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    Tdrd3 tudor domain containing 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306066, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Tdrd3provided by RGD
    Official Full Name
    tudor domain containing 3provided by RGD
    Primary source
    RGD:1310126
    See related
    EnsemblRapid:ENSRNOG00000009034 AllianceGenome:RGD:1310126
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    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, Dec 2024]
    Expression
    Biased expression in Kidney (RPKM 123.2), Adrenal (RPKM 83.2) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Tdrd3 in Genome Data Viewer
    Location:
    15q12
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 15 NC_086033.1 (69748754..69911605)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 15 NC_051350.1 (63340531..63497208)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 15 NC_005114.4 (70732164..70864855)

    Chromosome 15 - NC_086033.1Genomic Context describing neighboring genes Neighboring gene ATP synthase membrane subunit j, pseudogene 2 Neighboring gene microfibrillar-associated protein 1A, pseudogene 2 Neighboring gene uncharacterized LOC134482000 Neighboring gene small nucleolar RNA SNORA48

    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. Perceiving the epigenetic landscape through histone readers. Musselman CA, et al. Nat Struct Mol Biol, 2012 Dec. PMID 23211769, Free PMC Article
    2. TDRD3 is an effector molecule for arginine-methylated histone marks. Yang Y, et al. Mol Cell, 2010 Dec 22. PMID 21172665, Free PMC Article
    3. Tudor: a versatile family of histone methylation 'readers'. Lu R, et al. Trends Biochem Sci, 2013 Nov. PMID 24035451, Free PMC Article
    4. SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay. Kashima I, et al. Genes Dev, 2010 Nov 1. PMID 20930030, Free PMC Article
    5. Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth. Mertz J, et al. Mol Cell Proteomics, 2015 Jul. PMID 25931508, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    Function Evidence Code Pubs
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    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 biological_process ND
    No biological Data available
    more info
    		  
    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
    		  
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    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_001012043.2 → NP_001012043.1  tudor domain-containing protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001012043.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/Swiss-Prot
      Q66HC1
      UniProtKB/TrEMBL
      A0A096MIS7
      Related
      ENSRNOP00000083043.1, ENSRNOT00000110490.2
      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:556 → 608
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    2. NM_001431474.1 → NP_001418403.1  tudor domain-containing protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A0A8I5ZYD3

    3. NM_001431475.1 → NP_001418404.1  tudor domain-containing protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A0A8I5ZYD3

    4. NM_001431476.1 → NP_001418405.1  tudor domain-containing protein 3 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/Swiss-Prot
      Q66HC1
      UniProtKB/TrEMBL
      A0A096MIS7

    5. NM_001431477.1 → NP_001418406.1  tudor domain-containing protein 3 isoform 4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015
      UniProtKB/TrEMBL
      A0A096MIS7

    6. NM_001431478.1 → NP_001418407.1  tudor domain-containing protein 3 isoform 5

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015

    RNA

    1. NR_197221.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015

    2. NR_197222.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000015

    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_086033.1 Reference GRCr8

      Range
      69748754..69911605
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063274315.1 → XP_063130385.1  tudor domain-containing protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZYD3, A0A8I6A6B7
      Related
      ENSRNOP00000086500.1, ENSRNOT00000119103.2

    2. XM_039093362.2 → XP_038949290.1  tudor domain-containing protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYD3
      Conserved Domains (3) summary
      cd14282
      Location:287 → 325
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:15 → 165
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:649 → 701
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    3. XM_039093361.2 → XP_038949289.1  tudor domain-containing protein 3 isoform X1

      Related
      ENSRNOP00000077267.2, ENSRNOT00000117994.2
      Conserved Domains (3) summary
      cd14282
      Location:287 → 325
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam08585
      Location:15 → 165
      RMI1_N; RecQ mediated genome instability protein
      cd20413
      Location:649 → 701
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    4. XM_039093365.2 → XP_038949293.1  tudor domain-containing protein 3 isoform X3

      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:556 → 608
      Tudor_TDRD3; Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins

    RNA

    1. XR_005493732.2 RNA Sequence

    2. XR_005493733.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q66HC1.1 GenPept UniProtKB/Swiss-Prot:Q66HC1

    Gene LinkOut

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

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