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DDX4 DEAD-box helicase 4 [ Homo sapiens (human) ]

Gene ID: 54514, updated on 14-Nov-2024

Summary

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Official Symbol
DDX4provided by HGNC
Official Full Name
DEAD-box helicase 4provided by HGNC
Primary source
HGNC:HGNC:18700
See related
Ensembl:ENSG00000152670 MIM:605281; AllianceGenome:HGNC:18700
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
VASA
Summary
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a homolog of VASA proteins in Drosophila and several other species. The gene is specifically expressed in the germ cell lineage in both sexes and functions in germ cell development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
Expression
Restricted expression toward testis (RPKM 81.5) See more
Orthologs
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Genomic context

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See DDX4 in Genome Data Viewer
Location:
5q11.2
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (55738061..55817157)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (56566349..56645450)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (55033889..55112985)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900980 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:54899656-54900855 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:54921170-54921984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:54937991-54938490 Neighboring gene solute carrier family 38 member 9 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:54991046-54991576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22557 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:55008415-55009058 Neighboring gene S-phase kinase-associated protein 1-like Neighboring gene RNA, 5S ribosomal pseudogene 183 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:55098870-55099053 Neighboring gene heterogeneous nuclear ribonucleoprotein H1 pseudogene 3 Neighboring gene interleukin 31 receptor A Neighboring gene H3K4me1 hESC enhancers GRCh37_chr5:55198729-55199230 and GRCh37_chr5:55199231-55199730 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:55206646-55207845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:55218660-55219260 Neighboring gene interleukin 6 cytokine family signal transducer Neighboring gene CRISPRi-FlowFISH-validated IL6ST regulatory element GRCh37_chr5:55289559-55291877

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. The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells. Noyes C, et al. Commun Biol, 2023 Jan 18. PMID 36653474, Free PMC Article
  2. VASA is a specific marker for both normal and malignant human germ cells. Zeeman AM, et al. Lab Invest, 2002 Feb. PMID 11850529
  3. Differential expression of VASA gene in ejaculated spermatozoa from normozoospermic men and patients with oligozoospermia. Guo X, et al. Asian J Androl, 2007 May. PMID 17486274
  4. Germ cell specific protein VASA is over-expressed in epithelial ovarian cancer and disrupts DNA damage-induced G2 checkpoint. Hashimoto H, et al. Gynecol Oncol, 2008 Nov. PMID 18805576
  5. Tissue-specific differentially methylated regions of the human VASA gene are potentially associated with maturation arrest phenotype in the testis. Sugimoto K, et al. J Hum Genet, 2009 Aug. PMID 19629140

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Discriminating activities of DEAD-Box Helicase 41 from myeloid malignancy-associated germline variants by genetic rescue.
    Title: Discriminating activities of DEAD-Box Helicase 41 from myeloid malignancy-associated germline variants by genetic rescue.
  2. The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells.
    Title: The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells.
  3. VASA protein and gene expression analysis of human non-obstructive azoospermia and normal by immunohistochemistry, immunocytochemistry, and bioinformatics analysis.
    Title: VASA protein and gene expression analysis of human non-obstructive azoospermia and normal by immunohistochemistry, immunocytochemistry, and bioinformatics analysis.
  4. DEAD-Box Helicase 4 (Ddx4)(+) Stem Cells Sustain Tumor Progression in Non-Serous Ovarian Cancers.
    Title: DEAD-Box Helicase 4 (Ddx4)(+) Stem Cells Sustain Tumor Progression in Non-Serous Ovarian Cancers.
  5. This study clearly demonstrates that the C-terminus of DDX4 can be expressed on the cell surface despite its lack of a conventional membrane-targeting or secretory sequence.
    Title: Extracellular Localisation of the C-Terminus of DDX4 Confirmed by Immunocytochemistry and Fluorescence-Activated Cell Sorting.
  6. Described are adult ovarian cell populations. A fluorescence-activated cell sorting technique incorporating dual-detection of DDX4 with aldehyde dehydrogenase 1 (ALDH1) demonstrates the existence of two sub-populations of small DDX4-positive cells (approx. 7 microm diameter) with ALDH1 activity, distinguished by expression of differentially spliced DDX4 transcripts and of DAZL, a major regulator of germ cell differenti...
    Title: Initial characterisation of adult human ovarian cell populations isolated by DDX4 expression and aldehyde dehydrogenase activity.
  7. Four sterility-related genes, including BOLL, DDX4, HORMAD1, and MAEL, were found to have increased methylation at CpGs of the promoter regions and decreased mRNA expressions in nonobstructive azoospermia and hypospermatogenesis (HS) testis and are believed to be associated with HS.
    Title: Causes and Clinical Features of Infertile Men With Nonobstructive Azoospermia and Histopathologic Diagnosis of Hypospermatogenesis.
  8. positivity for DDX4 gene was detected in 17 of 39 males with nonobstructive azoospermia which was due to maturation arrest in 35.3% of cases, due to incomplete Sertoli cell only in 23.5% and due to complete Sertoli cell only in 41.2%.
    Title: Does detection of DDX4 mRNA in cell-free seminal plasma represents a reliable noninvasive germ cell marker in patients with nonobstructive azoospermia?
  9. Results suggest that DDX4 positively regulates cell cycle progression of diverse somatic-derived blood cancer cells, implying its broad contributions to the cancer cell phenotype.
    Title: Germline factor DDX4 functions in blood-derived cancer cell phenotypes.
  10. DDX4 cell-free seminal mRNA was absent in 44% of Sertoli cell-only syndrome cases diagnosed by testicular histopathology, but present in all patients presenting with maturation arrest or hypospermatogenesis
    Title: Discrimination and characterization of Sertoli cell-only syndrome in non-obstructive azoospermia using cell-free seminal DDX4.
Submit: New GeneRIF Correction See all GeneRIFs (22)

