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

    Gene ID: 163589, updated on 2-Nov-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 germ cell development and regulatory ncRNA-mediated gene silencing. Predicted to be located in chromatoid body and pi-body. Predicted to be active in P granule and synapse. [provided by Alliance of Genome Resources, Nov 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (179591613..179691272)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (178946579..179047028)
    RS_2024_09 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 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. Disruption of Tdrd5 decouples the stepwise processing of long precursor transcripts during pachytene PIWI-interacting RNA biogenesis. Sun YH, et al. Biol Reprod, 2018 Oct 1. PMID 29733347
    2. 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
    3. 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
    4. 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
    5. 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

    See all (17) 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 retrotransposon silencing by piRNA-directed DNA methylation 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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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