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tdrd1 tudor domain containing 1 [ Danio rerio (zebrafish) ]

Gene ID: 553522, updated on 2-Nov-2024

Summary

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Official Symbol
tdrd1provided by ZNC
Official Full Name
tudor domain containing 1provided by ZNC
Primary source
ZFIN:ZDB-GENE-070803-1
See related
Ensembl:ENSDARG00000007465 AllianceGenome:ZFIN:ZDB-GENE-070803-1
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
im:7155161
Summary
Enables piRNA binding activity. Acts upstream of or within P granule organization. Predicted to be located in pi-body. Predicted to be active in P granule. Is expressed in oocyte stage I; oocyte stage II; primordial germ cell; and testis. Orthologous to human TDRD1 (tudor domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See tdrd1 in Genome Data Viewer
Location:
chromosome: 12
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 12 NC_007123.7 (30345835..30359498, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 12 NC_007123.6 (30230933..30244596, complement)

Chromosome 12 - NC_007123.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108191726 Neighboring gene actin filament associated protein 1-like 2 Neighboring gene kelch repeat and BTB domain-containing protein 13 Neighboring gene von Willebrand factor A domain containing 2 Neighboring gene si:ch211-225b10.3 Neighboring gene si:ch211-225b10.4

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. Huang HY, et al. EMBO J, 2011 Jul 8. PMID 21743441, Free PMC Article
  2. Comparative studies on duplicated tdrd7 paralogs in teleosts: Molecular evolution caused neo-functionalization. Wang B, et al. Comp Biochem Physiol Part D Genomics Proteomics, 2019 Jun. PMID 31059868
  3. m(6)A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Zhao BS, et al. Nature, 2017 Feb 23. PMID 28192787, Free PMC Article
  4. tdrd1 is a germline-specific and sexually dimorphically expressed gene in Paralichthys olivaceus. Zhao J, et al. Gene, 2018 Oct 5. PMID 29920365
  5. Control over the morphology and segregation of Zebrafish germ cell granules during embryonic development. Strasser MJ, et al. BMC Dev Biol, 2008 May 28. PMID 18507824, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables piRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
acts_upstream_of_or_within P granule organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in germ cell development ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within meiotic cell cycle IEA
Inferred from Electronic Annotation
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
  
acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing IEA
Inferred from Electronic Annotation
more info
  
involved_in retrotransposon silencing by piRNA-directed DNA methylation 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 P granule ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in pi-body ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
tudor domain-containing protein 1

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)

  1. NM_001164028.1 → NP_001157500.1  tudor domain-containing protein 1

    See identical proteins and their annotated locations for NP_001157500.1

    Status: PROVISIONAL

    Source sequence(s)
    CR932360
    UniProtKB/Swiss-Prot
    Q58EK5
    UniProtKB/TrEMBL
    A0A8M9QMI9, F1Q7S6
    Related
    ENSDARP00000127267.1, ENSDART00000152981.3
    Conserved Domains (2) summary
    pfam00567
    Location:404 → 523
    TUDOR; Tudor domain
    pfam01753
    Location:83 → 119
    zf-MYND; MYND finger

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007123.7 Reference GRCz11 Primary Assembly

    Range
    30345835..30359498 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_068224596.1 → XP_068080697.1  tudor domain-containing protein 1 isoform X2

    Related
    ENSDARP00000148308.1, ENSDART00000189988.1

  2. XM_021480110.2 → XP_021335785.1  tudor domain-containing protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58EK5
    UniProtKB/TrEMBL
    A0A8M9QMI9, F1Q7S6
    Related
    ENSDARP00000150322.1, ENSDART00000192628.1
    Conserved Domains (2) summary
    pfam00567
    Location:404 → 523
    TUDOR; Tudor domain
    pfam01753
    Location:83 → 119
    zf-MYND; MYND finger

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394851.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    197244..210882 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q58EK5.2 GenPept UniProtKB/Swiss-Prot:Q58EK5

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