TDRD6 tudor domain containing 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TDRD6provided by HGNC
Official Full Name: tudor domain containing 6provided by HGNC
Primary source: HGNC:HGNC:21339
See related: Ensembl:ENSG00000180113 MIM:611200; AllianceGenome:HGNC:21339
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TDR2; CT41.2; SPATA36; NY-CO-45; bA446F17.4
Summary: This gene encodes a tudor domain-containing protein and component of the chromatoid body, a type of ribonucleoprotein granule present in male germ cells. Studies in rodents have demonstrated a role for the encoded protein in spermiogenesis and the nonsense mediated decay (NMD) pathway. This protein is a major autoantigen in human patients with autoimmune polyendocrine syndrome type 1 (APS1). [provided by RefSeq, Oct 2016]
Expression: Biased expression in testis (RPKM 11.7), thyroid (RPKM 1.3) and 5 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p12.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (46680268..46704319)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (46517917..46541966)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (46648005..46672056)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Bi-allelic variants in chromatoid body protein TDRD6 cause spermiogenesis defects and severe oligoasthenoteratozoospermia in humans.
Title: Bi-allelic variants in chromatoid body protein TDRD6 cause spermiogenesis defects and severe oligoasthenoteratozoospermia in humans.
Whole-exome sequencing results in a patient with oligoasthenoteratozoospermia (OAT) from a consanguineous family identified a rare homozygous variant in TDRD6 which co-segregated with the OAT phenotype.
Title: TDRD6 is associated with oligoasthenoteratozoospermia by sequencing the patient from a consanguineous family.

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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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Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in P granule organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in piRNA processing	IBA Inferred from Biological aspect of Ancestor 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 chromatoid body	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: tudor domain-containing protein 6

Names: antigen NY-CO-45; cancer/testis antigen 41.2; spermatogenesis associated 36

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.

Genomic

NG_051941.1 RefSeqGene

Range

12618..29052

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001010870.3 → NP_001010870.1 tudor domain-containing protein 6 isoform 1

See identical proteins and their annotated locations for NP_001010870.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).

Source sequence(s)

AK131455, AL591242

Consensus CDS

CCDS34470.1

UniProtKB/Swiss-Prot

B3KWU2, F5H5M3, O60522, Q5HYB1, Q5VTS4, Q6ZMX5

Related

ENSP00000346065.5, ENST00000316081.11

Conserved Domains (2) summary

cd04508
Location:1356 → 1401

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:1301 → 1422

TUDOR; Tudor domain
NM_001168359.2 → NP_001161831.1 tudor domain-containing protein 6 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AK125838, AK131455, AL591242

Consensus CDS

CCDS55017.1

UniProtKB/Swiss-Prot

O60522

Related

ENSP00000443299.1, ENST00000544460.5

Conserved Domains (2) summary

cd04508
Location:1356 → 1401

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:1301 → 1422

TUDOR; Tudor domain

RNA

NR_144468.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 5' exon compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.

Source sequence(s)

AL591242, CR936792