Human Gene DDX4 (ENST00000505374.6_7) from GENCODE V47lift37
  Description: DEAD-box helicase 4, transcript variant 1 (from RefSeq NM_024415.3)
Gencode Transcript: ENST00000505374.6_7
Gencode Gene: ENSG00000152670.19_15
Transcript (Including UTRs)
   Position: hg19 chr5:55,033,889-55,112,985 Size: 79,097 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg19 chr5:55,034,792-55,112,368 Size: 77,577 Coding Exon Count: 21 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:55,033,889-55,112,985)mRNA (may differ from genome)Protein (724 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX4_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX4; EC=3.6.4.13; AltName: Full=DEAD box protein 4; AltName: Full=Vasa homolog;
FUNCTION: May play a role in germ cell development. May play a role in sperm motility.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Found in a mRNP complex, at least composed of TDRD1, TDRD6, TDRD7 and DDX4. N-terminus interacts with RANBP9. Interacts with PIWIL2 and MAEL (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasm, perinuclear region (By similarity).
TISSUE SPECIFICITY: Expressed only in ovary and testis. Expressed in migratory primordial germ cells in the region of the gonadal ridge in both sexes.
SIMILARITY: Belongs to the DEAD box helicase family. DDX4/VASA subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DDX4
Diseases sorted by gene-association score: sertoli cell-only syndrome (4), male reproductive system disease (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 87.96 RPKM in Testis
Total median expression: 90.09 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -17.7055-0.322 Picture PostScript Text
3' UTR -128.60617-0.208 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011545 - DNA/RNA_helicase_DEAD/DEAH_N
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000629 - RNA-helicase_DEAD-box_CS
IPR014014 - RNA_helicase_DEAD_Q_motif

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q9NQI0
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATPase activity

Biological Process:
GO:0007140 male meiosis
GO:0007141 male meiosis I
GO:0007275 multicellular organism development
GO:0007283 spermatogenesis
GO:0010501 RNA secondary structure unwinding
GO:0010529 negative regulation of transposition
GO:0030154 cell differentiation
GO:0030317 flagellated sperm motility
GO:0031047 gene silencing by RNA
GO:0034587 piRNA metabolic process
GO:0043046 DNA methylation involved in gamete generation
GO:0051321 meiotic cell cycle
GO:1990511 piRNA biosynthetic process

Cellular Component:
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0043186 P granule
GO:0048471 perinuclear region of cytoplasm
GO:0071546 pi-body
GO:0071547 piP-body


-  Descriptions from all associated GenBank mRNAs
  BC030638 - Homo sapiens cDNA clone IMAGE:4822528, containing frame-shift errors.
AK308300 - Homo sapiens cDNA, FLJ98248.
AK292417 - Homo sapiens cDNA FLJ77603 complete cds, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 (DDX4), transcript variant 2, mRNA.
BC088362 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 4, mRNA (cDNA clone MGC:111074 IMAGE:30386875), complete cds.
BC047455 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 4, mRNA (cDNA clone MGC:48304 IMAGE:5298807), complete cds.
AF262962 - Homo sapiens VASA protein mRNA, complete cds.
AY004154 - Homo sapiens DEAD box RNA helicase (VASA) mRNA, complete cds.
JD062095 - Sequence 43119 from Patent EP1572962.
AL137462 - Homo sapiens mRNA; cDNA DKFZp434B1122 (from clone DKFZp434B1122); partial cds.
AK093439 - Homo sapiens cDNA FLJ36120 fis, clone TESTI2022738, highly similar to Probable ATP-dependent RNA helicase DDX4 (EC 3.6.1.-).
AX748127 - Sequence 1652 from Patent EP1308459.
JD292807 - Sequence 273831 from Patent EP1572962.
JD279418 - Sequence 260442 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NQI0 (Reactome details) participates in the following event(s):

R-HSA-5603062 Complexed PIWIL2 binds pre-piRNA
R-HSA-5601910 Complexed PIWIL2:2'-O-methyl-piRNA cleaves transposon RNA
R-HSA-5629218 HENMT1 methylates 2' hydroxyl at 3' end of piRNA in 6xMeR-PIWIL2:piRNA:TDRD1:TDRD12:DDX4:ASZ:MOV10L1
R-HSA-5601884 PIWI-interacting RNA (piRNA) biogenesis
R-HSA-211000 Gene Silencing by RNA
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: A8K8Q2, B3KSF4, D6RDK4, DDX4_HUMAN, E9PCD8, ENST00000505374.1, ENST00000505374.2, ENST00000505374.3, ENST00000505374.4, ENST00000505374.5, NM_024415, Q5M7Z3, Q86VX0, Q9NQI0, Q9NT92, Q9NYB1, uc322zrt.1, uc322zrt.2, VASA
UCSC ID: ENST00000505374.6_7
RefSeq Accession: NM_024415.3
Protein: Q9NQI0 (aka DDX4_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.