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DDX1 Gene

protein-coding   GIFtS: 65
GCID: GC02P015731

DEAD (Asp-Glu-Ala-Asp) Box Helicase 1

(Previous names: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1, DEAD (Asp-Glu-Ala-Asp)...)
  See DDX1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
DEAD (Asp-Glu-Ala-Asp) Box Helicase 11 2     ATP-Dependent RNA Helicase DDX12
DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 11 2     DEAD Box Polypeptide 12
DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 11 2     DEAD Box-12
DBP-RB2 3     EC 3.6.4.133
DEAD Box Protein 12 3     EC 3.6.18
DEAD Box Protein Retinoblastoma2 3     EC 3.6.1.108
UKVH5d2     

External Ids:    HGNC: 27341   Entrez Gene: 16532   Ensembl: ENSG000000797857   OMIM: 6012575   UniProtKB: Q924993   

Export aliases for DDX1 gene to outside databases

Previous GC identifers: GC02P015736 GC02P015753 GC02P015682


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for DDX1 Gene:
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. This gene encodes a DEAD box protein of unknown function. It shows high
transcription levels in 2 retinoblastoma cell lines and in tissues of neuroectodermal origin. (provided by
RefSeq, Jul 2008)

GeneCards Summary for DDX1 Gene:
DDX1 (DEAD (Asp-Glu-Ala-Asp) box helicase 1) is a protein-coding gene. Diseases associated with DDX1 include heavy chain disease, and retinoblastoma. GO annotations related to this gene include chromatin binding and transcription cofactor activity. An important paralog of this gene is DDX3X.

UniProtKB/Swiss-Prot: DDX1_HUMAN, Q92499
Function: Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5'
single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA
polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the
template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a
coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional
regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the
NF-kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage
and polyadenylation of pre-mRNAs. Required for HIV-1 Rev function as well as for HIV-1 replication. Binds to the
RRE sequence of HIV-1 mRNAs

Gene Wiki entry for DDX1 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NC_018913.2  NT_005334.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the DDX1 gene promoter:
         TBP   Elk-1   NCX/Ncx   HNF-1A   HEN1   PPAR-gamma1   NRF-2   Nkx6-1   HNF-1   PPAR-gamma2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDDX1 promoter sequence
   Search Chromatin IP Primers for DDX1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DDX1


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

Entrez Gene cytogenetic band: 2p24   Ensembl cytogenetic band:  2p24.3   HGNC cytogenetic band: 2p24

DDX1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DDX1 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P015731:  view genomic region     (about GC identifiers)

Start:
15,731,302 bp from pter      End:
15,771,235 bp from pter
Size:
39,934 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: DDX1_HUMAN, Q92499 (See protein sequence)
Recommended Name: ATP-dependent RNA helicase DDX1  
Size: 740 amino acids; 82432 Da
Subunit: Interacts with PHF5A (via C-terminus) (By similarity). Interacts with MBNL1. Interacts with CSTF2.
Interacts with HNRNPK. Interacts with ATM. Interacts with RELA (via C-terminus). Interacts (via C-terminus) with
the replicase polyprotein 1ab Nsp14 of the avian infectious bronchitis virus (IBV). Interacts with Rev of HIV-1.
Interacts with severe acute respiratory syndrome coronavirus (SARS-CoV) (via N-terminus). Component of the
tRNA-splicing ligase complex
Caution: According to some authors the unwinding activity is ADP-dependent and not ATP-dependent (PubMed:18710941)

Explore the universe of human proteins at neXtProt for DDX1: NX_Q92499

Explore proteomics data for DDX1 at MOPED

Post-translational modifications: 

  • Phosphorylated. Phosphorylated by ATM kinase; phosphorylation is increased in response to ionizing radiation (IR)1
  • Ubiquitination2 at Lys90, Lys132, Lys281, Lys288, Lys307, Lys358
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for DDX1 (Q92499) (see all 34)
     VHAKDNT  DGYIVKS  YIVKSQH  IVVGTPG 


    See DDX1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_004930.1  
    ENSEMBL proteins: 
     ENSP00000370745   ENSP00000413767   ENSP00000233084  

    DDX1 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for DDX1

     
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    antibodies-online proteins for DDX1 (7 products) 

     
    antibodies-online peptides for DDX1

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    DDX: DEAD-boxes

    Selected InterPro protein domains (see all 9):
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR001870 B30.2/SPRY
     IPR027417 P-loop_NTPase
     IPR003877 SPRY_rcpt
     IPR014014 RNA_helicase_DEAD_Q_motif

