Mouse Gene Ddx4 (ENSMUST00000075748.6) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 (Ddx4), transcript variant 2, mRNA. (from RefSeq NM_010029)
Gencode Transcript: ENSMUST00000075748.6
Gencode Gene: ENSMUSG00000021758.14
Transcript (Including UTRs)
   Position: mm10 chr13:112,598,333-112,652,301 Size: 53,969 Total Exon Count: 21 Strand: -
Coding Region
   Position: mm10 chr13:112,598,945-112,651,403 Size: 52,459 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:112,598,333-112,652,301)mRNA (may differ from genome)Protein (702 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: DDX4_MOUSE
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX4; EC=3.6.4.13; AltName: Full=DEAD box protein 4; AltName: Full=Mvh; AltName: Full=Vasa homolog;
FUNCTION: May play a role in germ cell development. May play a role in sperm motility (By similarity).
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.
SUBCELLULAR LOCATION: Cytoplasm. Cytoplasm, perinuclear region.
TISSUE SPECIFICITY: Testis.
DEVELOPMENTAL STAGE: Expressed in spermatogenic cells from the spermatocyte stage to the round spermatid stage.
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


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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -10.2041-0.249 Picture PostScript Text
3' UTR -127.10612-0.208 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 Q61496
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-  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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsemblEnsembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  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:0005515 protein binding
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:0032880 regulation of protein localization
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:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0033391 chromatoid body
GO:0048471 perinuclear region of cytoplasm
GO:0071546 pi-body
GO:0071547 piP-body
GO:1990904 ribonucleoprotein complex


-  Descriptions from all associated GenBank mRNAs
  AK133366 - Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:4932703A03 product:DEAD (Asp-Glu-Ala-Asp) box polypeptide 4, full insert sequence.
AK014844 - Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:4921508G22 product:DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide 4, full insert sequence.
BC137601 - Mus musculus DEAD (Asp-Glu-Ala-Asp) box polypeptide 4, mRNA (cDNA clone MGC:169225 IMAGE:8860620), complete cds.
BC144760 - Mus musculus DEAD (Asp-Glu-Ala-Asp) box polypeptide 4, mRNA (cDNA clone MGC:178316 IMAGE:9053308), complete cds.
BC072566 - Mus musculus DEAD (Asp-Glu-Ala-Asp) box polypeptide 4, mRNA (cDNA clone IMAGE:5708359), **** WARNING: chimeric clone ****.
JQ923486 - Mus musculus strain Kunming DEAD box polypeptide 4 mRNA, complete cds.
D14859 - Mus musculus mRNA for Drosophila vasa homologue, partial cds.

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

Protein Q61496 (Reactome details) participates in the following event(s):

R-MMU-5605349 Complexed Piwil2:2'-O-methyl-piRNA cleaves transposon RNA
R-MMU-5629217 Henmt1 methylates 2' hydroxyl at 3' end of piRNA in Asz1:Ddx4:Mov10l1:6xMeR-Piwil2:piRNA:Tdrd1:Tdrd12
R-MMU-5605279 Complexed Piwil2 binds pre-piRNA

-  Other Names for This Gene
  Alternate Gene Symbols: DDX4_MOUSE, NM_010029, Q61496, Q9D5X7, uc007rwm.1, uc007rwm.2, uc007rwm.3, Vasa
UCSC ID: uc007rwm.3
RefSeq Accession: NM_010029
Protein: Q61496 (aka DDX4_MOUSE)
CCDS: CCDS26774.1, CCDS49366.1

-  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.