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

Gene ID: 221400, updated on 5-Mar-2024

Summary

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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
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Genomic context

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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_000006.12Genomic Context describing neighboring genes Neighboring gene cytochrome P450 family 39 subfamily A member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46542802-46543302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:46543303-46543803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17273 Neighboring gene solute carrier family 25 member 27 Neighboring gene TDRD6 and SLC25A27 antisense RNA 1 Neighboring gene phospholipase A2 group VII Neighboring gene ankyrin repeat domain 66 Neighboring gene meprin A subunit alpha

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. TDRD6 is associated with oligoasthenoteratozoospermia by sequencing the patient from a consanguineous family. Sha YW, et al. Gene, 2018 Jun 15. PMID 29551503
  2. Pituitary autoantibodies in autoimmune polyendocrine syndrome type 1. Bensing S, et al. Proc Natl Acad Sci U S A, 2007 Jan 16. PMID 17215373, Free PMC Article
  3. Chromatoid Body Protein TDRD6 Supports Long 3' UTR Triggered Nonsense Mediated mRNA Decay. Fanourgakis G, et al. PLoS Genet, 2016 May. PMID 27149095, Free PMC Article
  4. Tudor-related proteins TDRD1/MTR-1, TDRD6 and TDRD7/TRAP: domain composition, intracellular localization, and function in male germ cells in mice. Hosokawa M, et al. Dev Biol, 2007 Jan 1. PMID 17141210
  5. Characterization of human colon cancer antigens recognized by autologous antibodies. Scanlan MJ, et al. Int J Cancer, 1998 May 29. PMID 9610721

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ43850, DKFZp781I1148

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

  1. NG_051941.1 RefSeqGene

    Range
    12618..29052
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  1. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    46680268..46704319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    46517917..46541966
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60522.2 GenPept UniProtKB/Swiss-Prot:O60522

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