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

    Gene ID: 54514, updated on 9-Dec-2024

    Summary

    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
    NEW
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_001142549.2NP_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:226626
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    2. NM_001166533.2NP_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:240640
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    3. NM_001166534.2NP_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:154357
      DEXDc; DEAD-like helicases superfamily
      cd00268
      Location:141355
      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:377486
      Helicase_C; Helicase conserved C-terminal domain
    4. NM_024415.3NP_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:260660
      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_024446119.2XP_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:260660
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    2. XM_011543495.3XP_011541797.1  probable ATP-dependent RNA helicase DDX4 isoform X2

      Conserved Domains (1) summary
      COG0513
      Location:234634
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
    3. XM_011543497.3XP_011541799.1  probable ATP-dependent RNA helicase DDX4 isoform X3

      Conserved Domains (3) summary
      cd00268
      Location:244458
      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:131633
      PTZ00110; helicase; Provisional
      pfam00271
      Location:480589
      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_054352838.1XP_054208813.1  probable ATP-dependent RNA helicase DDX4 isoform X2

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

    3. XM_054352837.1XP_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.