatoid body and pi-body. Predicted to be part of ribonucleoprotein complex. Predicted to be active in P granule and synapse. Orthologous to human TDRD1 (tudor domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Testes (RPKM 198.1) and Brain (RPKM 5.5) See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tdrd1 in Genome Data Viewer
    Location:
    1q55
    Exon count:
    33
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (265876858..265924357)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (255871939..255919222)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (277639670..277685236)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene adrenoceptor beta 1 Neighboring gene uncharacterized LOC102547814 Neighboring gene coiled-coil domain containing 186 Neighboring gene von Willebrand factor A domain containing 2 Neighboring gene actin filament associated protein 1-like 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. 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
    2. 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
    3. 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
    4. MVH in piRNA processing and gene silencing of retrotransposons. Kuramochi-Miyagawa S, et al. Genes Dev, 2010 May. PMID 20439430, Free PMC Article
    5. Tudor-related proteins TDRD1/MTR-1, TDRD6 and TDRD7/TRAP: domain composition, intracellular localization, and function in male germ cells in mice. Hosokawa M, et al. Dev Biol, 2007 Jan 1. PMID 17141210

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in P granule organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in germ cell development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in piRNA processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in piRNA processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transposable element silencing by piRNA-mediated DNA methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in transposable element silencing by piRNA-mediated DNA methylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in P granule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in P granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatoid body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in pi-body ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  

    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_001106202.1 → NP_001099672.1  tudor domain-containing protein 1

      See identical proteins and their annotated locations for NP_001099672.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473986
      UniProtKB/TrEMBL
      A6JI31, D4A3N0
      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:706 → 824
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      265876858..265924357
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039103224.2 → XP_038959152.1  tudor domain-containing protein 1 isoform X1

      Conserved Domains (5) summary
      pfam00567
      Location:709 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger
      cd20408
      Location:262 → 391
      Tudor_TDRD1_rpt1; first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cd20409
      Location:512 → 593
      Tudor_TDRD1_rpt2; second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:938 → 1053
      Tudor_SF; Tudor domain superfamily

    2. XM_039103243.2 → XP_038959171.1  tudor domain-containing protein 1 isoform X5

      Conserved Domains (4) summary
      pfam00567
      Location:571 → 687
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger
      cd20408
      Location:262 → 391
      Tudor_TDRD1_rpt1; first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:800 → 915
      Tudor_SF; Tudor domain superfamily

    3. XM_063282786.1 → XP_063138856.1  tudor domain-containing protein 1 isoform X1

      Related
      ENSRNOP00000023024.4, ENSRNOT00000023024.6

    4. XM_039103240.2 → XP_038959168.1  tudor domain-containing protein 1 isoform X3

      Conserved Domains (5) summary
      pfam00567
      Location:709 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger
      cd20408
      Location:262 → 391
      Tudor_TDRD1_rpt1; first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cd20409
      Location:512 → 593
      Tudor_TDRD1_rpt2; second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:938 → 1030
      Tudor_SF; Tudor domain superfamily

    5. XM_039103209.2 → XP_038959137.1  tudor domain-containing protein 1 isoform X1

      Conserved Domains (5) summary
      pfam00567
      Location:709 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger
      cd20408
      Location:262 → 391
      Tudor_TDRD1_rpt1; first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cd20409
      Location:512 → 593
      Tudor_TDRD1_rpt2; second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:938 → 1053
      Tudor_SF; Tudor domain superfamily

    6. XM_039103236.2 → XP_038959164.1  tudor domain-containing protein 1 isoform X1

      Conserved Domains (5) summary
      pfam00567
      Location:709 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger
      cd20408
      Location:262 → 391
      Tudor_TDRD1_rpt1; first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cd20409
      Location:512 → 593
      Tudor_TDRD1_rpt2; second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:938 → 1053
      Tudor_SF; Tudor domain superfamily

    7. XM_063282791.1 → XP_063138861.1  tudor domain-containing protein 1 isoform X4

    8. XM_063282787.1 → XP_063138857.1  tudor domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A6JI31, D4A3N0

    9. XM_063282788.1 → XP_063138858.1  tudor domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A6JI31, D4A3N0

    10. XM_063282792.1 → XP_063138862.1  tudor domain-containing protein 1 isoform X4

    11. XM_039103239.2 → XP_038959167.1  tudor domain-containing protein 1 isoform X1

      Conserved Domains (5) summary
      pfam00567
      Location:709 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger
      cd20408
      Location:262 → 391
      Tudor_TDRD1_rpt1; first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cd20409
      Location:512 → 593
      Tudor_TDRD1_rpt2; second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:938 → 1053
      Tudor_SF; Tudor domain superfamily

    12. XM_039103212.2 → XP_038959140.1  tudor domain-containing protein 1 isoform X1

      Conserved Domains (5) summary
      pfam00567
      Location:709 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger
      cd20408
      Location:262 → 391
      Tudor_TDRD1_rpt1; first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cd20409
      Location:512 → 593
      Tudor_TDRD1_rpt2; second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:938 → 1053
      Tudor_SF; Tudor domain superfamily

    13. XM_063282789.1 → XP_063138859.1  tudor domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A6JI31, D4A3N0
      Related
      ENSRNOP00000105132.1, ENSRNOT00000123796.1

    14. XM_039103219.2 → XP_038959147.1  tudor domain-containing protein 1 isoform X1

      Conserved Domains (5) summary
      pfam00567
      Location:709 → 825
      TUDOR; Tudor domain
      pfam01753
      Location:162 → 198
      zf-MYND; MYND finger
      cd20408
      Location:262 → 391
      Tudor_TDRD1_rpt1; first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cd20409
      Location:512 → 593
      Tudor_TDRD1_rpt2; second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:938 → 1053
      Tudor_SF; Tudor domain superfamily

    15. XM_039103246.2 → XP_038959174.1  tudor domain-containing protein 1 isoform X6

      Conserved Domains (3) summary
      pfam00567
      Location:272 → 388
      TUDOR; Tudor domain
      cd20409
      Location:75 → 156
      Tudor_TDRD1_rpt2; second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins
      cl02573
      Location:501 → 616
      Tudor_SF; Tudor domain superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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