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

Summary

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

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_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
A dual-activity topoisomerase complex regulates mRNA translation and turnover.
Title: A dual-activity topoisomerase complex regulates mRNA translation and turnover.
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.
TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution.
Title: TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH47176 (e-PCR)
- UniSTS:90153

SHGC-13721 (e-PCR)
- UniSTS:74875

WI-14979 (e-PCR)
- UniSTS:2217

RH11258 (e-PCR)
- UniSTS:87538

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	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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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)

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
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
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

NC_000013.11 Reference GRCh38.p14 Primary Assembly

Range

60395533..60573879

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047430685.1 → XP_047286641.1 tudor domain-containing protein 3 isoform X7
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
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
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
XM_047430682.1 → XP_047286638.1 tudor domain-containing protein 3 isoform X4
XM_047430688.1 → XP_047286644.1 tudor domain-containing protein 3 isoform X10
XM_047430681.1 → XP_047286637.1 tudor domain-containing protein 3 isoform X1
XM_024449416.2 → XP_024305184.2 tudor domain-containing protein 3 isoform X2
XM_047430683.1 → XP_047286639.1 tudor domain-containing protein 3 isoform X5
XM_047430687.1 → XP_047286643.1 tudor domain-containing protein 3 isoform X9
XM_047430684.1 → XP_047286640.1 tudor domain-containing protein 3 isoform X6