Human Gene DDX21 (uc001jov.2) Description and Page Index
  Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box helicase 21 (DDX21), transcript variant 1, mRNA.
RefSeq Summary (NM_004728): 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 an antigen recognized by autoimmune antibodies from a patient with watermelon stomach disease. This protein unwinds double-stranded RNA, folds single-stranded RNA, and may play important roles in ribosomal RNA biogenesis, RNA editing, RNA transport, and general transcription. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr10:70,715,879-70,744,825 Size: 28,947 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr10:70,715,982-70,742,568 Size: 26,587 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:70,715,879-70,744,825)mRNA (may differ from genome)Protein (783 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: DDX21_HUMAN
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. Involved in rRNA processing.
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.
SUBCELLULAR LOCATION: Nucleus, nucleolus.
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 (By similarity).
MISCELLANEOUS: Autoantibodies against DDX21 are found in patients with watermelon stomach disease, which is characterized by prominent stripes of ectatic vascular tissue in the stomach similar to stripes on a watermelon.
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.
SEQUENCE CAUTION: Sequence=AAB02546.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DDX21
CDC HuGE Published Literature: DDX21

-  MalaCards Disease Associations
  MalaCards Gene Search: DDX21
Diseases sorted by gene-association score: stomach disease (27), cerebral creatine deficiency syndrome 3 (2), cerebral creatine deficiency syndrome 2 (2), cerebral creatine deficiency syndrome (2), neurodermatitis (2), breast abscess (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: 55.08 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 739.18 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 -39.20103-0.381 Picture PostScript Text
3' UTR -586.562257-0.260 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

ModBase Predicted Comparative 3D Structure on Q9NR30
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
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:0001649 osteoblast differentiation
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
GO:0045815 positive regulation of gene expression, epigenetic

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  BC104671 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 21, mRNA (cDNA clone IMAGE:6744750), partial cds.
LP895197 - Sequence 61 from Patent EP3253886.
BC009432 - Homo sapiens cDNA clone IMAGE:3355439, containing frame-shift errors.
U41387 - Human Gu protein mRNA, partial cds.
AK315585 - Homo sapiens cDNA, FLJ96663, Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 (DDX21),mRNA.
BC008071 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 21, mRNA (cDNA clone MGC:2857 IMAGE:2987980), complete cds.
BC004182 - Homo sapiens cDNA clone IMAGE:2961423, containing frame-shift errors.
BC017228 - Homo sapiens cDNA clone IMAGE:4122673, containing frame-shift errors.
CU675917 - Synthetic construct Homo sapiens gateway clone IMAGE:100017494 5' read DDX21 mRNA.
AB527408 - Synthetic construct DNA, clone: pF1KB3472, Homo sapiens DDX21 gene for DEAD (Asp-Glu-Ala-Asp) box polypeptide 21, without stop codon, in Flexi system.
KJ892707 - Synthetic construct Homo sapiens clone ccsbBroadEn_02101 DDX21 gene, encodes complete protein.
JD173498 - Sequence 154522 from Patent EP1572962.
CR749598 - Homo sapiens mRNA; cDNA DKFZp686F21172 (from clone DKFZp686F21172).
BX648405 - Homo sapiens mRNA; cDNA DKFZp686A04240 (from clone DKFZp686A04240).
JD041906 - Sequence 22930 from Patent EP1572962.
KJ905991 - Synthetic construct Homo sapiens clone ccsbBroadEn_15661 DDX21 gene, encodes complete protein.
DQ896852 - Synthetic construct Homo sapiens clone IMAGE:100011312; FLH185139.01L; RZPDo839F09145D DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 (DDX21) gene, encodes complete protein.
DQ893631 - Synthetic construct clone IMAGE:100006261; FLH185143.01X; RZPDo839F09146D DEAD (Asp-Glu-Ala-Asp) box polypeptide 21 (DDX21) gene, encodes complete protein.
AK025629 - Homo sapiens cDNA: FLJ21976 fis, clone HEP05883, highly similar to HSU41387 Human Gu protein mRNA.
AB062394 - Homo sapiens OK/SW-cl.65 mRNA for DEAD/H(Asp-Glu-Ala-Asp/His)box polypeptide 21, complete cds.
JD377804 - Sequence 358828 from Patent EP1572962.
JD237365 - Sequence 218389 from Patent EP1572962.
JD101781 - Sequence 82805 from Patent EP1572962.
JD441977 - Sequence 423001 from Patent EP1572962.
JD234854 - Sequence 215878 from Patent EP1572962.
JD553759 - Sequence 534783 from Patent EP1572962.
JD295283 - Sequence 276307 from Patent EP1572962.
JD491099 - Sequence 472123 from Patent EP1572962.

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

Protein Q9NR30 (Reactome details) participates in the following event(s):

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

-  Other Names for This Gene
  Alternate Gene Symbols: B2RDL0, DDX21_HUMAN, NM_004728, NP_001243839, Q13436, Q5VX41, Q68D35, Q9NR30, uc001jov.1
UCSC ID: uc001jov.2
RefSeq Accession: NM_004728
Protein: Q9NR30 (aka DDX21_HUMAN or DD21_HUMAN)
CCDS: CCDS31211.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004728.3
exon count: 15CDS single in 3' UTR: no RNA size: 4720
ORF size: 2352CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4904.00frame shift in genome: no % Coverage: 99.83
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.