Tdrkh tudor and KH domain containing protein [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Tdrkhprovided by MGI
Official Full Name: tudor and KH domain containing proteinprovided by MGI
Primary source: MGI:MGI:1919884
See related: Ensembl:ENSMUSG00000041912 AllianceGenome:MGI:1919884
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: Tdrd2; 2700091C21Rik
Summary: Predicted to enable RNA binding activity. Involved in fertilization; gamete generation; and piRNA metabolic process. Located in mitochondrion; pi-body; and piP-body. Is expressed in central nervous system; reproductive system; and retina. Orthologous to human TDRKH (tudor and KH domain containing). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in testis adult (RPKM 43.0), CNS E18 (RPKM 3.9) and 5 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F2.1; 3 40.62 cM

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (94320551..94342161)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (94413243..94434854)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

we show that mitochondria-anchored TDRKH controls multiple steps of pachytene piRNA biogenesis in mice. TDRKH specifically recruits MIWI, but not MILI, to engage the piRNA pathway. It is required for the production of the entire MIWI-bound piRNA population and enables trimming of MILI-bound piRNAs.
Title: Mitochondrial membrane-based initial separation of MIWI and MILI functions during pachytene piRNA biogenesis.
Unlike most other Tudor domains TDRD2 preferentially recognizes an unmethylated arginine-rich sequence from PIWIL1.
Title: Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2.
Loss of Tdrkh is associated with impaired spermatogenesis.
Title: Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Endonuclease-mediated (2)
Targeted (5) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH137835 (e-PCR)
- UniSTS:219922

Tdrkh (e-PCR), detects polymorphism
- UniSTS:479045

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables nucleic acid 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 fertilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in male meiotic nuclear division	IMP Inferred from Mutant Phenotype more info	PubMed
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 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 cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in mitochondrion	HDA more info	PubMed
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in pi-body	IDA Inferred from Direct Assay more info	PubMed
located_in piP-body	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tudor and KH domain-containing protein

Names: tudor domain-containing protein 2

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_001357711.1 → NP_001344640.1 tudor and KH domain-containing protein isoform 1

Status: VALIDATED

Source sequence(s)

AC122808, BC057030

Consensus CDS

CCDS38534.1

UniProtKB/Swiss-Prot

Q80VL1

UniProtKB/TrEMBL

Q6PGG8

Related

ENSMUSP00000129635.2, ENSMUST00000166032.8

Conserved Domains (2) summary

pfam00013
Location:54 → 117

KH_1; KH domain

pfam00567
Location:303 → 422

TUDOR; Tudor domain
NM_001357712.1 → NP_001344641.1 tudor and KH domain-containing protein isoform 1

Status: VALIDATED

Source sequence(s)

AC122808

Consensus CDS

CCDS38534.1

UniProtKB/Swiss-Prot

Q80VL1

UniProtKB/TrEMBL

Q6PGG8

Related

ENSMUSP00000142561.2, ENSMUST00000197901.5

Conserved Domains (2) summary

pfam00013
Location:54 → 117

KH_1; KH domain

pfam00567
Location:303 → 422

TUDOR; Tudor domain
NM_001357713.1 → NP_001344642.1 tudor and KH domain-containing protein isoform 2

Status: VALIDATED

Source sequence(s)

AC122808

Consensus CDS

CCDS89664.1

UniProtKB/TrEMBL

A0A0G2JE08

Related

ENSMUSP00000142584.2, ENSMUST00000200486.5

Conserved Domains (1) summary

pfam00013
Location:54 → 117

KH_1; KH domain
NM_001357714.1 → NP_001344643.1 tudor and KH domain-containing protein isoform 3

Status: VALIDATED

Source sequence(s)

AC122808

Consensus CDS

CCDS89663.1

UniProtKB/TrEMBL

A0A0G2JFP5

Related

ENSMUSP00000143256.2, ENSMUST00000196386.5

Conserved Domains (1) summary

pfam00013
Location:54 → 117

KH_1; KH domain
NM_028307.2 → NP_082583.1 tudor and KH domain-containing protein isoform 1

See identical proteins and their annotated locations for NP_082583.1

Status: VALIDATED

Source sequence(s)

AC122808, BC049363, BE945944

Consensus CDS

CCDS38534.1

UniProtKB/Swiss-Prot

Q80VL1

UniProtKB/TrEMBL

Q6PGG8

Related

ENSMUSP00000041002.6, ENSMUST00000045245.10

Conserved Domains (2) summary

pfam00013
Location:54 → 117

KH_1; KH domain

pfam00567
Location:303 → 422

TUDOR; Tudor domain

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_000069.7 Reference GRCm39 C57BL/6J

Range

94320551..94342161

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030252843.2 → XP_030108703.1 tudor and KH domain-containing protein isoform X1

Conserved Domains (1) summary

pfam00567
Location:66 → 179

TUDOR; Tudor domain