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DDX21 Gene(Protein Coding)

DEAD-Box Helicase 21

GCID:
GC10P068956
GIFtS:
56
Genes Participants
UDN Logo

Aliases for DDX21 Gene

Aliases for DDX21 Gene

  • DEAD-Box Helicase 21 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Helicase 21 2 3 5
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 21 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 21 2 3
  • Nucleolar RNA Helicase Gu 3 4
  • Nucleolar RNA Helicase II 3 4
  • DEAD Box Protein 21 3 4
  • RH II/Gu 3 4
  • Gu-Alpha 3 4
  • RNA Helicase II/Gu Alpha 3
  • EC 3.6.4.13 4
  • Gu Protein 3
  • RH-II/GuA 3
  • RH-II/GU 3
  • EC 3.6.1 63
  • GURDB 3
  • GUA 3

External Ids for DDX21 Gene

Previous GeneCards Identifiers for DDX21 Gene

  • GC10P069527
  • GC10P069802
  • GC10P070608
  • GC10P070060
  • GC10P070385
  • GC10P070715
  • GC10P064717

Summaries for DDX21 Gene

Entrez Gene Summary for DDX21 Gene

  • 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]

GeneCards Summary for DDX21 Gene

DDX21 (DEAD-Box Helicase 21) is a Protein Coding gene. Diseases associated with DDX21 include Stomach Disease and Cerebral Creatine Deficiency Syndrome 3. Among its related pathways are Gene Expression and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. GO annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is DDX50.

UniProtKB/Swiss-Prot for DDX21 Gene

  • RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at Ser-77 (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292).

Gene Wiki entry for DDX21 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX21 Gene

Genomics for DDX21 Gene

Products:

  1. Regulatory Element

Regulatory Elements for DDX21 Gene

Enhancers for DDX21 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around DDX21 on UCSC Golden Path with GeneCards custom track

Promoters for DDX21 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around DDX21 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the DDX21 gene promoter:

Genomic Location for DDX21 Gene

Chromosome:
10
Start:
68,956,123 bp from pter
End:
68,985,073 bp from pter
Size:
28,951 bases
Orientation:
Plus strand

Genomic View for DDX21 Gene

Genes around DDX21 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX21 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX21 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for DDX21 Gene

Proteins for DDX21 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for DDX21 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NR30-DDX21_HUMAN
    Recommended name:
    Nucleolar RNA helicase 2
    Protein Accession:
    Q9NR30
    Secondary Accessions:
    • B2RDL0
    • Q13436
    • Q5VX41
    • Q68D35

    Protein attributes for DDX21 Gene

    Size:
    783 amino acids
    Molecular mass:
    87344 Da
    Quaternary structure:
    • Component of the B-WICH complex, at least composed of SMARCA5/SNF2H, BAZ1B/WSTF, SF3B1, DEK, MYO1C, ERCC6, MYBBP1A and DDX21. Interacts with C1QBP. Interacts with JUN (PubMed:11823437, PubMed:18180292). Interacts with WDR46 (PubMed:23848194).
    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.
    SequenceCaution:
    • Sequence=AAB02546.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for DDX21 Gene

    Alternative splice isoforms for DDX21 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX21 Gene

Proteomics data for DDX21 Gene at MOPED

Protein Expression for DDX21 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for DDX21 Gene

Q9NR30:

Post-translational modifications for DDX21 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DDX21 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for DDX21 Gene

Gene Families for DDX21 Gene

HGNC:

Protein Domains for DDX21 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for DDX21 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NR30

UniProtKB/Swiss-Prot:

DDX21_HUMAN :
  • The helicase and foldase activities reside in two separate domains, the helicase in the N-terminus and the foldase in the C-terminus.
  • Belongs to the DEAD box helicase family. DDX21/DDX50 subfamily.
Domain:
  • The helicase and foldase activities reside in two separate domains, the helicase in the N-terminus and the foldase in the C-terminus.
  • The 3 X 5 AA repeats seem to be critical for the RNA folding activity.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the DEAD box helicase family. DDX21/DDX50 subfamily.
genes like me logo Genes that share domains with DDX21: view

Function for DDX21 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for DDX21 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2-O-methylation, possibly by promoting the recruitment of late-acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at Ser-77 (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292).

