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

Gene ID: 54514, updated on 24-Dec-2019

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
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

Genomic context

See DDX4 in Genome Data Viewer
Location:
5q11.2
Exon count:
24
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (55737994..55817157)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (55033845..55112975)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378975 Neighboring gene solute carrier family 38 member 9 Neighboring gene S-phase kinase-associated protein 1 pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 183 Neighboring gene heterogeneous nuclear ribonucleoprotein H1 pseudogene 3 Neighboring gene interleukin 31 receptor A

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

Homology

Clone Names

  • MGC111074

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATPase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA helicase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA methylation involved in gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
 
cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
flagellated sperm motility IMP
Inferred from Mutant Phenotype
more info
PubMed 
gamete generation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
gene silencing by RNA IEA
Inferred from Electronic Annotation
more info
 
male meiosis I ISS
Inferred from Sequence or Structural Similarity
more info
 
male meiotic nuclear division ISS
Inferred from Sequence or Structural Similarity
more info
 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transposition ISS
Inferred from Sequence or Structural Similarity
more info
 
piRNA biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
piRNA metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
P granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 
pi-body ISS
Inferred from Sequence or Structural Similarity
more info
 
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

NCBI Reference Sequences (RefSeq)

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_001142549.1NP_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)
    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_001166533.1NP_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)
    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_001166534.1NP_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)
    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
    Q9NQI0
    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: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    55737994..55817157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543495.2XP_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]
  2. XM_011543497.2XP_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
  3. XM_024446119.1XP_024301887.1  probable ATP-dependent RNA helicase DDX4 isoform X1

    Conserved Domains (1) summary
    COG0513
    Location:260660
    SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

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.
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