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TDRD5 tudor domain containing 5 [ Homo sapiens (human) ]

Gene ID: 163589, updated on 5-Mar-2024

Summary

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Official Symbol
TDRD5provided by HGNC
Official Full Name
tudor domain containing 5provided by HGNC
Primary source
HGNC:HGNC:20614
See related
Ensembl:ENSG00000162782 MIM:617748; AllianceGenome:HGNC:20614
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
TUDOR3
Summary
Predicted to be involved in DNA methylation involved in gamete generation; P granule organization; and spermatid development. Predicted to be located in chromatoid body and pi-body. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward testis (RPKM 11.6) See more
Orthologs
mouse all
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Genomic context

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See TDRD5 in Genome Data Viewer
Location:
1q25.2
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (179591613..179691272)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (178946579..179047028)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (179560748..179660407)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, U5F small nuclear 2, pseudogene Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2152 Neighboring gene uncharacterized LOC105371635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2153 Neighboring gene uncharacterized LOC128071543 Neighboring gene family with sequence similarity 163 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179713723-179714415 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:179757425-179757972 Neighboring gene microRNA 12116

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. Testicular expression of TDRD1, TDRD5, TDRD9 and TDRD12 in azoospermia. Babakhanzadeh E, et al. BMC Med Genet, 2020 Feb 14. PMID 32059713, Free PMC Article
  2. TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice. Yabuta Y, et al. J Cell Biol, 2011 Mar 7. PMID 21383078, Free PMC Article
  3. Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study. Ehret GB, et al. Eur J Hum Genet, 2009 Dec. PMID 19536175, Free PMC Article
  4. Molecular genetics of successful smoking cessation: convergent genome-wide association study results. Uhl GR, et al. Arch Gen Psychiatry, 2008 Jun. PMID 18519826, Free PMC Article
  5. Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage. Drissi R, et al. Mol Cell Proteomics, 2015 Jul. PMID 25963833, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Here we evaluate gene and protein expression levels of four key TDRDs (TDRD1, TDRD5, TDRD9 and TDRD12) in testicular biopsy samples obtained from men with obstructive azoospermia (OA, n = 29), as controls, and various types of non-obstructive azoospermia containing hypospermatogenesis (HP, 28), maturation arrest (MA, n = 30), and Sertoli cell-only syndrome (SCOS, n = 32) as cases.
    Title: Testicular expression of TDRD1, TDRD5, TDRD9 and TDRD12 in azoospermia.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study.
Submit: New GeneRIF Correction

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ34823, MGC163404

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 P granule organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in piRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in siRNA-mediated retrotransposon silencing by heterochromatin formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatid development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatogenesis IBA
Inferred from Biological aspect of Ancestor
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 pi-body ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in synapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
tudor domain-containing protein 5
Names
testicular tissue protein Li 194

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_053092.1 RefSeqGene

    Range
    5220..104660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001199085.3 → NP_001186014.1  tudor domain-containing protein 5 isoform 1

    See identical proteins and their annotated locations for NP_001186014.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 2 both encode the same isoform (1).
    Source sequence(s)
    AK127370, BC089387, BC144058, DA418635
    Consensus CDS
    CCDS55663.1
    UniProtKB/Swiss-Prot
    Q8NAT2
    Related
    ENSP00000406052.1, ENST00000444136.6
    Conserved Domains (5) summary
    cd04508
    Location:529 → 575
    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 ...
    cd09975
    Location:132 → 201
    LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09976
    Location:296 → 369
    LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09985
    Location:4 → 98
    LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
    pfam00567
    Location:471 → 594
    TUDOR; Tudor domain

  2. NM_001199089.3 → NP_001186018.1  tudor domain-containing protein 5 isoform 1

    See identical proteins and their annotated locations for NP_001186018.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (1).
    Source sequence(s)
    AK127370, BC043368, BC089387, BC130532, DA418635, DB073297
    Consensus CDS
    CCDS55663.1
    UniProtKB/Swiss-Prot
    Q8NAT2
    Conserved Domains (5) summary
    cd04508
    Location:529 → 575
    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 ...
    cd09975
    Location:132 → 201
    LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09976
    Location:296 → 369
    LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09985
    Location:4 → 98
    LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
    pfam00567
    Location:471 → 594
    TUDOR; Tudor domain

  3. NM_001199091.2 → NP_001186020.1  tudor domain-containing protein 5 isoform 2

    See identical proteins and their annotated locations for NP_001186020.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an in-frame coding exon compared to variant 1. The resulting isoform (2) lacks an internal segment compared to isoform 1. Variants 3, 4, and 6 all encode the same isoform (2).
    Source sequence(s)
    AK126889, AL160286, BC043368, BC089387
    Consensus CDS
    CCDS1332.1
    UniProtKB/Swiss-Prot
    A1L4G5, B7ZLV0, Q5EBN4, Q5VTV0, Q6ZSK2, Q8NAT2
    UniProtKB/TrEMBL
    A0A024R910, A0A140VJW7
    Related
    ENSP00000356586.1, ENST00000367614.5
    Conserved Domains (4) summary
    cd09975
    Location:132 → 201
    LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09976
    Location:296 → 369
    LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09985
    Location:4 → 98
    LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
    pfam00567
    Location:471 → 594
    TUDOR; Tudor domain

