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    TDRD3 tudor domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 81550, updated on 3-Nov-2024

    Summary

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    Official Symbol
    TDRD3provided by HGNC
    Official Full Name
    tudor domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:20612
    See related
    Ensembl:ENSG00000083544 MIM:614392; AllianceGenome:HGNC:20612
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables 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. Located in Golgi apparatus; cytosol; and nucleus. Part of DNA topoisomerase III-beta-TDRD3 complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 6.2), thyroid (RPKM 5.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TDRD3 in Genome Data Viewer
    Location:
    13q21.2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (60395533..60573879)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (59615225..59793547)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (60970591..61148013)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene TARDBP pseudogene 2 Neighboring gene uncharacterized LOC105370228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7800 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:60970714-60971226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7803 Neighboring gene uncharacterized LOC124903178 Neighboring gene uncharacterized LOC124903274 Neighboring gene Sharpr-MPRA regulatory region 4317 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:61159285-61159859 Neighboring gene uncharacterized LOC105370230 Neighboring gene RNA, 5S ribosomal pseudogene 31

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The TDRD3-USP9X complex and MIB1 regulate TOP3B homeostasis and prevent deleterious TOP3B cleavage complexes. Saha S, et al. Nat Commun, 2023 Nov 18. PMID 37980342, Free PMC Article
    2. Tudor Domain Containing Protein 3 Promotes Tumorigenesis and Invasive Capacity of Breast Cancer Cells. Morettin A, et al. Sci Rep, 2017 Jul 11. PMID 28698590, Free PMC Article
    3. Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit. Liu J, et al. FEBS J, 2018 Jun. PMID 29645362
    4. PRMT1 and TDRD3 promote stress granule assembly by rebuilding the protein-RNA interaction network. Qin M, et al. Int J Biol Macromol, 2024 Oct. PMID 39097054
    5. Involvement of SYCP2L and TDRD3 gene variants on ovarian reserve and reproductive outcomes: a cross-sectional study. Rosa IR, et al. JBRA Assist Reprod, 2023 Sep 12. PMID 37417852, Free PMC Article

    See all (77) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PRMT1 and TDRD3 promote stress granule assembly by rebuilding the protein-RNA interaction network.
      Title: PRMT1 and TDRD3 promote stress granule assembly by rebuilding the protein-RNA interaction network.
    2. Involvement of SYCP2L and TDRD3 gene variants on ovarian reserve and reproductive outcomes: a cross-sectional study.
      Title: Involvement of SYCP2L and TDRD3 gene variants on ovarian reserve and reproductive outcomes: a cross-sectional study.
    3. A dual-activity topoisomerase complex regulates mRNA translation and turnover.
      Title: A dual-activity topoisomerase complex regulates mRNA translation and turnover.
    4. TDRD3 is an antiviral restriction factor that promotes IFN signaling with G3BP1.
      Title: TDRD3 is an antiviral restriction factor that promotes IFN signaling with G3BP1.
    5. TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution.
      Title: TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution.
    6. Our work depicts the structural plasticity of the TDRD3 Tudor domain and paves the way for the subsequent structure-guided discovery of selective inhibitors targeting Tudor domains
      Title: Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit.
    7. Study reports TDRD3 as a novel regulator of cell proliferation and invasion in breast cancer cells. Its depletion inhibits tumor formation and metastasis to the lung in vivo. Furthermore, TDRD3 regulates the expression of a number of key genes associated with promotion of breast cancer tumorigenesis and disease progression at the level of translation.
      Title: Tudor Domain Containing Protein 3 Promotes Tumorigenesis and Invasive Capacity of Breast Cancer Cells.
    8. Structural basis of the interaction between TOP3B and the TDRD3 auxiliary factor has been reported.
      Title: Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor.
    9. Top3b proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3b-polyribosome association requires TDRD3, which directly interacts with Top3beta and is present in animals but not bacteria or yeast.
      Title: RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals.
    10. The binding specificity and affinity of the Tudor domains of TDRD3, SMN and SPF30 proteins were characterized quantitatively.
      Title: Crystal structure of TDRD3 and methyl-arginine binding characterization of TDRD3, SMN and SPF30.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetic variants associated with breast size also influence breast cancer risk.
    EBI GWAS Catalog
    Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21007

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    part_of exon-exon junction complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    tudor domain-containing protein 3

    NCBI Reference Sequences (RefSeq)

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    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_001146070.2 → NP_001139542.1  tudor domain-containing protein 3 isoform 1

