DDX60 Gene (Protein Coding)

DExD/H-Box Helicase 60

GC04M168216
GIFtS:
35
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases which are implicated in a number of cellular procsses involving RNA binding and alteration of RNA secondary structure. This gene encodes a DEXD/H box RNA helicase that functions as an antiviral factor and promotes RIG-I-like receptor-mediated signaling. [provided by RefSeq... See more...

Aliases for DDX60 Gene

Aliases for DDX60 Gene

  • DExD/H-Box Helicase 60 2 3 5
  • Probable ATP-Dependent RNA Helicase DDX60 3 4
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 60 2 3
  • DEAD Box Protein 60 3 4
  • ATP-Dependent RNA Helicase DDX60 3
  • DEAD-Box Helicase 60 3
  • EC 3.6.4.13 4

External Ids for DDX60 Gene

Previous GeneCards Identifiers for DDX60 Gene

  • GC04M169375
  • GC04M169137
  • GC04M164890

Summaries for DDX60 Gene

Entrez Gene Summary for DDX60 Gene

  • DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases which are implicated in a number of cellular procsses involving RNA binding and alteration of RNA secondary structure. This gene encodes a DEXD/H box RNA helicase that functions as an antiviral factor and promotes RIG-I-like receptor-mediated signaling. [provided by RefSeq, Apr 2017]

GeneCards Summary for DDX60 Gene

DDX60 (DExD/H-Box Helicase 60) is a Protein Coding gene. Diseases associated with DDX60 include Autosomal Recessive Alport Syndrome. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and hydrolase activity. An important paralog of this gene is DDX60L.

UniProtKB/Swiss-Prot Summary for DDX60 Gene

  • Positively regulates DDX58/RIG-I- and IFIH1/MDA5-dependent type I interferon and interferon inducible gene expression in response to viral infection. Binds ssRNA, dsRNA and dsDNA and can promote the binding of DDX58/RIG-I to dsRNA. Exhibits antiviral activity against hepatitis C virus and vesicular stomatitis virus (VSV).

Additional gene information for DDX60 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DDX60 Gene

Genomics for DDX60 Gene

GeneHancer (GH) Regulatory Elements for DDX60 Gene

Promoters and enhancers for DDX60 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH04J168317 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 -0.1 -88 3 TCF12 SP1 PHF8 CTCF ZIC2 POLR2A ZBTB26 RCOR1 TRIM22 HDAC2 DDX60 lnc-ANXA10-6 DDX60L
GH04J168479 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 35.4 -165.3 -165322 12.7 TCF12 POLR2G JUND PHF8 FOS ZIC2 ZBTB10 POLR2A ZNF423 ZBTB26 DDX60L DDX60 PALLD ENSG00000207171 lnc-DDX60L-3
GH04J169007 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11.1 -690.3 -690328 4.3 ZBTB40 ZNF217 CTCF ZSCAN5C SIN3A MYC NRF1 POLR2G NCOR1 GTF2E2 CBR4 ENSG00000251445 DDX60 ENSG00000251171 lnc-SH3RF1-2
GH04J168501 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11.3 -188.1 -188093 11.8 ZBTB40 ZNF217 EP300 TCF12 JUND FOS FOXA1 CUX1 GATAD2B CTBP1 DDX60L DDX60 ENSG00000207171 ENSG00000249623 PALLD lnc-DDX60L-3
GH04J168557 Enhancer 1.5 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.2 -241.8 -241787 6 TCF12 JUND FOS ZNF639 ZIC2 FOXA1 EP300 CTBP1 ZBTB17 NR3C1 DDX60L PALLD RNU6-1336P ENSG00000249623 DDX60 lnc-ANXA10-1 lnc-DDX60L-3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DDX60 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DDX60

Top Transcription factor binding sites by QIAGEN in the DDX60 gene promoter:
  • AP-4
  • C/EBPalpha
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • p300
  • RORalpha1

Genomic Locations for DDX60 Gene

Genomic Locations for DDX60 Gene
chr4:168,216,291-168,318,807
(GRCh38/hg38)
Size:
102,517 bases
Orientation:
Minus strand
chr4:169,137,442-169,239,958
(GRCh37/hg19)
Size:
102,517 bases
Orientation:
Minus strand

Genomic View for DDX60 Gene

Genes around DDX60 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX60 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX60 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for DDX60 Gene