Enzyme Numbers (IUBMB) for DDX21 Gene

Gene Ontology (GO) - Molecular Function for DDX21 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA --
GO:0004386 helicase activity IEA --
GO:0005524 ATP binding IEA --
GO:0019843 rRNA binding IDA 25470060
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with DDX21: view

Phenotypes for DDX21 Gene

MGI mutant phenotypes for DDX21:
inferred from 1 alleles
GenomeRNAi human phenotypes for DDX21:
genes like me logo Genes that share phenotypes with DDX21: view

Animal Model Products

miRNA for DDX21 Gene

miRTarBase miRNAs that target DDX21

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DDX21 Gene

Localization for DDX21 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX21 Gene

Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Present both in nucleolus and nucleoplasm. Interaction with JUN promotes translocation from the nucleolus to the nucleoplasm (PubMed:11823437, PubMed:18180292). Interaction with WDR46 is required for localization to the nucleolus (PubMed:23848194). {ECO:0000269 PubMed:11823437, ECO:0000269 PubMed:18180292, ECO:0000269 PubMed:23848194}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DDX21 Gene COMPARTMENTS Subcellular localization image for DDX21 gene
Compartment Confidence
nucleus 5
cytosol 3
chloroplast 2
mitochondrion 1

No data available for Gene Ontology (GO) - Cellular Components for DDX21 Gene

Pathways & Interactions for DDX21 Gene

genes like me logo Genes that share pathways with DDX21: view

Gene Ontology (GO) - Biological Process for DDX21 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006366 transcription from RNA polymerase II promoter IMP 25470060
genes like me logo Genes that share ontologies with DDX21: view

No data available for SIGNOR curated interactions for DDX21 Gene

Drugs & Compounds for DDX21 Gene

Products:

  1. Drug

(1) Drugs for DDX21 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine triphosphate Approved Nutra 0

(3) Additional Compounds for DDX21 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
 Full agonist, Agonist 58-64-0
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
 7664-38-2
Water
  • Dihydrogen oxide
  • Steam
 7732-18-5
genes like me logo Genes that share compounds with DDX21: view

Transcripts for DDX21 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for DDX21 Gene

(3) REFSEQ mRNAs :
(11) Additional mRNA sequences :
(650) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for DDX21 Gene

DEAD (Asp-Glu-Ala-Asp) box helicase 21:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX21 Gene

No ASD Table

Relevant External Links for DDX21 Gene

GeneLoc Exon Structure for
DDX21
ECgene alternative splicing isoforms for
DDX21

Expression for DDX21 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for DDX21 Gene

mRNA expression in normal human tissues for DDX21 Gene
mRNA expression by BioGPS for DDX21 GenemRNA expression by GTEx for DDX21 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDX21 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (21.0), Tlymphocyte (6.3), and Stomach (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for DDX21 Gene



SOURCE GeneReport for Unigene cluster for DDX21 Gene Hs.223141

genes like me logo Genes that share expression patterns with DDX21: view

Protein tissue co-expression partners for DDX21 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for DDX21 Gene

