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    Tdrd3 tudor domain containing 3 [ Mus musculus (house mouse) ]

    Gene ID: 219249, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Tdrd3provided by MGI
    Official Full Name
    tudor domain containing 3provided by MGI
    Primary source
    MGI:MGI:2444023
    See related
    Ensembl:ENSMUSG00000022019 AllianceGenome:MGI:2444023
    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
    6720468N18; 4732418C03Rik
    Summary
    Predicted to enable chromatin binding activity; methylated histone binding activity; and transcription coactivator activity. Predicted to be involved in chromatin organization and positive regulation of DNA-templated transcription. Predicted to be located in Golgi apparatus; cytosol; and nucleoplasm. Predicted to be part of DNA topoisomerase III-beta-TDRD3 complex and exon-exon junction complex. Predicted to be active in nucleus. Orthologous to human TDRD3 (tudor domain containing 3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 1.6), limb E14.5 (RPKM 1.5) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Tdrd3 in Genome Data Viewer
    Location:
    14 E1; 14 44.17 cM
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (87647598..87782944)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (87416178..87545508)

    Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene diaphanous related formin 3 Neighboring gene STARR-seq mESC enhancer starr_37335 Neighboring gene predicted gene, 41222 Neighboring gene STARR-seq mESC enhancer starr_37337 Neighboring gene STARR-seq mESC enhancer starr_37338 Neighboring gene STARR-seq mESC enhancer starr_37339 Neighboring gene STARR-seq mESC enhancer starr_37340 Neighboring gene STARR-positive B cell enhancer ABC_E758 Neighboring gene STARR-seq mESC enhancer starr_37342 Neighboring gene STARR-seq mESC enhancer starr_37343 Neighboring gene STARR-seq mESC enhancer starr_37344 Neighboring gene STARR-positive B cell enhancer mm9_chr14:87815570-87815871 Neighboring gene predicted gene, 23278 Neighboring gene STARR-positive B cell enhancer mm9_chr14:87852017-87852318 Neighboring gene STARR-seq mESC enhancer starr_37345 Neighboring gene ATP synthase subunit d, mitochondrial pseudogene Neighboring gene STARR-seq mESC enhancer starr_37346 Neighboring gene STARR-seq mESC enhancer starr_37347 Neighboring gene STARR-seq mESC enhancer starr_37348 Neighboring gene STARR-seq mESC enhancer starr_37349 Neighboring gene STARR-seq mESC enhancer starr_37350 Neighboring gene predicted gene, 57617 Neighboring gene STARR-seq mESC enhancer starr_37351 Neighboring gene STARR-seq mESC enhancer starr_37352 Neighboring gene NOP2 nucleolar protein homolog pseudogene

    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. Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity. Zhu X, et al. Prog Neurobiol, 2024 Feb. PMID 38216113,
    2. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Yang Y, et al. Mol Cell, 2014 Feb 6. PMID 24507716, Free PMC Article
    3. Genetic, morphometric, and behavioral factors linked to the midsagittal area of the corpus callosum. Newbury AJ, et al. Front Genet, 2012. PMID 22666227, Free PMC Article
    4. Top3β is an RNA topoisomerase that works with fragile X syndrome protein to promote synapse formation. Xu D, et al. Nat Neurosci, 2013 Sep. PMID 23912945, Free PMC Article
    5. Epilepsy- and intellectual disability-associated CYFIP2 interacts with both actin regulators and RNA-binding proteins in the neonatal mouse forebrain. Lee Y, et al. Biochem Biophys Res Commun, 2020 Aug 13. PMID 32560809

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity.
      Title: Tdrd3-null mice show post-transcriptional and behavioral impairments associated with neurogenesis and synaptic plasticity.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 
    • Gene trapped (1) 

    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 chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables methylated histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription coactivator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA topological change NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of DNA topoisomerase III-beta-TDRD3 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of DNA topoisomerase III-beta-TDRD3 complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of exon-exon junction complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of exon-exon junction complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    tudor domain-containing protein 3

    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_001253755.1 → NP_001240684.1  tudor domain-containing protein 3 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons and its transcription extends past a splice site that is used in variant 1, resulting in a novel 3' coding region and 3' UTR compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK028617, AK032892, AK078326, AK162275, AW047213, BB126096, BC066144
      Consensus CDS
      CCDS56972.1
      UniProtKB/Swiss-Prot
      Q91W18
      Related
      ENSMUSP00000131542.2, ENSMUST00000169504.8
      Conserved Domains (3) summary
      cd04508
      Location:651 → 699
      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 ...
      cd14282
      Location:287 → 325
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:15 → 162
      RMI1_N; RecQ mediated genome instability protein

    2. NM_172605.3 → NP_766193.3  tudor domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_766193.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AK032892, AK033390, AW047213, BB668608, BE983697
      Consensus CDS
      CCDS27305.2
      UniProtKB/Swiss-Prot
      E9Q2Q4, Q6NZG7, Q8BZW6, Q8C1A4, Q91W18
      Related
      ENSMUSP00000129019.2, ENSMUST00000168275.9
      Conserved Domains (3) summary
      cd14282
      Location:287 → 325
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      cd20413
      Location:648 → 700
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:15 → 165
      RMI1_N; RecQ mediated genome instability protein

    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_000080.7 Reference GRCm39 C57BL/6J

      Range
      87647598..87782944
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006518911.5 → XP_006518974.1  tudor domain-containing protein 3 isoform X2

      See identical proteins and their annotated locations for XP_006518974.1

      Conserved Domains (3) summary
      cd14282
      Location:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:555 → 607
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    2. XM_006518909.4 → XP_006518972.1  tudor domain-containing protein 3 isoform X1

      Conserved Domains (3) summary
      cd04508
      Location:629 → 677
      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 ...
      cd14282
      Location:265 → 303
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:43 → 143
      RMI1_N; RecQ mediated genome instability protein

    3. XM_006518910.5 → XP_006518973.1  tudor domain-containing protein 3 isoform X2

      See identical proteins and their annotated locations for XP_006518973.1

      Conserved Domains (3) summary
      cd14282
      Location:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:555 → 607
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    4. XM_036158571.1 → XP_036014464.1  tudor domain-containing protein 3 isoform X2

      Conserved Domains (3) summary
      cd14282
      Location:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:555 → 607
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    5. XM_036158573.1 → XP_036014466.1  tudor domain-containing protein 3 isoform X2

      Conserved Domains (3) summary
      cd14282
      Location:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:555 → 607
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    6. XM_030247773.2 → XP_030103633.1  tudor domain-containing protein 3 isoform X2

      Conserved Domains (3) summary
      cd14282
      Location:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:555 → 607
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    7. XM_036158572.1 → XP_036014465.1  tudor domain-containing protein 3 isoform X2

      Conserved Domains (3) summary
      cd14282
      Location:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:555 → 607
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    8. XM_006518912.5 → XP_006518975.1  tudor domain-containing protein 3 isoform X2

      See identical proteins and their annotated locations for XP_006518975.1

      Conserved Domains (3) summary
      cd14282
      Location:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:555 → 607
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    RNA

    1. XR_004938390.1 RNA Sequence

    2. XR_383170.3 RNA Sequence

    3. XR_004938389.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91W18.4 GenPept UniProtKB/Swiss-Prot:Q91W18

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