      See identical proteins and their annotated locations for NP_001139542.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer protein (isoform 1).
      Source sequence(s)
      AK024660, AL359920, BC030514, EU643838
      Consensus CDS
      CCDS53872.1
      UniProtKB/Swiss-Prot
      Q9H7E2
      Related
      ENSP00000367113.2, ENST00000377881.8
      Conserved Domains (3) summary
      cd04508
      Location:652 → 700
      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:41 → 162
      RMI1_N; RecQ mediated genome instability protein

    2. NM_001146071.1 → NP_001139543.1  tudor domain-containing protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001139543.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains a distinct 5' UTR and uses two different splice sites in its UTRs, compared to variant 1. These differences cause translation initiation at a downstream start codon. The encoded protein (isoform 2) is shorter than isoform 1.
      Source sequence(s)
      BG219444, BX537910
      Consensus CDS
      CCDS9441.1
      UniProtKB/Swiss-Prot
      B2MWP9, Q53XA6, Q6P992, Q9H7E2
      Related
      ENSP00000196169.3, ENST00000196169.7
      Conserved Domains (4) summary
      cd04508
      Location:559 → 607
      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:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam06003
      Location:523 → 647
      SMN; Survival motor neuron protein (SMN)
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein

    3. NM_030794.2 → NP_110421.1  tudor domain-containing protein 3 isoform 2

      See identical proteins and their annotated locations for NP_110421.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and uses a different splice site in its 5' UTR, compared to variant 1. These differences cause translation initiation at a downstream start codon. The encoded protein (isoform 2) is shorter than isoform 1.
      Source sequence(s)
      AA004370, AK024660, BG191408, BX537910
      Consensus CDS
      CCDS9441.1
      UniProtKB/Swiss-Prot
      B2MWP9, Q53XA6, Q6P992, Q9H7E2
      Related
      ENSP00000367126.2, ENST00000377894.6
      Conserved Domains (4) summary
      cd04508
      Location:559 → 607
      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:194 → 232
      UBA_TDRD3; UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins
      pfam06003
      Location:523 → 647
      SMN; Survival motor neuron protein (SMN)
      pfam08585
      Location:1 → 72
      RMI1_N; RecQ mediated genome instability protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      60395533..60573879
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047430685.1 → XP_047286641.1  tudor domain-containing protein 3 isoform X7

    2. XM_024449417.2 → XP_024305185.1  tudor domain-containing protein 3 isoform X8

      Conserved Domains (3) summary
      cd04508
      Location:559 → 607
      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: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

    3. XM_005266560.3 → XP_005266617.1  tudor domain-containing protein 3 isoform X8

      Conserved Domains (3) summary
      cd04508
      Location:559 → 607
      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: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

    4. XM_005266556.5 → XP_005266613.1  tudor domain-containing protein 3 isoform X3

      Conserved Domains (3) summary
      cd04508
      Location:652 → 700
      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:41 → 162
      RMI1_N; RecQ mediated genome instability protein

    5. XM_047430682.1 → XP_047286638.1  tudor domain-containing protein 3 isoform X4

    6. XM_047430688.1 → XP_047286644.1  tudor domain-containing protein 3 isoform X10

    7. XM_047430681.1 → XP_047286637.1  tudor domain-containing protein 3 isoform X1

    8. XM_024449416.2 → XP_024305184.2  tudor domain-containing protein 3 isoform X2

    9. XM_047430683.1 → XP_047286639.1  tudor domain-containing protein 3 isoform X5

    10. XM_047430687.1 → XP_047286643.1  tudor domain-containing protein 3 isoform X9

    11. XM_047430684.1 → XP_047286640.1  tudor domain-containing protein 3 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      59615225..59793547
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375047.1 → XP_054231022.1  tudor domain-containing protein 3 isoform X7

    2. XM_054375048.1 → XP_054231023.1  tudor domain-containing protein 3 isoform X8

    3. XM_054375049.1 → XP_054231024.1  tudor domain-containing protein 3 isoform X8

    4. XM_054375043.1 → XP_054231018.1  tudor domain-containing protein 3 isoform X3

    5. XM_054375044.1 → XP_054231019.1  tudor domain-containing protein 3 isoform X4

    6. XM_054375051.1 → XP_054231026.1  tudor domain-containing protein 3 isoform X10

    7. XM_054375041.1 → XP_054231016.1  tudor domain-containing protein 3 isoform X1

    8. XM_054375042.1 → XP_054231017.1  tudor domain-containing protein 3 isoform X2

    9. XM_054375045.1 → XP_054231020.1  tudor domain-containing protein 3 isoform X5

    10. XM_054375050.1 → XP_054231025.1  tudor domain-containing protein 3 isoform X9

    11. XM_054375046.1 → XP_054231021.1  tudor domain-containing protein 3 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H7E2.1 GenPept UniProtKB/Swiss-Prot:Q9H7E2

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