Proteins for DDX60 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for DDX60 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IY21-DDX60_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase DDX60
    Protein Accession:
    Q8IY21
    Secondary Accessions:
    • Q6PK35
    • Q9NVE3

    Protein attributes for DDX60 Gene

    Size:
    1712 amino acids
    Molecular mass:
    197853 Da
    Quaternary structure:
    • Interacts with EXOSC1, EXOSC4, DDX58/RIG-I, IFIH1/MDA5 and DHX58/LGP2.

neXtProt entry for DDX60 Gene

Protein Expression for DDX60 Gene

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

Post-translational modifications for DDX60 Gene

  • Ubiquitination at Lys834
  • Modification sites at PhosphoSitePlus

Other Protein References for DDX60 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for DDX60 Gene

Domains & Families for DDX60 Gene

Gene Families for DDX60 Gene

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

Protein Domains for DDX60 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for DDX60 Gene

GenScript: Design optimal peptide antigens:
  • DEAD box protein 60 (DDX60_HUMAN)
  • DDX60 protein (Q6B0F7_HUMAN)
  • cDNA: FLJ22680 fis, clone HSI10688 (Q9H616_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8IY21

UniProtKB/Swiss-Prot:

DDX60_HUMAN :
  • Belongs to the helicase family.
Family:
  • Belongs to the helicase family.
genes like me logo Genes that share domains with DDX60: view

Function for DDX60 Gene

Products:

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

Molecular function for DDX60 Gene

UniProtKB/Swiss-Prot Function:
Positively regulates DDX58/RIG-I- and IFIH1/MDA5-dependent type I interferon and interferon inducible gene expression in response to viral infection. Binds ssRNA, dsRNA and dsDNA and can promote the binding of DDX58/RIG-I to dsRNA. Exhibits antiviral activity against hepatitis C virus and vesicular stomatitis virus (VSV).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;.
UniProtKB/Swiss-Prot Induction:
By interferon (IFN). Up-regulated during vesicular stomatitis virus (VSV), or poliovirus (PV) infection.

Enzyme Numbers (IUBMB) for DDX60 Gene

Phenotypes From GWAS Catalog for DDX60 Gene

Gene Ontology (GO) - Molecular Function for DDX60 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003690 double-stranded DNA binding IDA 21791617
GO:0003723 RNA binding IEA --
GO:0003724 RNA helicase activity IEA --
GO:0003725 double-stranded RNA binding IDA 21791617
genes like me logo Genes that share ontologies with DDX60: view
genes like me logo Genes that share phenotypes with DDX60: view

Animal Models for DDX60 Gene

MGI Knock Outs for DDX60:
  • Ddx60 Ddx60<tm1b(EUCOMM)Wtsi>
  • Ddx60 Ddx60<tm1d(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

miRNA for DDX60 Gene

miRTarBase miRNAs that target DDX60

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DDX60 Gene

Localization for DDX60 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX60 Gene

Cytoplasm.

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 DDX60 gene
Compartment Confidence
cytosol 5
cytoskeleton 4
plasma membrane 3
nucleus 2
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Intermediate filaments (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX60 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA,IEA 21791617
GO:0005829 cytosol IDA --
GO:0045111 intermediate filament cytoskeleton IDA --
genes like me logo Genes that share ontologies with DDX60: view

Pathways & Interactions for DDX60 Gene

PathCards logo

SuperPathways for DDX60 Gene

No Data Available

Gene Ontology (GO) - Biological Process for DDX60 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002376 immune system process IEA --
GO:0009615 response to virus IDA 21791617
GO:0045087 innate immune response IEA --
GO:0051607 defense response to virus IEA --
GO:1900245 positive regulation of MDA-5 signaling pathway IMP 21791617
genes like me logo Genes that share ontologies with DDX60: view

No data available for Pathways by source and SIGNOR curated interactions for DDX60 Gene

Drugs & Compounds for DDX60 Gene

Products:

  1. Drug

(3) Drugs for DDX60 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, Activator, Full agonist, Antagonist, Pore Blocker, Potentiation 0

(1) Additional Compounds for DDX60 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
 Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with DDX60: view

Transcripts for DDX60 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for DDX60 Gene

1 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX60 Gene

No ASD Table

Relevant External Links for DDX60 Gene

GeneLoc Exon Structure for
DDX60

Expression for DDX60 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for DDX60 Gene

mRNA expression in normal human tissues for DDX60 Gene
mRNA expression by GTEx for DDX60 GenemRNA expression by BioGPS for DDX60 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDX60 Gene

