Free for academic non-profit institutions. Other users need a Commercial license

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 61
  • 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. 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

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
GH07G044079 1.7 Ensembl ENCODE dbSUPER 28.8 +492.3 492250 6.4 CREB3L1 MLX AGO1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D POLM RASA4CP DDX56 ENSG00000239556 ENSG00000228434 AEBP1
GH07G044613 1.9 FANTOM5 Ensembl ENCODE dbSUPER 22.1 -45.3 -45341 13.0 HDGF FOXA2 ATF1 WRNIP1 FEZF1 DMAP1 GTF3C2 ZNF121 FOS ZHX2 PURB DDX56 ZMIZ2 SNORA5C ENSG00000228434 SNORA5B SNORA5A ENSG00000228596 TBRG4 MYO1G
GH07G044755 1.4 ENCODE dbSUPER 25.2 -181.8 -181805 2.3 CREB3L1 MLX AGO1 DMAP1 YY1 ZNF548 SP3 NFYC TBX21 MEF2D DDX56 SNORA5C SNORA5B TBRG4 ENSG00000228434 SNHG15 PIR36062 ENSG00000228596
GH07G043688 1.1 dbSUPER 24.5 +885.7 885733 2.2 HDGF CREB3L1 ARNT AGO1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 STK17A DDX56 ENSG00000228434 COA1 MRPS24 GC07M043624
GH07G044733 1.5 FANTOM5 Ensembl ENCODE 16 -160.4 -160424 4.1 NFIB KLF17 SIN3A RAD21 RFX5 GTF3C2 ZNF121 GATA2 SCRT2 FOS PURB SNORA5C DDX56 ENSG00000228434 SNORA5B SNORA5A MYO1G TBRG4 ZMIZ2 OGDH
- 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 CREB3L1 AGO1 ARID4B SIN3A DMAP1 YY1 SLC30A9 FOS

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 Lys45
  • Modification sites at PhosphoSitePlus

Domains & Families for DDX56 Gene

Gene Families for DDX56 Gene

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

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 IDA,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

Clone 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

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,TAS --
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with DDX56: view

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,IEA --
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
Adenosine triphosphate Approved Nutra 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

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 34 35
  • 99.45 (n)
cow
(Bos Taurus)
Mammalia DDX56 34 35
  • 87.67 (n)
mouse
(Mus musculus)
Mammalia Ddx56 34 16 35
  • 85.47 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 85 (a)
OneToMany
-- 35
  • 75 (a)
OneToMany
-- 35
  • 74 (a)
OneToMany
-- 35
  • 72 (a)
OneToMany
dog
(Canis familiaris)
Mammalia DDX56 34 35
  • 84.85 (n)
rat
(Rattus norvegicus)
Mammalia Ddx56 34
  • 84.65 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX56 35
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx56 34
  • 64.29 (n)
zebrafish
(Danio rerio)
Actinopterygii ddx56 34 35
  • 63.17 (n)
fruit fly
(Drosophila melanogaster)
Insecta Hlc 35 34
  • 55.17 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP011147 34
  • 54.38 (n)
worm
(Caenorhabditis elegans)
Secernentea CELE_C24H12.4 34
  • 52.03 (n)
C24H12.4 35
  • 34 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR278C 34
  • 51.46 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C04576g 34
  • 50.38 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DBP9 34 35 37
  • 50.32 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G34910 34
  • 47.3 (n)
rice
(Oryza sativa)
Liliopsida Os03g0728800 34
  • 49.72 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU07070 34
  • 52.2 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 52 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC1494.06c 34
  • 49.84 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.7432 34
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

Relevant External Links for DDX56

Genetic Association Database (GAD)
DDX56
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DDX56

No disorders were found for DDX56 Gene.

No data available for MalaCards , 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 R.F. … Schmidt-Zachmann M.S. (Mol. Biol. Cell 2000) 2 3 4 22 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. Human chromosome 7: DNA sequence and biology. (PMID: 12690205) Scherer S.W. … Tsui L.-C. (Science 2003) 3 4 64
  5. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A. … Diaz J.-J. (Mol. Biol. Cell 2002) 3 4 64

Products for DDX56 Gene

Sources for DDX56 Gene

Content
Loading form....