Tdrd1 tudor domain containing 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tdrd1provided by MGI
Official Full Name: tudor domain containing 1provided by MGI
Primary source: MGI:MGI:1933218
See related: Ensembl:ENSMUSG00000025081 AllianceGenome:MGI:1933218
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: MTR-1
Summary: Predicted to enable metal ion binding activity. Involved in gamete generation; gene silencing by RNA; and piRNA metabolic process. Located in chromatoid body and pi-body. Part of ribonucleoprotein complex. Is expressed in several structures, including reproductive system. Orthologous to human TDRD1 (tudor domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in testis adult (RPKM 23.7) and limb E14.5 (RPKM 0.9) See more
Orthologs: human all
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Genomic context

Location:: 19 D2; 19 52.0 cM

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	19	NC_000085.7 (56814603..56858444)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	19	NC_000085.6 (56826171..56870012)

Chromosome 19 - NC_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TDRD1 can accommodate different peptides from different proteins, and can therefore act as a scaffold protein for complex assembly in the piRNA pathway.
Title: The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors.
Data suggest that the formation of complexes between MILI, MIWI and TDRD1/MTR-1 is critical for the integrated subcellular localizations of these proteins, and is presumably essential for spermatogenesis.
Title: Associations between PIWI proteins and TDRD1/MTR-1 are critical for integrated subcellular localization in murine male germ cells.
Tdrd1 ensures the entry of correct transcripts into the normal piRNA pool.
Title: Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile.
Results suggest that Mili interacts with Tdrd1 in the nuage and chromatoid body, and that this interaction does not contribute to piRNA biogenesis but represents a regulatory mechanism that is critical for spermatogenesis.
Title: Mili interacts with tudor domain-containing protein 1 in regulating spermatogenesis.
targeted mutation in Tudor domain containing 1/mouse tudor repeat 1 (Tdrd1/Mtr-1), a tudor-related gene in mice, leads to male sterility because of postnatal spermatogenic defects
Title: Tdrd1/Mtr-1, a tudor-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice.
isolated Mouse tudor repeat-1 (Mtr-1) which encodes a MYND domain and four copies of the tudor domain. Mtr-1 is expressed in germ-line cells and is most abundant in fetal prospermatogonia and postnatal primary spermatocytes.
Title: Mouse Tudor Repeat-1 (MTR-1) is a novel component of chromatoid bodies/nuages in male germ cells and forms a complex with snRNPs.
Tudor-related proteins, which contain multiple repeats of the Tudor domain, constitute an evolutionarily conserved class of nuage components in the germ-line, and their localization or accumulation to nuage is likely conferred by a Tudor domain structure
Title: Tudor-related proteins TDRD1/MTR-1, TDRD6 and TDRD7/TRAP: domain composition, intracellular localization, and function in male germ cells in mice.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Tdrd1 (e-PCR), detects polymorphism
- UniSTS:274199

G65212 (e-PCR)
- UniSTS:225881

G65786 (e-PCR)
- UniSTS:225923

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in P granule organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in germ cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within meiotic cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in piRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in piRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing	IEA Inferred from Electronic Annotation more info
involved_in siRNA-mediated retrotransposon silencing by heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in P granule	IBA Inferred from Biological aspect of Ancestor more info
located_in P granule	IDA Inferred from Direct Assay more info	PubMed
located_in chromatoid body	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in pi-body	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in synapse	EXP Inferred from Experiment more info	PubMed
is_active_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tudor domain-containing protein 1

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_001002238.2 → NP_001002238.1 tudor domain-containing protein 1

See identical proteins and their annotated locations for NP_001002238.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 3. All four variants encode the same protein.

Source sequence(s)

AC125150, AC158549

Consensus CDS

CCDS29922.1

UniProtKB/Swiss-Prot

A2VDG6, Q6F3G0, Q8CDN7, Q8K1G3, Q99MV1

Related

ENSMUSP00000107233.2, ENSMUST00000111606.8

Conserved Domains (3) summary

cd04508
Location:760 → 805

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 ...

pfam00567
Location:487 → 606

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
NM_001002240.2 → NP_001002240.1 tudor domain-containing protein 1

See identical proteins and their annotated locations for NP_001002240.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 3. All four variants encode the same protein.

Source sequence(s)

AC125150, AC158549

Consensus CDS

CCDS29922.1

UniProtKB/Swiss-Prot

A2VDG6, Q6F3G0, Q8CDN7, Q8K1G3, Q99MV1

Related

ENSMUSP00000077785.5, ENSMUST00000078723.11

Conserved Domains (3) summary

cd04508
Location:760 → 805

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 ...

pfam00567
Location:487 → 606

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
NM_001002241.2 → NP_001002241.1 tudor domain-containing protein 1

See identical proteins and their annotated locations for NP_001002241.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) represents the longest transcript. All four variants encode the same protein.

Source sequence(s)

AC125150, AC158549

Consensus CDS

CCDS29922.1

UniProtKB/Swiss-Prot

A2VDG6, Q6F3G0, Q8CDN7, Q8K1G3, Q99MV1

Related

ENSMUSP00000107231.2, ENSMUST00000111604.2

Conserved Domains (3) summary

cd04508
Location:760 → 805

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 ...

pfam00567
Location:487 → 606

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
NM_031387.3 → NP_113564.2 tudor domain-containing protein 1

See identical proteins and their annotated locations for NP_113564.2

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 3. All four variants encode the same protein.

Source sequence(s)

AC125150, AK029806

Consensus CDS

CCDS29922.1

UniProtKB/Swiss-Prot

A2VDG6, Q6F3G0, Q8CDN7, Q8K1G3, Q99MV1

Related

ENSMUSP00000112786.2, ENSMUST00000121249.8

Conserved Domains (3) summary

cd04508
Location:760 → 805

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 ...

pfam00567
Location:487 → 606

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger

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

NC_000085.7 Reference GRCm39 C57BL/6J

Range

56814603..56858444

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006527473.1 → XP_006527536.1 tudor domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_006527536.1

Conserved Domains (2) summary

pfam00567
Location:718 → 825

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
XM_006527478.1 → XP_006527541.1 tudor domain-containing protein 1 isoform X2

Conserved Domains (2) summary

pfam00567
Location:718 → 825

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
XM_006527475.4 → XP_006527538.1 tudor domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_006527538.1

Conserved Domains (2) summary

pfam00567
Location:718 → 825

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
XM_006527474.1 → XP_006527537.1 tudor domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_006527537.1

Conserved Domains (2) summary

pfam00567
Location:718 → 825

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
XM_006527476.2 → XP_006527539.1 tudor domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_006527539.1

Conserved Domains (2) summary

pfam00567
Location:718 → 825

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
XM_006527477.4 → XP_006527540.1 tudor domain-containing protein 1 isoform X1

See identical proteins and their annotated locations for XP_006527540.1

Conserved Domains (2) summary

pfam00567
Location:718 → 825

TUDOR; Tudor domain

pfam01753
Location:163 → 199

zf-MYND; MYND finger
XM_006527479.3 → XP_006527542.1 tudor domain-containing protein 1 isoform X3

Conserved Domains (2) summary

pfam00567
Location:613 → 720

TUDOR; Tudor domain

pfam01753
Location:58 → 94

zf-MYND; MYND finger