TDRKH tudor and KH domain containing [Homo sapiens (human)] - Gene

Summary

Official Symbol: TDRKHprovided by HGNC
Official Full Name: tudor and KH domain containingprovided by HGNC
Primary source: HGNC:HGNC:11713
See related: Ensembl:ENSG00000182134 MIM:609501; AllianceGenome:HGNC:11713
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
Also known as: TDRD2
Summary: Predicted to enable RNA binding activity. Predicted to be involved in several processes, including P granule organization; male meiotic nuclear division; and piRNA processing. Located in mitochondrion. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in testis (RPKM 11.8), brain (RPKM 4.0) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q21.3

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (151766486..151790534, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (150889872..150914019, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (151744044..151763010, complement)

Chromosome 1 - NC_000001.11 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 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?

Whole genome sequencing identifies a homozygous splicing variant in TDRKH segregating with non-obstructive azoospermia in an Iranian family.
Title: Whole genome sequencing identifies a homozygous splicing variant in TDRKH segregating with non-obstructive azoospermia in an Iranian family.
TDRKH missense mutation segregates with dominant distal hereditary motor neuropathy in a four generation pedigree.
Title: TDRKH is a candidate gene for an autosomal dominant distal hereditary motor neuropathy.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Tudor domain proteins interact with arginine-glycine-rich motifs in a methylarginine-dependent manner.
Title: Tudor domains bind symmetrical dimethylated arginines.

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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

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

SHGC-155176 (e-PCR)
- UniSTS:182720

SHGC-155178 (e-PCR)
- UniSTS:182722

RH69511 (e-PCR)
- UniSTS:92897

RH102157 (e-PCR)
- UniSTS:96491

D1S2120 (e-PCR)
- UniSTS:151795

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA 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
involved_in fertilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in male meiotic nuclear division	ISS Inferred from Sequence or Structural Similarity more info
involved_in piRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in piRNA processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in spermatogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in P granule	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	HTP more info	PubMed
located_in mitochondrion	ISS Inferred from Sequence or Structural Similarity more info
located_in pi-body	ISS Inferred from Sequence or Structural Similarity more info
located_in piP-body	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: tudor and KH domain-containing protein

Names: putative RNA binding protein; tudor domain containing 2; 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_001083963.1 → NP_001077432.1 tudor and KH domain-containing protein isoform a

See identical proteins and their annotated locations for NP_001077432.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 all encode isoform a.

Source sequence(s)

AK226092, BC022467, DA796638

Consensus CDS

CCDS41394.1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Related

ENSP00000395718.2, ENST00000458431.6

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561
NM_001083964.1 → NP_001077433.1 tudor and KH domain-containing protein isoform b

See identical proteins and their annotated locations for NP_001077433.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an alternate inframe segment in the coding region compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.

Source sequence(s)

AK226092, BC022467, DA796638

Consensus CDS

CCDS41395.1

UniProtKB/TrEMBL

B4DZR8

Related

ENSP00000357817.3, ENST00000368825.7

Conserved Domains (4) summary

cd04508
Location:312 → 359

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 ...

pfam00013
Location:54 → 112

KH_1; KH domain

pfam00567
Location:258 → 377

TUDOR; Tudor domain

pfam10573
Location:147 → 204

UPF0561; uncharacterized protein family UPF0561
NM_001083965.2 → NP_001077434.1 tudor and KH domain-containing protein isoform a

See identical proteins and their annotated locations for NP_001077434.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2, and 3 all encode isoform a.

Source sequence(s)

AF227192, AK226092, AL589765, BC022467, DA796638

Consensus CDS

CCDS41394.1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Related

ENSP00000357815.3, ENST00000368824.8

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561
NM_006862.4 → NP_006853.2 tudor and KH domain-containing protein isoform a

See identical proteins and their annotated locations for NP_006853.2

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 3' UTR compared to variant 1. Variants 1, 2, and 3 all encode isoform a.

Source sequence(s)

AF119121, AL589765, BC032690, DA796638

Consensus CDS

CCDS41394.1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Related

ENSP00000357819.6, ENST00000368827.10

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561

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_000001.11 Reference GRCh38.p14 Primary Assembly

Range

151766486..151790534 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047441989.1 → XP_047297945.1 tudor and KH domain-containing protein isoform X1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6
XM_047442008.1 → XP_047297964.1 tudor and KH domain-containing protein isoform X1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6
XM_017000123.3 → XP_016855612.1 tudor and KH domain-containing protein isoform X1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561
XM_017000126.2 → XP_016855615.1 tudor and KH domain-containing protein isoform X1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561
XM_017000127.2 → XP_016855616.1 tudor and KH domain-containing protein isoform X1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561
XM_017000128.2 → XP_016855617.1 tudor and KH domain-containing protein isoform X2

UniProtKB/TrEMBL

B4DJ68

Conserved Domains (2) summary

cd04508
Location:133 → 180

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:79 → 198

TUDOR; Tudor domain
XM_017000124.2 → XP_016855613.1 tudor and KH domain-containing protein isoform X1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561
XM_017000125.2 → XP_016855614.1 tudor and KH domain-containing protein isoform X1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Related

ENSP00000357812.1, ENST00000368822.5

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561
XM_017000122.3 → XP_016855611.1 tudor and KH domain-containing protein isoform X1

UniProtKB/Swiss-Prot

D3DV24, Q5SZR3, Q5SZR5, Q8N582, Q9NYV5, Q9Y2W6

UniProtKB/TrEMBL

B4DZR8

Conserved Domains (4) summary

cd04508
Location:357 → 404

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 ...

cd00105
Location:54 → 116

KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...

pfam00567
Location:303 → 422

TUDOR; Tudor domain

pfam10573
Location:192 → 249

UPF0561; uncharacterized protein family UPF0561