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ddx4 DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 [ Danio rerio (zebrafish) ]

Gene ID: 30263, updated on 21-Apr-2024

Summary

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Official Symbol
ddx4provided by ZNC
Official Full Name
DEAD (Asp-Glu-Ala-Asp) box polypeptide 4provided by ZNC
Primary source
ZFIN:ZDB-GENE-990415-272
See related
Ensembl:ENSDARG00000014373 AllianceGenome:ZFIN:ZDB-GENE-990415-272
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
vas; vlg; vasa; wu:fi24g05; zgc:109812; zgc:158535
Summary
Predicted to enable RNA binding activity and RNA helicase activity. Acts upstream of or within germ cell development; gonad development; and regulation of meiotic cell cycle. Located in P granule. Is expressed in several structures, including blastodisc; germ line cell; reproductive system; shield; and unfertilized egg. Orthologous to human DDX4 (DEAD-box helicase 4). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 10
Exon count:
27
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 10 NC_007121.7 (6884126..6905588)
105 previous assembly GRCz10 (GCF_000002035.5) 10 NC_007121.6 (6925426..6946885)

Chromosome 10 - NC_007121.7Genomic Context describing neighboring genes Neighboring gene macrophage immunometabolism regulator Neighboring gene diphosphoinositol pentakisphosphate kinase 2 Neighboring gene solute carrier family 38 member 9 Neighboring gene SH2 domain containing 4A

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
  • 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. Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis. Bogoch Y, et al. Front Cell Dev Biol, 2022. PMID 35733854, Free PMC Article
  2. Germline Specific Expression of a vasa Homologue Gene in the Viviparous Fish Black Rockfish (Sebastes schlegelii) and Functional Analysis of the vasa 3' Untranslated Region. Zhou L, et al. Front Cell Dev Biol, 2020. PMID 33330452, Free PMC Article
  3. Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish. Redl S, et al. Development, 2021 Jan 20. PMID 33298460, Free PMC Article
  4. Preservation of zebrafish genetic resources through testis cryopreservation and spermatogonia transplantation. Marinović Z, et al. Sci Rep, 2019 Sep 25. PMID 31554831, Free PMC Article
  5. Visualization of Turbot (Scophthalmus maximus) Primordial Germ Cells in vivo Using Fluorescent Protein Mediated by the 3' Untranslated Region of nanos3 or vasa Gene. Zhou L, et al. Mar Biotechnol (NY), 2019 Oct. PMID 31502176

See all (229) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Bucky Ball Is a Novel Zebrafish Vasa ATPase Activator.
    Title: Bucky Ball Is a Novel Zebrafish Vasa ATPase Activator.
  2. Nanog suppresses the expression of vasa by directly regulating nlk1 in the early zebrafish embryo
    Title: Nanog suppresses the expression of vasa by directly regulating nlk1 in the early zebrafish embryo.
  3. studies provide insight into the function of zebrafish vasa during female meiosis, differentiation, and maintenance of germ-line stem cells.
    Title: Zebrafish vasa is required for germ-cell differentiation and maintenance.
  4. Gene includes a peculiar tandem repeat with three units each containing several tandemly arranged RNA-binding motifs (RGG boxes).
    Title: The vasa locus in zebrafish: multiple RGG boxes from duplications.
  5. characterisation of the zebrafish vasa locus
    Title: Expression of a vas::EGFP transgene in primordial germ cells of the zebrafish.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Clone Names

  • MGC158535

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in gamete generation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in germ cell development IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within germ cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within gonad development IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within regulation of meiotic cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in P granule IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in P granule IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
probable ATP-dependent RNA helicase DDX4
Names
vasa homolog
NP_571132.1
XP_005156510.1
XP_017213415.1
XP_017213416.1
XP_021334777.1
XP_021334778.1
XP_021334779.1
XP_021334780.1

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_131057.1 → NP_571132.1  probable ATP-dependent RNA helicase DDX4

    See identical proteins and their annotated locations for NP_571132.1

    Status: PROVISIONAL

    Source sequence(s)
    AB005147
    UniProtKB/TrEMBL
    O42107
    Conserved Domains (3) summary
    smart00487
    Location:292 → 506
    DEXDc; DEAD-like helicases superfamily
    cd00268
    Location:279 → 493
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:514 → 624
    Helicase_C; Helicase conserved C-terminal domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007121.7 Reference GRCz11 Primary Assembly

    Range
    6884126..6905588
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021479102.1 → XP_021334777.1  probable ATP-dependent RNA helicase DDX4 isoform X4

    UniProtKB/TrEMBL
    A0A8M9PTC4
    Related
    ENSDARP00000096157.4, ENSDART00000105384.5
    Conserved Domains (1) summary
    COG0513
    Location:233 → 633
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

  2. XM_017357927.2 → XP_017213416.1  probable ATP-dependent RNA helicase DDX4 isoform X3

    UniProtKB/TrEMBL
    A0A8M6Z8Q8

  3. XM_005156453.4 → XP_005156510.1  probable ATP-dependent RNA helicase DDX4 isoform X1

    See identical proteins and their annotated locations for XP_005156510.1

    UniProtKB/TrEMBL
    A0A8M2B2J0, Q8QGG8
    Related
    ENSDARP00000125001.1, ENSDART00000149334.3
    Conserved Domains (3) summary
    smart00487
    Location:291 → 505
    DEXDc; DEAD-like helicases superfamily
    cd00268
    Location:278 → 492
    DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...
    pfam00271
    Location:513 → 623
    Helicase_C; Helicase conserved C-terminal domain

  4. XM_017357926.2 → XP_017213415.1  probable ATP-dependent RNA helicase DDX4 isoform X2

    UniProtKB/TrEMBL
    A0A8M6Z2W1

  5. XM_021479104.1 → XP_021334779.1  probable ATP-dependent RNA helicase DDX4 isoform X6

    UniProtKB/TrEMBL
    A0A8M9QBU4
    Related
    ENSDARP00000110084.2, ENSDART00000125262.3
    Conserved Domains (1) summary
    COG0513
    Location:221 → 621
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

  6. XM_021479103.1 → XP_021334778.1  probable ATP-dependent RNA helicase DDX4 isoform X5

    UniProtKB/TrEMBL
    A0A8M9Q5S2
    Related
    ENSDARP00000124026.1, ENSDART00000149095.3
    Conserved Domains (1) summary
    COG0513
    Location:232 → 632
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

  7. XM_021479105.1 → XP_021334780.1  probable ATP-dependent RNA helicase DDX4 isoform X7

    UniProtKB/TrEMBL
    A0A8M9QKJ0
    Related
    ENSDARP00000123870.1, ENSDART00000148772.3
    Conserved Domains (1) summary
    COG0513
    Location:220 → 620
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
Nucleotide Protein Strain
Heading Accession and Version

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