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Aliases for DDX56 Gene

Aliases for DDX56 Gene

  • DEAD-Box Helicase 56 2 3 5
  • ATP-Dependent 61 KDa Nucleolar RNA Helicase 3 4
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 56 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Helicase 56 2 3
  • Nucleolar Helicase Of 61 KDa 2 3
  • DEAD Box Protein 21 3 4
  • DEAD Box Protein 56 3 4
  • DDX21 3 4
  • NOH61 3 4
  • Probable ATP-Dependent RNA Helicase DDX56 3
  • Putative Nucleolar RNA Helicase 3
  • 61-Kd Nucleolar Helicase 3
  • DEAD-Box RNA Helicase 3
  • EC 4
  • EC 3.6.1 56
  • DDX26 3

External Ids for DDX56 Gene

Previous GeneCards Identifiers for DDX56 Gene

  • GC07M044311
  • GC07M044346
  • GC07M044378
  • GC07M044571
  • GC07M044489

Summaries for DDX56 Gene

Entrez Gene Summary for DDX56 Gene

  • This gene encodes a member of the DEAD box protein family. 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. The protein encoded by this gene shows ATPase activity in the presence of polynucleotides and associates with nucleoplasmic 65S preribosomal particles. This gene may be involved in ribosome synthesis, most likely during assembly of the large 60S ribosomal subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]

GeneCards Summary for DDX56 Gene

DDX56 (DEAD-Box Helicase 56) is a Protein Coding gene. Diseases associated with DDX56 include West Nile Virus. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and hydrolase activity.

UniProtKB/Swiss-Prot for DDX56 Gene

  • May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity.

Gene Wiki entry for DDX56 Gene

Additional gene information for DDX56 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX56 Gene

Genomics for DDX56 Gene

GeneHancer (GH) Regulatory Elements for DDX56 Gene

Promoters and enhancers for DDX56 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH07I044572 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 558.3 +1.2 1226 3 PKNOX1 SMAD1 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B E2F8 DDX56 NUDCD3 NPC1L1
GH07I044576 Enhancer 0.5 FANTOM5 559.2 -1.7 -1662 0.4 ZNF362 GLIS1 DDX56 NUDCD3 PIR40932 GC07M044579
GH07I044845 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 46.5 -272.5 -272533 4.2 FEZF1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC GLIS1 LINC01952 H2AFV CICP20 DDX56 SNORA5C POLM SNORA5B ENSG00000228434 SPDYE1 TMED4
GH07I044488 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 32.4 +84.8 84760 2.6 CLOCK ZFP64 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC MEF2D NUDCD3 DDX56 TMED4 URGCP SNORA5B SNORA5C PURB GC07M044473 GC07M044472
GH07I044121 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 28.5 +452.0 452011 3.4 HDGF PKNOX1 CLOCK MLX ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF213 POLD2 POLM TMED4 SPDYE1 SNORA5B ENSG00000228434 DDX56 SNORA5C TBRG4 TUBG1P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DDX56 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DDX56 gene promoter:

Genomic Locations for DDX56 Gene

Genomic Locations for DDX56 Gene
9,635 bases
Minus strand

Genomic View for DDX56 Gene

Genes around DDX56 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX56 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX56 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX56 Gene

Proteins for DDX56 Gene

  • Protein details for DDX56 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Probable ATP-dependent RNA helicase DDX56
    Protein Accession:
    Secondary Accessions:
    • A4D2K9
    • C9JV95
    • Q6IAE2
    • Q9H9I8

    Protein attributes for DDX56 Gene

    547 amino acids
    Molecular mass:
    61590 Da
    Quaternary structure:
    • May form homooligomeric complexes.

    Alternative splice isoforms for DDX56 Gene


neXtProt entry for DDX56 Gene

Selected DME Specific Peptides for DDX56 Gene


Post-translational modifications for DDX56 Gene

  • Ubiquitination at Lys45
  • Modification sites at PhosphoSitePlus

Domains & Families for DDX56 Gene

Gene Families for DDX56 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for DDX56 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the DEAD box helicase family. DDX56/DBP9 subfamily.
  • Belongs to the DEAD box helicase family. DDX56/DBP9 subfamily.
genes like me logo Genes that share domains with DDX56: view

Function for DDX56 Gene

Molecular function for DDX56 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity.

