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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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