Orthologs for DDX21 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX21 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
 Mammalia DDX21 35
  • 89.34 (n)
  • 89.26 (a)
-- 36
  • 75 (a)
 OneToMany
DDX21 36
  • 89 (a)
 OneToMany
dog
(Canis familiaris)
 Mammalia DDX21 35
  • 89.31 (n)
  • 89.66 (a)
DDX21 36
  • 89 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Ddx21 35
  • 86.07 (n)
  • 89.97 (a)
Ddx21 16
Ddx21 36
  • 77 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia DDX21 35
  • 99.83 (n)
  • 99.87 (a)
DDX21 36
  • 100 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Ddx21 35
  • 83.83 (n)
  • 84.85 (a)
oppossum
(Monodelphis domestica)
 Mammalia DDX21 36
  • 71 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia DDX21 36
  • 66 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves DDX50 35
  • 70.39 (n)
  • 69.85 (a)
-- 36
  • 67 (a)
 ManyToMany
-- 36
  • 65 (a)
 ManyToMany
lizard
(Anolis carolinensis)
 Reptilia -- 36
  • 61 (a)
 OneToMany
tropical clawed frog
(Silurana tropicalis)
 Amphibia ddx21 35
  • 63.18 (n)
  • 59.87 (a)
zebrafish
(Danio rerio)
 Actinopterygii -- 35
ddx21 35
  • 64.37 (n)
  • 71.11 (a)
ddx21 36
  • 55 (a)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes DBP3 36
  • 29 (a)
 ManyToMany
TIF1 36
  • 32 (a)
 ManyToMany
TIF2 36
  • 32 (a)
 ManyToMany
thale cress
(Arabidopsis thaliana)
 eudicotyledons PRH75 35
  • 49.35 (n)
  • 43.29 (a)
rice
(Oryza sativa)
 Liliopsida Os09g0520700 35
  • 51.24 (n)
  • 46.1 (a)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.2984 36
  • 50 (a)
 OneToMany
Species with no ortholog for DDX21:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for DDX21 Gene

ENSEMBL:
Gene Tree for DDX21 (if available)
TreeFam:
Gene Tree for DDX21 (if available)

Paralogs for DDX21 Gene

Paralogs for DDX21 Gene

(8) SIMAP similar genes for DDX21 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with DDX21: view

Variants for DDX21 Gene

Sequence variations from dbSNP and Humsavar for DDX21 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs17556220 - 68,956,305(+) GCAAA(C/T)CGAGG upstream-variant-2KB, reference, missense
rs1539163 -- 68,979,874(-) ATGGT(A/G)TTGGT intron-variant
rs4554 -- 68,983,666(-) GCCCC(C/T)TACTC utr-variant-3-prime
rs7920 -- 68,984,923(+) TTACT(A/G)TTTTC utr-variant-3-prime
rs9197 -- 68,974,703(+) CTTCT(G/T)CAACA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for DDX21 Gene

Variant ID Type Subtype PubMed ID
nsv831907 CNV Gain 17160897
nsv519999 CNV Loss 19592680

Variation tolerance for DDX21 Gene

Residual Variation Intolerance Score: 39.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.10; 38.40% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for DDX21 Gene

Disorders for DDX21 Gene

MalaCards: The human disease database

(6) MalaCards diseases for DDX21 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
stomach disease
  • gastric disease
cerebral creatine deficiency syndrome 3
  • agat deficiency
cerebral creatine deficiency syndrome 2
  • guanidinoacetate methyltransferase deficiency
neurodermatitis
cerebral creatine deficiency syndrome
  • cerebral creatine deficiency syndromes
- elite association - COSMIC cancer census association via MalaCards
Search DDX21 in MalaCards View complete list of genes associated with diseases

Relevant External Links for DDX21

Genetic Association Database (GAD)
DDX21
Human Genome Epidemiology (HuGE) Navigator
DDX21
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DDX21
genes like me logo Genes that share disorders with DDX21: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DDX21 Gene

Publications for DDX21 Gene

  1. c-Jun supports ribosomal RNA processing and nucleolar localization of RNA helicase DDX21. (PMID: 18180292) HolmstrAPm T.H. … Westermarck J. (J. Biol. Chem. 2008) 2 3 4 67
  2. Genomic structure of newly identified paralogue of RNA helicase II/Gu: detection of pseudogenes and multiple alternatively spliced mRNAs. (PMID: 11891046) Valdez B.C. … Sequitin A.M. (Gene 2002) 3 23
  3. A nucleolar RNA helicase recognized by autoimmune antibodies from a patient with watermelon stomach disease. (PMID: 8614622) Valdez B.C. … Busch H. (Nucleic Acids Res. 1996) 2 3
  4. RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. (PMID: 25470060) Calo E. … Wysocka J. (Nature 2015) 3
  5. The association of late-acting snoRNPs with human pre-ribosomal complexes requires the RNA helicase DDX21. (PMID: 25477391) Sloan K.E. … Bohnsack M.T. (Nucleic Acids Res. 2015) 3

Products for DDX21 Gene

Sources for DDX21 Gene

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