Enzyme Numbers (IUBMB) for DDX56 Gene

Phenotypes From GWAS Catalog for DDX56 Gene

Gene Ontology (GO) - Molecular Function for DDX56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA,IEA 22658674
GO:0004004 ATP-dependent RNA helicase activity TAS 10749921
GO:0004386 helicase activity IEA --
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with DDX56: view
genes like me logo Genes that share phenotypes with DDX56: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DDX56 Gene

Localization for DDX56 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX56 Gene

Nucleus, nucleolus.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DDX56 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for DDX56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IBA --
GO:0016020 membrane HDA,IDA 19946888
genes like me logo Genes that share ontologies with DDX56: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for DDX56 Gene

Pathways & Interactions for DDX56 Gene

SuperPathways for DDX56 Gene

No Data Available

Gene Ontology (GO) - Biological Process for DDX56 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing IBA --
GO:0010501 RNA secondary structure unwinding IBA --
GO:0010976 positive regulation of neuron projection development IEA --
GO:0042254 ribosome biogenesis IEA --
genes like me logo Genes that share ontologies with DDX56: view

No data available for Pathways by source and SIGNOR curated interactions for DDX56 Gene

Drugs & Compounds for DDX56 Gene

(3) Drugs for DDX56 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for DDX56 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with DDX56: view

Transcripts for DDX56 Gene

Unigene Clusters for DDX56 Gene

DEAD (Asp-Glu-Ala-Asp) box helicase 56:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX56 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15a ·
SP1: - -
SP2: -
SP4: -
SP5: -

ExUns: 15b ^ 16
SP1: -
SP2: -

Relevant External Links for DDX56 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for DDX56 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX56 Gene

Protein differential expression in normal tissues from HIPED for DDX56 Gene

This gene is overexpressed in Lung (59.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DDX56 Gene

Protein tissue co-expression partners for DDX56 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DDX56 Gene:


SOURCE GeneReport for Unigene cluster for DDX56 Gene:


mRNA Expression by UniProt/SwissProt for DDX56 Gene:

Tissue specificity: Detected in heart, brain, liver, pancreas, placenta and lung.

Evidence on tissue expression from TISSUES for DDX56 Gene

  • Nervous system(4.9)
  • Skin(4.6)
  • Liver(4.2)
  • Intestine(3.1)
  • Lung(2.5)
  • Kidney(2)
genes like me logo Genes that share expression patterns with DDX56: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX56 Gene

Orthologs for DDX56 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX56 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia DDX56 33 34
  • 99.45 (n)
(Bos Taurus)
Mammalia DDX56 33 34
  • 87.67 (n)
(Mus musculus)
Mammalia Ddx56 33 16 34
  • 85.47 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 85 (a)
-- 34
  • 75 (a)
-- 34
  • 74 (a)
-- 34
  • 72 (a)
(Canis familiaris)
Mammalia DDX56 33 34
  • 84.85 (n)
(Rattus norvegicus)
Mammalia Ddx56 33
  • 84.65 (n)
(Monodelphis domestica)
Mammalia DDX56 34
  • 80 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx56 33
  • 64.29 (n)
(Danio rerio)
Actinopterygii ddx56 33 34
  • 63.17 (n)
fruit fly
(Drosophila melanogaster)
Insecta Hlc 33 34
  • 55.17 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011147 33
  • 54.38 (n)
(Caenorhabditis elegans)
Secernentea CELE_C24H12.4 33
  • 52.03 (n)
C24H12.4 34
  • 34 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR278C 33
  • 51.46 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C04576g 33
  • 50.38 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DBP9 33 34 36
  • 50.32 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G34910 33
  • 47.3 (n)
(Oryza sativa)
Liliopsida Os03g0728800 33
  • 49.72 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU07070 33
  • 52.2 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 52 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC1494.06c 33
  • 49.84 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7432 33
Species where no ortholog for DDX56 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • 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)

Evolution for DDX56 Gene

Gene Tree for DDX56 (if available)
Gene Tree for DDX56 (if available)

Paralogs for DDX56 Gene Pseudogenes for DDX56 Gene

genes like me logo Genes that share paralogs with DDX56: view

No data available for Paralogs for DDX56 Gene

Variants for DDX56 Gene

Sequence variations from dbSNP and Humsavar for DDX56 Gene

SNP ID Clin Chr 07 pos Variation AA Info Type
rs1000250141 -- 44,572,266(-) A/C intron_variant
rs1000873245 -- 44,573,524(-) G/A intron_variant
rs1000953468 -- 44,566,935(-) G/A intron_variant
rs1001288224 -- 44,571,277(-) G/A intron_variant
rs1001317809 -- 44,566,051(-) C/G/T coding_sequence_variant, missense_variant

Variation tolerance for DDX56 Gene

Residual Variation Intolerance Score: 32.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.27; 70.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX56 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for DDX56 Gene

Disorders for DDX56 Gene

MalaCards: The human disease database

(1) MalaCards diseases for DDX56 Gene - From: GeneCards

Disorder Aliases PubMed IDs
west nile virus
  • west nile virus, susceptibility to
- elite association - COSMIC cancer census association via MalaCards
Search DDX56 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for DDX56

genes like me logo Genes that share disorders with DDX56: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DDX56 Gene

Publications for DDX56 Gene

  1. A novel helicase-type protein in the nucleolus: protein NOH61. (PMID: 10749921) Zirwes RF … Schmidt-Zachmann MS (Molecular biology of the cell 2000) 2 3 4 22 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4 58
  5. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A … Diaz JJ (Molecular biology of the cell 2002) 3 4 58

Products for DDX56 Gene

Sources for DDX56 Gene

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