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

Gene ID: 289129, updated on 2-Nov-2024

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 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 piRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrotransposon silencing by piRNA-directed DNA methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in retrotransposon silencing by piRNA-directed DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in siRNA-mediated retrotransposon silencing by heterochromatin formation ISO
Inferred from Sequence Orthology
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in P granule IBA
Inferred from Biological aspect of Ancestor
more info
  
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

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

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