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    Tdrd5 tudor domain containing 5 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 289129, updated on 4-Jan-2025

    Summary

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    Official Symbol
    Tdrd5provided by RGD
    Official Full Name
    tudor domain containing 5provided by RGD
    Primary source
    RGD:1307078
    See related
    EnsemblRapid:ENSRNOG00000004018 AllianceGenome:RGD:1307078
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    This gene encodes a member of the tudor domain-containing protein family. Tudor domain-containing proteins regulate a variety of processes including RNA metabolism, histone modification, and the DNA damage response. The tudor domain commonly functions to link methylated arginine or lysine marks to downstream effector proteins. In mouse, this gene is expressed in the primordial germ cells and in male germ cells during embryogenesis. In addition, it is expressed in adult testis cells where the protein is a component of the intermitochondrial cement and chromatoid bodies. Loss-of-function mutations in mouse result in arrest of spermatogenesis. [provided by RefSeq, Mar 2015]
    Expression
    Biased expression in Testes (RPKM 72.2), Thymus (RPKM 53.6) and 2 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tdrd5 in Genome Data Viewer
    Location:
    13q22
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (70944441..70992345, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (68394180..68447745, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (73872637..73922640, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene ATP synthase F1 subunit gamma, pseudogene 3 Neighboring gene eukaryotic translation elongation factor 1 alpha 1, pseudogene 15 Neighboring gene NPHS2 stomatin family member, podocin Neighboring gene uncharacterized LOC134481573 Neighboring gene axonemal dynein light chain domain containing 1

    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. Tudor domain proteins in development. Pek JW, et al. Development, 2012 Jul. PMID 22669818
    2. TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice. Yabuta Y, et al. J Cell Biol, 2011 Mar 7. PMID 21383078, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC188201

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in P granule organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in P granule organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in P granule organization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in germ cell development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatid development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatid development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatid development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    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
    		  
    involved_in transposable element silencing by piRNA-mediated DNA methylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatoid body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in chromatoid body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatoid body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in pi-body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in pi-body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in pi-body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    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 5

    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_001134740.1 → NP_001128212.1  tudor domain-containing protein 5

      See identical proteins and their annotated locations for NP_001128212.1

      Status: REVIEWED

      Source sequence(s)
      BC168218
      UniProtKB/Swiss-Prot
      B4F7C4
      UniProtKB/TrEMBL
      A0A0G2KAX5
      Related
      ENSRNOP00000075564.2, ENSRNOT00000090848.3
      Conserved Domains (5) summary
      cd04508
      Location:537 → 583
      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 ...
      cd09975
      Location:127 → 196
      LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09976
      Location:292 → 365
      LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09985
      Location:4 → 98
      LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
      pfam00567
      Location:483 → 602
      TUDOR; Tudor domain

    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_086031.1 Reference GRCr8

      Range
      70944441..70992345 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006250039.4 → XP_006250101.1  tudor domain-containing protein 5 isoform X2

      UniProtKB/TrEMBL
      A0A8I5XVL8
      Conserved Domains (4) summary
      cd04508
      Location:460 → 506
      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 ...
      cd09976
      Location:215 → 288
      LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09985
      Location:4 → 98
      LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
      pfam00567
      Location:406 → 525
      TUDOR; Tudor domain

    2. XM_006250037.4 → XP_006250099.1  tudor domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_006250099.1

      UniProtKB/TrEMBL
      A0A0H2UHC6, A0A8I5XVL8
      Related
      ENSRNOP00000005353.6, ENSRNOT00000005353.9
      Conserved Domains (4) summary
      cd09975
      Location:127 → 196
      LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09976
      Location:292 → 365
      LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09985
      Location:4 → 98
      LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd20419
      Location:484 → 601
      Tudor_TDRD5; Tudor domain found in Tudor domain-containing protein 5 (TDRD5) and similar proteins

    3. XM_008769615.4 → XP_008767837.1  tudor domain-containing protein 5 isoform X1

      See identical proteins and their annotated locations for XP_008767837.1

      UniProtKB/TrEMBL
      A0A0H2UHC6, A0A8I5XVL8
      Conserved Domains (4) summary
      cd09975
      Location:127 → 196
      LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09976
      Location:292 → 365
      LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09985
      Location:4 → 98
      LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd20419
      Location:484 → 601
      Tudor_TDRD5; Tudor domain found in Tudor domain-containing protein 5 (TDRD5) and similar proteins

    4. XM_063272103.1 → XP_063128173.1  tudor domain-containing protein 5 isoform X3

      UniProtKB/TrEMBL
      A0A8I5XVL8

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001134739.1: Suppressed sequence

      Description
      NM_001134739.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    B4F7C4.1 GenPept UniProtKB/Swiss-Prot:B4F7C4

    Gene LinkOut

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

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