  4. NM_001199092.2 → NP_001186021.1  tudor domain-containing protein 5 isoform 3

    See identical proteins and their annotated locations for NP_001186021.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks multiple exons from the 5' end and contains an alternate 5' exon, and lacks an in-frame coding exon compared to variant 1. The resulting isoform (3) has a shorter N-terminus and lacks an internal segment compared to isoform 1.
    Source sequence(s)
    AK092142, BC089387
    UniProtKB/TrEMBL
    A0A0C4DG74
    Conserved Domains (2) summary
    cd04508
    Location:84 → 130
    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:26 → 149
    TUDOR; Tudor domain

  5. NM_001349923.1 → NP_001336852.1  tudor domain-containing protein 5 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and 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. Variants 3, 4, and 6 all encode the same isoform (2).
    Source sequence(s)
    AL160286, AL590987
    Consensus CDS
    CCDS1332.1
    UniProtKB/Swiss-Prot
    A1L4G5, B7ZLV0, Q5EBN4, Q5VTV0, Q6ZSK2, Q8NAT2
    UniProtKB/TrEMBL
    A0A024R910, A0A140VJW7
    Conserved Domains (4) summary
    cd09975
    Location:132 → 201
    LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09976
    Location:296 → 369
    LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09985
    Location:4 → 98
    LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
    pfam00567
    Location:471 → 594
    TUDOR; Tudor domain

  6. NM_173533.5 → NP_775804.2  tudor domain-containing protein 5 isoform 2

    See identical proteins and their annotated locations for NP_775804.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame coding exon compared to variant 1. The resulting isoform (2) lacks an internal segment compared to isoform 1. Variants 3, 4, and 6 all encode the same isoform (2).
    Source sequence(s)
    AK127370, BC043368, BC089387, DA418635
    Consensus CDS
    CCDS1332.1
    UniProtKB/Swiss-Prot
    A1L4G5, B7ZLV0, Q5EBN4, Q5VTV0, Q6ZSK2, Q8NAT2
    UniProtKB/TrEMBL
    A0A024R910, A0A140VJW7
    Related
    ENSP00000294848.8, ENST00000294848.12
    Conserved Domains (4) summary
    cd09975
    Location:132 → 201
    LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09976
    Location:296 → 369
    LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09985
    Location:4 → 98
    LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
    pfam00567
    Location:471 → 594
    TUDOR; Tudor domain

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    179591613..179691272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047447750.1 → XP_047303706.1  tudor domain-containing protein 5 isoform X1

  2. XM_005244934.2 → XP_005244991.1  tudor domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_005244991.1

    UniProtKB/Swiss-Prot
    Q8NAT2
    Conserved Domains (5) summary
    cd04508
    Location:529 → 575
    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 ...
    cd09975
    Location:132 → 201
    LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09976
    Location:296 → 369
    LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09985
    Location:4 → 98
    LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
    pfam00567
    Location:471 → 594
    TUDOR; Tudor domain

  3. XM_047447752.1 → XP_047303708.1  tudor domain-containing protein 5 isoform X2

    UniProtKB/Swiss-Prot
    A1L4G5, B7ZLV0, Q5EBN4, Q5VTV0, Q6ZSK2, Q8NAT2
    UniProtKB/TrEMBL
    A0A024R910, A0A140VJW7

  4. XM_005244935.5 → XP_005244992.1  tudor domain-containing protein 5 isoform X1

    See identical proteins and their annotated locations for XP_005244992.1

    UniProtKB/Swiss-Prot
    Q8NAT2
    Conserved Domains (5) summary
    cd04508
    Location:529 → 575
    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 ...
    cd09975
    Location:132 → 201
    LOTUS_2_TDRD5; The second LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09976
    Location:296 → 369
    LOTUS_3_TDRD5; The third LOTUS domain on Tudor-containing protein 5 (TDRD5)
    cd09985
    Location:4 → 98
    LOTUS_1_TDRD5; The first LOTUS domain on Tudor-containing protein 5 (TDRD5)
    pfam00567
    Location:471 → 594
    TUDOR; Tudor domain

  5. XM_047447753.1 → XP_047303709.1  tudor domain-containing protein 5 isoform X2

    UniProtKB/Swiss-Prot
    A1L4G5, B7ZLV0, Q5EBN4, Q5VTV0, Q6ZSK2, Q8NAT2
    UniProtKB/TrEMBL
    A0A024R910, A0A140VJW7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    178946579..179047028
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334731.1 → XP_054190706.1  tudor domain-containing protein 5 isoform X2

  2. XM_054334729.1 → XP_054190704.1  tudor domain-containing protein 5 isoform X1

  3. XM_054334728.1 → XP_054190703.1  tudor domain-containing protein 5 isoform X1

  4. XM_054334732.1 → XP_054190707.1  tudor domain-containing protein 5 isoform X2

  5. XM_054334730.1 → XP_054190705.1  tudor domain-containing protein 5 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NAT2.3 GenPept UniProtKB/Swiss-Prot:Q8NAT2

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