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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 3.6.4.13 4
  • EC 3.6.1 58
  • 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. 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

Regulatory Elements for DDX56 Gene

Enhancers for DDX56 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH07H044628 2 FANTOM5 Ensembl ENCODE dbSUPER 31 -60.2 -60154 13 HDGF PKNOX1 SIN3A FEZF1 YY1 ZNF766 ZNF143 FOS DEK JUNB DDX56 OGDH H2AFV SNORA5C PURB SNORA5B NACAD NUDCD3 TMED4 ENSG00000228434
GH07H043582 2 FANTOM5 Ensembl ENCODE dbSUPER 23.5 +987.0 987038 11 HDGF PKNOX1 FOXA2 ARID4B SIN3A FEZF1 ZNF2 YY1 CBX5 ZNF207 STK17A COA1 DDX56 BLVRA POLM URGCP PIR39554
GH07H044488 1.4 ENCODE dbSUPER 32.4 +84.8 84761 2 HDGF PKNOX1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 DDX56 NUDCD3 TMED4 URGCP SNORA5B SNORA5C PURB GC07M044473 GC07M044472
GH07H044121 1.1 ENCODE 40.2 +452.0 452012 3 HDGF PKNOX1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF143 FOS ENSG00000228680 DDX56 POLM TMED4 SPDYE1 SNORA5B ENSG00000228434 SNORA5C SNHG15 TBRG4
GH07H044613 1.9 FANTOM5 Ensembl ENCODE dbSUPER 22.1 -45.3 -45341 13 HDGF FOXA2 ATF1 FEZF1 DMAP1 GTF3C2 ZNF121 FOS ATF7 RUNX3 PURB DDX56 ZMIZ2 SNORA5C POLM ENSG00000228434 SNORA5B URGCP SNORA5A TMED4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DDX56 on UCSC Golden Path with GeneCards custom track

Promoters for DDX56 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000211849 1151 1401 PKNOX1 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 FOS MXD4 NFYC

Genomic Location for DDX56 Gene

Chromosome:
7
Start:
44,565,417 bp from pter
End:
44,575,051 bp from pter
Size:
9,635 bases
Orientation:
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:
    Q9NY93-DDX56_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase DDX56
    Protein Accession:
    Q9NY93
    Secondary Accessions:
    • A4D2K9
    • C9JV95
    • Q6IAE2
    • Q9H9I8

    Protein attributes for DDX56 Gene

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

    Alternative splice isoforms for DDX56 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX56 Gene

Selected DME Specific Peptides for DDX56 Gene

Q9NY93:
  • ARTGSGKT
  • LDPRLLQA
  • VLNFDLP
  • IPLALEGKD

Post-translational modifications for DDX56 Gene

  • Ubiquitination at posLast=4545
  • Modification sites at PhosphoSitePlus

Domains & Families for DDX56 Gene

Gene Families for DDX56 Gene

HGNC:
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

Q9NY93

UniProtKB/Swiss-Prot:

DDX56_HUMAN :
  • Belongs to the DEAD box helicase family. DDX56/DBP9 subfamily.
Family:
  • 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 IEA,IDA 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

Clone Products

  • Applied Biological Materials Clones for DDX56
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

COMPARTMENTS
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 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 Nutra Agonist 0

(1) Additional Compounds for DDX56 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
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

Clone Products

  • Applied Biological Materials Clones for DDX56
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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: -
SP3:
SP4: -
SP5: -
SP6:
SP7:
SP8:
SP9:

ExUns: 15b ^ 16
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for DDX56 Gene

GeneLoc Exon Structure for
DDX56
ECgene alternative splicing isoforms for
DDX56

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:

DDX56

SOURCE GeneReport for Unigene cluster for DDX56 Gene:

Hs.654762

mRNA Expression by UniProt/SwissProt for DDX56 Gene:

Q9NY93-DDX56_HUMAN
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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia DDX56 33 34
  • 99.45 (n)
cow
(Bos Taurus)
Mammalia DDX56 33 34
  • 87.67 (n)
mouse
(Mus musculus)
Mammalia Ddx56 33 16 34
  • 85.47 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 85 (a)
OneToMany
-- 34
  • 75 (a)
OneToMany
-- 34
  • 74 (a)
OneToMany
-- 34
  • 72 (a)
OneToMany
dog
(Canis familiaris)
Mammalia DDX56 33 34
  • 84.85 (n)
rat
(Rattus norvegicus)
Mammalia Ddx56 33
  • 84.65 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX56 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx56 33
  • 64.29 (n)
zebrafish
(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)
worm
(Caenorhabditis elegans)
Secernentea CELE_C24H12.4 33
  • 52.03 (n)
C24H12.4 34
  • 34 (a)
OneToOne
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)
rice
(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)
OneToOne
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

ENSEMBL:
Gene Tree for DDX56 (if available)
TreeFam:
Gene Tree for DDX56 (if available)

Paralogs for DDX56 Gene

Pseudogenes.org 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 Sequence Context AA Info Type
rs1000250141 -- 44,572,266(+) CACCA(A/C)AGAAT intron-variant
rs1000873245 -- 44,573,524(+) GAACC(A/G)CCCTT intron-variant
rs1000953468 -- 44,566,935(+) CACCT(A/G)GGCCC intron-variant
rs1001288224 -- 44,571,277(+) CAGGC(A/G)ATCCG intron-variant
rs1001317809 -- 44,566,051(+) TGAAG(C/T)TGCGC reference, missense

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)

Relevant External Links for DDX56 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX56

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 encephalitis
- elite association - COSMIC cancer census association via MalaCards
Search DDX56 in MalaCards View complete list of genes associated with diseases

Relevant External Links for DDX56

Genetic Association Database (GAD)
DDX56
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  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 60
  4. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer SW … Tsui LC (Science (New York, N.Y.) 2003) 3 4 60
  5. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A … Diaz JJ (Molecular biology of the cell 2002) 3 4 60

Products for DDX56 Gene

Sources for DDX56 Gene

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