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)

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

  • MGC111074

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables ATP-dependent H2AZ histone chaperone activity IEA
Inferred from Electronic Annotation
more info
  
enables ATP-dependent H3-H4 histone complex chaperone activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA clamp loader activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chromatin extrusion motor activity IEA
Inferred from Electronic Annotation
more info
  
enables cohesin loader activity IEA
Inferred from Electronic Annotation
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables molecular condensate scaffold activity EXP
Inferred from Experiment
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin looping IEA
Inferred from Electronic Annotation
more info
  
involved_in flagellated sperm motility IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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
  
involved_in male meiosis I ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in male meiotic nuclear division ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in piRNA processing ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in transposable element silencing by piRNA-mediated DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_positive_effect transposable element silencing by piRNA-mediated heterochromatin formation 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 cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in pi-body ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in piP-body ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
probable ATP-dependent RNA helicase DDX4
Names
DEAD (Asp-Glu-Ala-Asp) box polypeptide 4
DEAD box protein 4
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4
vasa homolog
NP_001136021.1
NP_001160005.1
NP_001160006.1
NP_077726.1
XP_011541797.1
XP_011541799.1
XP_024301887.1
XP_054208812.1
XP_054208813.1
XP_054208814.1

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_001142549.2 → NP_001136021.1  probable ATP-dependent RNA helicase DDX4 isoform 2

    See identical proteins and their annotated locations for NP_001136021.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame coding exon, as compared to variant 1. The resulting isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC016632, AL137462, BC047455, DB457419, DB508256
    Consensus CDS
    CCDS47208.1
    UniProtKB/Swiss-Prot
    Q9NQI0
    Related
    ENSP00000334167.7, ENST00000353507.9
    Conserved Domains (1) summary
    COG0513
    Location:226 → 626
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

  2. NM_001166533.2 → NP_001160005.1  probable ATP-dependent RNA helicase DDX4 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame coding exon compared to variant 1 resulting in a shorter protein isoform (3).
    Source sequence(s)
    AC016632, BC030638, BC088362, BI559479, DB457419
    Consensus CDS
    CCDS54854.1
    UniProtKB/Swiss-Prot
    Q9NQI0
    Related
    ENSP00000425359.2, ENST00000514278.6
    Conserved Domains (1) summary
    COG0513
    Location:240 → 640
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

  3. NM_001166534.2 → NP_001160006.1  probable ATP-dependent RNA helicase DDX4 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has a novel first exon representing use of an alternate internal promoter site compared to variant 1. The predicted protein isoform (4) is shorter and has a distinct N-terminus.
    Source sequence(s)
    AC016632, AK093439, DB022413, DB051674, DB508256
    Consensus CDS
    CCDS54855.1
    UniProtKB/Swiss-Prot
    Q9NQI0
    Related
    ENSP00000423123.1, ENST00000511853.1
    Conserved Domains (3) summary
    smart00487
    Location:154 → 357
    DEXDc; DEAD-like helicases superfamily
    cd00268
    Location:141 → 355
    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:377 → 486
    Helicase_C; Helicase conserved C-terminal domain

  4. NM_024415.3 → NP_077726.1  probable ATP-dependent RNA helicase DDX4 isoform 1

    See identical proteins and their annotated locations for NP_077726.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC016632, BC088362, DB508256
    Consensus CDS
    CCDS3969.1
    UniProtKB/Swiss-Prot
    A8K8Q2, B3KSF4, D6RDK4, E9PCD8, Q5M7Z3, Q86VX0, Q9NQI0, Q9NT92, Q9NYB1
    Related
    ENSP00000424838.1, ENST00000505374.6
    Conserved Domains (1) summary
    COG0513
    Location:260 → 660
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    55738061..55817157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446119.2 → XP_024301887.1  probable ATP-dependent RNA helicase DDX4 isoform X1

    UniProtKB/Swiss-Prot
    A8K8Q2, B3KSF4, D6RDK4, E9PCD8, Q5M7Z3, Q86VX0, Q9NQI0, Q9NT92, Q9NYB1
    Conserved Domains (1) summary
    COG0513
    Location:260 → 660
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

  2. XM_011543495.3 → XP_011541797.1  probable ATP-dependent RNA helicase DDX4 isoform X2

    Conserved Domains (1) summary
    COG0513
    Location:234 → 634
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

  3. XM_011543497.3 → XP_011541799.1  probable ATP-dependent RNA helicase DDX4 isoform X3

    Conserved Domains (3) summary
    cd00268
    Location:244 → 458
    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 ...
    PTZ00110
    Location:131 → 633
    PTZ00110; helicase; Provisional
    pfam00271
    Location:480 → 589
    Helicase_C; Helicase conserved C-terminal domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    56566349..56645450
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352838.1 → XP_054208813.1  probable ATP-dependent RNA helicase DDX4 isoform X2

  2. XM_054352839.1 → XP_054208814.1  probable ATP-dependent RNA helicase DDX4 isoform X3

  3. XM_054352837.1 → XP_054208812.1  probable ATP-dependent RNA helicase DDX4 isoform X1

    UniProtKB/Swiss-Prot
    A8K8Q2, B3KSF4, D6RDK4, E9PCD8, Q5M7Z3, Q86VX0, Q9NQI0, Q9NT92, Q9NYB1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_019039.1: Suppressed sequence

    Description
    NM_019039.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NQI0.2 GenPept UniProtKB/Swiss-Prot:Q9NQI0

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