This gene is overexpressed in Cervix (13.3), CD8 Tcells (9.7), Peripheral blood mononuclear cells (8.3), and Placenta (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DDX60 Gene



Protein tissue co-expression partners for DDX60 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DDX60

SOURCE GeneReport for Unigene cluster for DDX60 Gene:

Hs.591710

mRNA Expression by UniProt/SwissProt for DDX60 Gene:

Q8IY21-DDX60_HUMAN
Tissue specificity: Brain, lymph node, prostate, stomach, thyroid, tongue, trachea, uterus, skeletal muscle, spleen, kidney, liver and small intestine.

Evidence on tissue expression from TISSUES for DDX60 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with DDX60: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX60 Gene

Orthologs for DDX60 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for DDX60 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia DDX60 31 30
  • 99.51 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia DDX60 31 30
  • 84.48 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Ddx60 17 31 30
  • 79.55 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 62 (a)
 OneToMany
-- 31
  • 46 (a)
 OneToMany
oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 49 (a)
 OneToMany
chicken
(Gallus gallus)
 Aves DDX60 31 30
  • 63.31 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia DDX60 31
  • 57 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia ddx60 30
  • 59.46 (n)
worm
(Caenorhabditis elegans)
 Secernentea C28H8.3 31 30
  • 45.2 (n)
 OneToMany
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes MTR4 31
  • 16 (a)
 OneToMany
Species where no ortholog for DDX60 was found in the sources mined by GeneCards:
  • 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)
  • cow (Bos Taurus)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for DDX60 Gene

ENSEMBL:
Gene Tree for DDX60 (if available)
TreeFam:
Gene Tree for DDX60 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DDX60: view image

Paralogs for DDX60 Gene

Paralogs for DDX60 Gene

(3) SIMAP similar genes for DDX60 Gene using alignment to 6 proteins:

  • DDX60_HUMAN
  • D6R944_HUMAN
  • H0Y8Z7_HUMAN
  • H0Y9B2_HUMAN
  • Q6B0F7_HUMAN
  • Q9H616_HUMAN

Pseudogenes.org Pseudogenes for DDX60 Gene

genes like me logo Genes that share paralogs with DDX60: view

Variants for DDX60 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DDX60 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
rs864622021 Uncertain Significance: Malignant tumor of prostate 168,280,400(-) T/C MISSENSE_VARIANT
rs550625 - p.Val672Met
rs576619 - p.Ile998Val

Additional dbSNP identifiers (rs#s) for DDX60 Gene

Structural Variations from Database of Genomic Variants (DGV) for DDX60 Gene

Variant ID Type Subtype PubMed ID
esv2728712 CNV deletion 23290073
esv2728713 CNV deletion 23290073
nsv4596 CNV insertion 18451855
nsv474625 CNV novel sequence insertion 20440878
nsv830146 CNV gain 17160897

Variation tolerance for DDX60 Gene

Residual Variation Intolerance Score: 4.36% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.76; 73.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX60 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX60

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX60 Gene

Disorders for DDX60 Gene

MalaCards: The human disease database

(1) MalaCards diseases for DDX60 Gene - From: DISEASES

Disorder Aliases PubMed IDs
autosomal recessive alport syndrome
  • alport syndrome autosomal recessive
- elite association - COSMIC cancer census association via MalaCards
Search DDX60 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for DDX60

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with DDX60: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DDX60 Gene

Publications for DDX60 Gene

  1. DDX60, a DEXD/H box helicase, is a novel antiviral factor promoting RIG-I-like receptor-mediated signaling. (PMID: 21791617) Miyashita M … Seya T (Molecular and cellular biology 2011) 2 3 4 54
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  3. A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape. (PMID: 30833792) Hubel P … Pichlmair A (Nature immunology 2019) 3 54
  4. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. (PMID: 29987050) Xiao T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2018) 3 54
  5. Interactome and Proteome Dynamics Uncover Immune Modulatory Associations of the Pathogen Sensing Factor cGAS. (PMID: 30471916) Lum KK … Cristea IM (Cell systems 2018) 3 54

ExternalLinks

View latest publications for DDX60 gene in Mastermind

Products for DDX60 Gene

Sources for DDX60 Gene