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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

DDX60 Gene

protein-coding   GIFtS: 43
GCID: GC04M169137

DEAD (Asp-Glu-Ala-Asp) box polypeptide 60
 Explore 12 diseases affiliated with
DDX60 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for DDX60    

Aliases
for DDX60 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 601 2
DEAD Box Protein 602 3
FLJ200351
Probable ATP-Dependent RNA Helicase DDX602
EC 3.6.4.133

External Ids:    HGNC: 259421   Entrez Gene: 556012   Ensembl: ENSG000001376287   OMIM: 6139745   UniProtKB: Q8IY213   

Export aliases for DDX60 gene to outside databases

Previous GC identifers: GC04M169375 GC04M164890


Summaries
for DDX60 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
UniProtKB/Swiss-Prot: DDX60_HUMAN, Q8IY21
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)




Genomic Views
for DDX60 gene

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_016354.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the DDX60 gene promoter:
         RORalpha1   NF-AT4   NF-AT2   p300   NF-AT3   AP-4   NF-AT   NF-AT1   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: DDX60 promoter sequence
   Search SABiosciences Chromatin IP Primers for DDX60

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat DDX60


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 4q32.3   Ensembl cytogenetic band:  4q32.3   HGNC cytogenetic band: 4q32.3

DDX60 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DDX60 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M169137:  view genomic region     (about GC identifiers)

Start:
 169,137,442 bp from pter      End:
 169,239,958 bp from pter
Size:
 102,517 bases      Orientation:
 minus strand

Proteins
for DDX60 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB/Swiss-Prot: DDX60_HUMAN, Q8IY21 (See protein sequence)
Recommended Name: Probable ATP-dependent RNA helicase DDX60  
Size: 1712 amino acids; 197853 Da
Subunit: Interacts with EXOSC1, EXOSC4, DDX58/RIG-I, IFIH1/MDA5 and DHX58/LGP2
Subcellular location: Cytoplasm
Secondary accessions: Q6PK35 Q9NVE3

Explore the universe of human proteins at neXtProt for DDX60: NX_Q8IY21

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8IY21

    • DDX60 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_060101.3  
    ENSEMBL proteins: 
     ENSP00000377344   ENSP00000422669   ENSP00000423678   ENSP00000423647  

    Human Recombinant Protein Products: 
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    Novus Biologicals DDX60 Lysate
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    Uscn Proteins for DDX60

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005737cytoplasm IDA--


    DDX60 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for DDX60

    Protein Domains /
    Families
    for DDX60 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    DDX60 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR014001 Helicase_ATP-bd
     IPR001650 Helicase_C

    Graphical View of Domain Structure for InterPro Entry Q8IY21

    ProtoNet protein and cluster: Q8IY21

    UniProtKB/Swiss-Prot: DDX60_HUMAN, Q8IY21
    Similarity: Belongs to the helicase family
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain


    Function
    for DDX60 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

         UniProtKB/Swiss-Prot: DDX60_HUMAN, Q8IY21
    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)
    Catalytic activity: ATP + H(2)O = ADP + phosphate
    Induction: By interferon (IFN). Up-regulated during vesicular stomatitis virus (VSV), or poliovirus (PV) infection

    Enzyme Number (IUBMB): EC 3.6.4.131

    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmid: DDX60 3' UTR sequence
    Inhib. RNA
    Products:            		Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for DDX60 (see all 3)
    OriGene siRNA: DDX60
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    Gene Editing
    Products:    		DNA2.0 Custom Protein Engineering Service for DDX60

    Clone
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    Cell Line
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    Search LifeMap BioReagents cell lines for DDX60

    In Situ Assay
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    Gene Ontology (GO): 5/7 molecular function terms (GO ID links to tree view) (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003690double-stranded DNA binding IDA--
    GO:0003723RNA binding ----
    GO:0003725double-stranded RNA binding IDA--
    GO:0003727single-stranded RNA binding IDA--
    GO:0005515protein binding IPI--


    DDX60 for ontologies           About GeneDecksing



    Pathways & Interactions
    for DDX60 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for DDX60

    STRING Interaction Network Preview (showing 5 interactants - click image to see more details)

    5 Interacting proteins for DDX60 (ENSP000003773444) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EXOSC1ENSP000003599394STRING: ENSP00000359939
    DDX58ENSP000003692134STRING: ENSP00000369213
    DHX58ENSP000002516424STRING: ENSP00000251642
    EXOSC4ENSP000003154764STRING: ENSP00000315476
    IFIH1ENSP000002636424STRING: ENSP00000263642
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0009615response to virus IDA--
    GO:0045087innate immune response IEA--
    GO:0051607defense response to virus IEA--
    GO:1900245positive regulation of MDA-5 signaling pathway IMP--
    GO:1900246positive regulation of RIG-I signaling pathway IMP--


    DDX60 for ontologies           About GeneDecksing



    Drugs & Compounds
    for DDX60 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for DDX60
    Search CenterWatch for drugs/clinical trials and news about DDX60 

