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

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: mouse all
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Genomic context

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_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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?
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.
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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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH92050 (e-PCR)
- UniSTS:91400

DDX4 (e-PCR)
- UniSTS:505759

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 RNA helicase activity	IBA Inferred from Biological aspect of Ancestor 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 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
acts_upstream_of_positive_effect piRNA-mediated retrotransposon silencing by heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in retrotransposon silencing by piRNA-directed DNA methylation	ISS Inferred from Sequence or Structural Similarity 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 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

EC 3.6.4.13

NP_001160005.1

EC 3.6.4.13

NP_001160006.1

EC 3.6.4.13

NP_077726.1

EC 3.6.4.13

XP_011541797.1

EC 3.6.4.13

XP_011541799.1

EC 3.6.4.13

XP_024301887.1

EC 3.6.4.13

XP_054208812.1

EC 3.6.4.13

XP_054208813.1

EC 3.6.4.13

XP_054208814.1

EC 3.6.4.13

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)

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]
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]
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
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

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

55738061..55817157

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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]
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]
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

NC_060929.1 Alternate T2T-CHM13v2.0

Range

56566349..56645450

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054352838.1 → XP_054208813.1 probable ATP-dependent RNA helicase DDX4 isoform X2
XM_054352839.1 → XP_054208814.1 probable ATP-dependent RNA helicase DDX4 isoform X3
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

NM_019039.1: Suppressed sequence

Description

NM_019039.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.