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

Gene ID: 81550, updated on 4-Jun-2023

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 transcription, DNA-templated. Located in Golgi apparatus; cytosol; and nucleoplasm. Colocalizes with exon-exon junction complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 6.2), thyroid (RPKM 5.5) and 25 other tissues See more
Orthologs
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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_2023_03 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (60395533..60573879)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (59615225..59793547)
105.20220307 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 H3K27ac hESC enhancer GRCh37_chr13:60970714-60971226 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

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
  • 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. Structural plasticity of the TDRD3 Tudor domain probed by a fragment screening hit. Liu J, et al. FEBS J, 2018 Jun. PMID 29645362
  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. A dual-activity topoisomerase complex regulates mRNA translation and turnover. Su S, et al. Nucleic Acids Res, 2022 Jul 8. PMID 35748872, Free PMC Article
  4. TDRD3 is an antiviral restriction factor that promotes IFN signaling with G3BP1. Deater M, et al. PLoS Pathog, 2022 Jan. PMID 35085371, Free PMC Article
  5. RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals. Ahmad M, et al. Nucleic Acids Res, 2016 Jul 27. PMID 27257063, Free PMC Article

See all (67) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A dual-activity topoisomerase complex regulates mRNA translation and turnover.
    Title: A dual-activity topoisomerase complex regulates mRNA translation and turnover.
  2. 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.
  3. TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution.
    Title: TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. The TDRD3 is an effector molecule that promotes transcription by binding methylarginine marks on histone tails.
    Title: TDRD3 is an effector molecule for arginine-methylated histone marks.
  10. propose a contribution of Tdrd3 to FMRP-mediated translational repression and suggest that the loss of the FMRP-Tdrd3 interaction caused by the I304N mutation might contribute to the pathogenesis of Fragile X syndrome
    Title: Tdrd3 is a novel stress granule-associated protein interacting with the Fragile-X syndrome protein FMRP.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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)

Genotypes

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 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
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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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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
    Q6P992, Q9H7E2
    UniProtKB/TrEMBL
    A0A024QZE0
    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
    Q6P992, Q9H7E2
    UniProtKB/TrEMBL
    A0A024QZE0
    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_2023_03

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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