    Transcripts
    for DDX60 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section
    REFSEQ mRNAs for DDX60 gene: 
    NM_017631.5  

    Unigene Cluster for DDX60:

    DEAD (Asp-Glu-Ala-Asp) box polypeptide 60
    Hs.591710  [show with all ESTs]
    Unigene Representative Sequence: NM_017631
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000393743(uc003irp.3 uc003iro.3) ENST00000511317 ENST00000507815
    ENST00000505393 ENST00000513997 ENST00000514995

    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmid: DDX60 3' UTR sequence
    Inhib. RNA
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    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for DDX60 (see all 3)
    OriGene siRNA: DDX60
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    Clone
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    Primer
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    Additional cDNA sequence: 

    AK000042.1 AK001649.1 AK026333.1 AK223184.1 AK225191.1 AK307404.1 AL137464.1 BC007820.2 
    BC020601.1 BC038115.2 BC074781.2 BX648655.1 

    6 DOTS entries:

    DT.40121440  DT.100779132  DT.92417354  DT.100861376  DT.95269757  DT.95269760 

    24/102 AceView cDNA sequences (see all 102):

    CR620318 BF508126 AI990745 BP346012 BU161524 AW512348 BC007820 AW150758 
    AI383115 AK026333 BX648655 CB126090 AI926267 BQ425955 CA390354 AI687639 
    BG622111 AK001649 BU185203 AI625970 AL137464 AI520911 BX646368 BC074781 

    GeneLoc Exon Structure


    Expression
    for DDX60 gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    DDX60 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: AATACTCACA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    DDX60 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Primordial germ cell-like cells (Reconstitution of mo...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See DDX60 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for DDX60

    SOURCE GeneReport for Unigene cluster: Hs.591710

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

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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DDX60

    Orthologs
    for DDX60 gene

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section
    This gene was present in the common ancestor of animals.

    Orthologs for DDX60 gene from 3/14 species (see all 14)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    chicken
    (Gallus gallus)    		 Aves DDX601 DEAD (Asp-Glu-Ala-Asp) box polypeptide 60 63.27(n)
    55.28(a)    		   422427  XM_003641151.1  XP_003641199.1 
    lizard
    (Anolis carolinensis)    		 Reptilia --
    		 --
    		 58(a)
    		 possible ortholog
    		 GL343216.1(130853-184202)
    worm
    (Caenorhabditis elegans)    		 Secernentea C28H8.31 Protein C28H8.3 44.77(n)
    31.46(a)    		   175834  NM_065882.3  NP_498283.1 


    ENSEMBL Gene Tree for DDX60 (if available)
    TreeFam Gene Tree for DDX60 (if available) 

    Paralogs
    for DDX60 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for DDX60 gene
    DDX60L2  SKIV2L2  
    3 SIMAP similar genes for DDX60 using alignment to 6 protein entries:     DDX60_HUMAN (see all proteins):
    DKFZp434E1722    DKFZp686E11248    DDX60L

    DDX60 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for DDX60
    PGOHUM00000244479


    Genomic Variants
    for DDX60 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing DDX60
    DNA2.0 Custom Variant and Variant Library Synthesis for DDX60

    Disorders / Diseases
    for DDX60 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    DDX60 for disorders           About GeneDecksing

    OMIM gene information: 613974    OMIM disorders: --

    12 diseases for DDX60:    About MalaCards
    venezuelan equine encephalitis    yellow fever    chikungunya    encephalitis
    hepatitis c    hepatitis    tuberculosis    malaria
    stomatitis    mycobacterium tuberculosis    thyroiditis    prostatitis


    Export disorders for DDX60 gene to outside databases

    Publications
    for DDX60 gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for DDX60 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with DDX60)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. DDX60, a DEXD/H box helicase, is a novel antiviral fa ctor promoting RIG-I-like receptor-mediated signaling. (PubMed id 21791617)1, 2 Miyashita M....Seya T. (2011)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
    4. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    5. A diverse range of gene products are effectors of the type I interferon antiviral response. (PubMed id 21478870)2 Schoggins J.W.... Rice C.M. (2011)
    6. Tandem immunoprecipitation of phosphotyrosine-mass spectrometry (TIPY-MS) indicates C19ORF19 becomes tyrosine-phosphorylated and associated with activated epidermal growth factor receptor. (PubMed id 18271526)1 Tong J....Moran M.F. (2008)
    7. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W....Wilson R.K. (2005)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    9. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. (PubMed id 8125298)1 Maruyama K. and Sugano S. (1994)

    External Searches for DDX60 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Free Text  
      Query String
    		PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing DDX60 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 55601 HGNC: 25942 AceView: FLJ20035 Ensembl:ENSG00000137628 euGenes: HUgn55601
    ECgene: DDX60 H-InvDB: DDX60

    Other Databases showing DDX60 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing DDX60 gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for DDX60 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for DDX60 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for DDX60 gene:
    Search GeneIP for patents involving DDX60

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for DDX60 gene

    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
    In Situ Hybridization Assays from
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     QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat DDX60
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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    VWF
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    von Willebrand factor
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