U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Tdrd5 tudor domain containing 5 [ Mus musculus (house mouse) ]

    Gene ID: 214575, updated on 14-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Tdrd5provided by MGI
    Official Full Name
    tudor domain containing 5provided by MGI
    Primary source
    MGI:MGI:2684949
    See related
    Ensembl:ENSMUSG00000060985 AllianceGenome:MGI:2684949
    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
    Gm103
    Summary
    Involved in P granule organization; retrotransposon silencing by piRNA-directed DNA methylation; and spermatid development. Located in chromatoid body and pi-body. Is active in synapse. Is expressed in genitourinary system. Orthologous to human TDRD5 (tudor domain containing 5). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in testis adult (RPKM 8.7), thymus adult (RPKM 3.7) and 3 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Tdrd5 in Genome Data Viewer
    Location:
    1 G3; 1 67.71 cM
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (156082866..156131874, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (156255296..156304304, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_02733 Neighboring gene family with sequence similarity 163, member A Neighboring gene predicted gene, 30472 Neighboring gene STARR-seq mESC enhancer starr_02734 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:158194711-158194894 Neighboring gene STARR-seq mESC enhancer starr_02735 Neighboring gene nephrosis 2, podocin Neighboring gene axonemal dynein light chain domain containing 1 Neighboring gene ribosomal protein L35, retrotransposed

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Disruption of Tdrd5 decouples the stepwise processing of long precursor transcripts during pachytene PIWI-interacting RNA biogenesis. Sun YH, et al. Biol Reprod, 2018 Oct 1. PMID 29733347
    2. TDRD5 binds piRNA precursors and selectively enhances pachytene piRNA processing in mice. Ding D, et al. Nat Commun, 2018 Jan 9. PMID 29317670, Free PMC Article
    3. Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors. Sun YH, et al. Nat Cell Biol, 2020 Feb. PMID 32015435, Free PMC Article
    4. Expression of the tudor-related gene Tdrd5 during development of the male germline in mice. Smith JM, et al. Gene Expr Patterns, 2004 Oct. PMID 15465492
    5. ZFP628 Is a TAF4b-Interacting Transcription Factor Required for Mouse Spermiogenesis. Gustafson EA, et al. Mol Cell Biol, 2020 Mar 16. PMID 31932482, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. By conditional inactivation of Tdrd5 in postnatal male germ cells (Tdrd5cKO), we show that spermatogenesis is arrested at the round spermatid stage, and the testes of Tdrd5cKO mice are about half the weight of wildtype controls.
      Title: Disruption of Tdrd5 decouples the stepwise processing of long precursor transcripts during pachytene PIWI-interacting RNA biogenesis.
    2. Conditional inactivation of TDRD5 in mouse postnatal germ cells reveals that TDRD5 selectively regulates the production of pachytene piRNAs from abundant piRNA-producing precursors, with little effect on low-abundant piRNAs.
      Title: TDRD5 binds piRNA precursors and selectively enhances pachytene piRNA processing in mice.
    3. TDRD5 is a novel component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis.
      Title: TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice.
    4. Tdrd5 expression is restricted to the male germline throughout development to adulthood
      Title: Expression of the tudor-related gene Tdrd5 during development of the male germline in mice.
    Submit: New GeneRIF Correction

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (3)  1 citation

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in P granule organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in spermatid development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transposable element silencing by piRNA-mediated DNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatoid body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in pi-body 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

    Go to the top of the page Help
    Preferred Names
    tudor domain-containing protein 5
    Names
    tudor domain containing protein 5

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001134741.1 → NP_001128213.1  tudor domain-containing protein 5 isoform 1

      See identical proteins and their annotated locations for NP_001128213.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK132674, BC099972, DV655037, DV659775
      Consensus CDS
      CCDS56647.1
      UniProtKB/Swiss-Prot
      A7YQ76, D3YXM4, Q5VCS6
      Related
      ENSMUSP00000137298.2, ENSMUST00000121146.10
      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

    2. NM_001277730.1 → NP_001264659.1  tudor domain-containing protein 5 isoform 2

      See identical proteins and their annotated locations for NP_001264659.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, and uses two alternate splice sites that result in the loss of an in-frame segment in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK132674, BC099972, DV659775
      UniProtKB/Swiss-Prot
      Q5VCS6
      Conserved Domains (3) summary
      cd09976
      Location:197 → 270
      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:388 → 507
      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_000067.7 Reference GRCm39 C57BL/6J

      Range
      156082866..156131874 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006496733.3 → XP_006496796.1  tudor domain-containing protein 5 isoform X8

      See identical proteins and their annotated locations for XP_006496796.1

      UniProtKB/Swiss-Prot
      Q5VCS6
      Conserved Domains (3) summary
      cd09976
      Location:197 → 270
      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:388 → 507
      TUDOR; Tudor domain

    2. XM_006496731.3 → XP_006496794.1  tudor domain-containing protein 5 isoform X6

      UniProtKB/TrEMBL
      J3QPB7
      Related
      ENSMUSP00000137182.2, ENSMUST00000167528.9
      Conserved Domains (3) summary
      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

    3. XM_006496728.3 → XP_006496791.1  tudor domain-containing protein 5 isoform X3

      Conserved Domains (4) summary
      cd09975
      Location:127 → 196
      LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09976
      Location:274 → 347
      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:465 → 584
      TUDOR; Tudor domain

    4. XM_006496726.4 → XP_006496789.1  tudor domain-containing protein 5 isoform X1

      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)
      pfam00567
      Location:482 → 601
      TUDOR; Tudor domain

    5. XM_006496727.4 → XP_006496790.1  tudor domain-containing protein 5 isoform X2

      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)
      pfam00567
      Location:483 → 602
      TUDOR; Tudor domain

    6. XM_006496729.4 → XP_006496792.1  tudor domain-containing protein 5 isoform X4

      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)
      pfam00567
      Location:483 → 602
      TUDOR; Tudor domain

    7. XM_006496734.1 → XP_006496797.1  tudor domain-containing protein 5 isoform X9

      Conserved Domains (3) summary
      cd09975
      Location:24 → 93
      LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
      cd09976
      Location:189 → 262
      LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
      pfam00567
      Location:380 → 499
      TUDOR; Tudor domain

    8. XM_006496730.3 → XP_006496793.1  tudor domain-containing protein 5 isoform X5

      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)
      pfam00567
      Location:483 → 602
      TUDOR; Tudor domain

    9. XM_006496732.3 → XP_006496795.1  tudor domain-containing protein 5 isoform X7

      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)
      pfam00567
      Location:483 → 602
      TUDOR; Tudor domain

    10. XM_030252864.1 → XP_030108724.1  tudor domain-containing protein 5 isoform X11

      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

    11. XM_011238780.3 → XP_011237082.1  tudor domain-containing protein 5 isoform X10

      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)
      pfam00567
      Location:483 → 602
      TUDOR; Tudor domain

    12. XM_036163492.1 → XP_036019385.1  tudor domain-containing protein 5 isoform X11

      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

    RNA

    1. XR_004941506.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VCS6.3 GenPept UniProtKB/Swiss-Prot:Q5VCS6

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools