Mouse Gene Ddx21 (ENSMUST00000045866.8) Description and Page Index
  Description: Mus musculus DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 (Ddx21), mRNA. (from RefSeq NM_019553)
Gencode Transcript: ENSMUST00000045866.8
Gencode Gene: ENSMUSG00000020075.8
Transcript (Including UTRs)
   Position: mm10 chr10:62,580,251-62,602,281 Size: 22,031 Total Exon Count: 15 Strand: -
Coding Region
   Position: mm10 chr10:62,582,350-62,602,214 Size: 19,865 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated: 2019-09-20

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:62,580,251-62,602,281)mRNA (may differ from genome)Protein (851 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DDX21_MOUSE
DESCRIPTION: RecName: Full=Nucleolar RNA helicase 2; EC=3.6.4.13; AltName: Full=DEAD box protein 21; AltName: Full=Gu-alpha; AltName: Full=Nucleolar RNA helicase Gu; AltName: Full=Nucleolar RNA helicase II; AltName: Full=RH II/Gu;
FUNCTION: Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase). Functions as cofactor for JUN-activated transcription (By similarity).
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Component of the B-WICH complex, at least composed of SMARCA5/SNF2H, BAZ1B/WSTF, SF3B1, DEK, MYO1C, ERCC6, MYBBP1A and DDX21 (By similarity).
SUBCELLULAR LOCATION: Nucleus, nucleolus.
TISSUE SPECIFICITY: Highly expressed in liver and testis. Expressed at lower level in brain, lungs, and skeletal muscle.
DOMAIN: The two enzymatic activities reside in two separate domains, the helicase in the N-terminus and the foldase in the C- terminus.
DOMAIN: The 3 X 5 AA repeats seem to be critical for the RNA folding activity.
DOMAIN: The 3 X 37 AA tandem repeats may be important for nuclear localization and/or interaction with nucleic acids or other proteins.
SIMILARITY: Belongs to the DEAD box helicase family. DDX21/DDX50 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.

-  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 -18.4067-0.275 Picture PostScript Text
3' UTR -624.102099-0.297 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
IPR012562 - GUCT
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR014014 - RNA_helicase_DEAD_Q_motif

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain
PF04851 - Type III restriction enzyme, res subunit
PF08152 - GUCT (NUC152) domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q9JIK5
FrontTopSide
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0003725 double-stranded RNA 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:0019843 rRNA binding
GO:0030515 snoRNA binding
GO:0035198 miRNA binding
GO:0097322 7SK snRNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006364 rRNA processing
GO:0006366 transcription from RNA polymerase II promoter
GO:0009615 response to virus
GO:0010501 RNA secondary structure unwinding
GO:0043330 response to exogenous dsRNA

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC060220 - Mus musculus cDNA clone IMAGE:6843088, containing frame-shift errors.
BC043655 - Mus musculus DEAD (Asp-Glu-Ala-Asp) box polypeptide 21, mRNA (cDNA clone MGC:49064 IMAGE:5363948), complete cds.
BC059237 - Mus musculus DEAD (Asp-Glu-Ala-Asp) box polypeptide 21, mRNA (cDNA clone MGC:66928 IMAGE:6412782), complete cds.
AF159131 - Mus musculus nucleolar RNA helicase II/Gu mRNA, complete cds.
AK160095 - Mus musculus osteoclast-like cell cDNA, RIKEN full-length enriched library, clone:I420048M08 product:DEAD (Asp-Glu-Ala-Asp) box polypeptide 21, full insert sequence.
BC030895 - Mus musculus DEAD (Asp-Glu-Ala-Asp) box polypeptide 21, mRNA (cDNA clone IMAGE:4488898), partial cds.
AK010281 - Mus musculus ES cells cDNA, RIKEN full-length enriched library, clone:2400004F19 product:DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21 (RNA helicase II/Gu), full insert sequence.
AK145578 - Mus musculus blastocyst blastocyst cDNA, RIKEN full-length enriched library, clone:I1C0017E01 product:DEAD (Asp-Glu-Ala-Asp) box polypeptide 21, full insert sequence.
AK012125 - Mus musculus 10 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2610511L22 product:DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21 (RNA helicase II/Gu), full insert sequence.

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

Protein Q9JIK5 (Reactome details) participates in the following event(s):

R-MMU-5250947 B-WICH complex binds rDNA promoter
R-MMU-5250930 B-WICH recruits histone acetyltransferases
R-MMU-5250938 B-WICH:histone acetyltransferase acetylates histone H3 at lysine-9
R-MMU-5250924 B-WICH complex positively regulates rRNA expression
R-MMU-5250913 Positive epigenetic regulation of rRNA expression
R-MMU-212165 Epigenetic regulation of gene expression
R-MMU-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: DDX21_MOUSE, NM_019553, Q3TVJ3, Q9JIK5, Q9WV45, uc007fhn.1, uc007fhn.2
UCSC ID: uc007fhn.2
RefSeq Accession: NM_019553
Protein: Q9JIK5 (aka DDX21_MOUSE or DD21_MOUSE)
CCDS: CCDS23891.1

-  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.