    Graphical View of Domain Structure for InterPro Entry Q92499

    ProtoNet protein and cluster: Q92499

    1 Blocks protein domain: IPB000629 ATP-dependent helicase

    UniProtKB/Swiss-Prot: DDX1_HUMAN, Q92499
    Domain: The helicase domain is involved in the stimulation of RELA transcriptional activity
    Similarity: Belongs to the DEAD box helicase family. DDX1 subfamily
    Similarity: Contains 1 B30.2/SPRY domain
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain


    Find genes that share domains with DDX1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DDX1_HUMAN, Q92499
    Function: Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5'
    single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA
    polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the
    template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a
    coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional
    regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the
    NF-kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage
    and polyadenylation of pre-mRNAs. Required for HIV-1 Rev function as well as for HIV-1 replication. Binds to the
    RRE sequence of HIV-1 mRNAs
    Catalytic activity: ATP + H(2)O = ADP + phosphate

         Genatlas biochemistry entry for DDX1:
    DEAD/H box protein 1,frequently amplified in retinoblastoma,neuroblastoma,small cell carcinoma of the lung,with
    poor prognosis

         Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.1.102 EC 3.6.4.131

         Gene Ontology (GO): Selected molecular function terms (see all 15):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003677DNA binding IEA--
    GO:0003682chromatin binding IDA19058135
    GO:0003712transcription cofactor activity IDA19058135
    GO:0003724RNA helicase activity TAS7689221
         
    Find genes that share ontologies with DDX1           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for DDX1:
     G0/1 arrest  Increased G1 DNA content  Nuclear pre-40S maturation def 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for DDX1

    miRNA
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    miRTarBase miRNAs that target DDX1:
    hsa-mir-1260a (MIRT035849), hsa-mir-342-5p (MIRT038224)

    Block miRNA regulation of human, mouse, rat DDX1 using miScript Target Protectors
    4 qRT-PCR Assays for microRNAs that regulate DDX1:
    hsa-miR-200c hsa-miR-499-5p hsa-miR-429 hsa-miR-200b
    SwitchGear 3'UTR luciferase reporter plasmidDDX1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat DDX1

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    GenScript: all cDNA clones in your preferred vector: DDX1 (NM_004939)
    Sino Biological Human cDNA Clone for DDX1
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DDX1

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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    DDX1_HUMAN, Q92499: Nucleus. Cytoplasm. Cytoplasmic granule. Note=Localized with MBNL1, TIAL1 and YBX1 in stress
    granules upon stress. Localized with CSTF2 in cleavage bodies. Forms large aggregates called DDX1 bodies.
    Relocalized into multiple foci (IR-induced foci or IRIF) after IR treatment, a process that depends on the
    presence of chromosomal DNA and/or RNA-DNA duplexes. Relocalized at sites of DNA double-strand breaks (DSBs) in
    an ATM-dependent manner after IR treatment. Colocalized with RELA in the nucleus upon TNF-alpha induction.
    Relocalized to the cytoplasm with a perinuclear staining pattern in avian infectious bronchitis virus
    (IBV)-infected cells. Required for proper localization of HIV-1 Rev
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol3

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0010494cytoplasmic stress granule IDA18335541
    GO:0030529ribonucleoprotein complex IDA18809582

    Find genes that share ontologies with DDX1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for DDX1 About    
    See pathways by source

    SuperPathContained pathways About
    1mRNA Splicing - Major Pathway
    mRNA processing0.44


    1 BioSystems Pathway for DDX1
        mRNA processing



        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for DDX1
    Interactions:

        Search GeneGlobe Interaction Network for DDX1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for DDX1 (Q924992, 3 ENSP000002330844) via UniProtKB, MINT, STRING, and/or I2D (see all 681)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HNRNPKP619782, 3, ENSP000003654394MINT-7945693 I2D: score=3 STRING: ENSP00000365439
    ATMQ133152, 3, ENSP000002786164MINT-7945693 I2D: score=1 STRING: ENSP00000278616
    NBNO609342, 3, ENSP000002654334MINT-7945693 I2D: score=1 STRING: ENSP00000265433
    SRRM2Q9UQ352, 3, ENSP000003017404MINT-7945693 I2D: score=1 STRING: ENSP00000301740
    RELBQ012012, 3MINT-49034 I2D: score=2 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000245spliceosomal complex assembly NAS7689221
    GO:0006200ATP catabolic process IDA12183465
    GO:0006302double-strand break repair IDA18710941
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated IEA--

    Find genes that share ontologies with DDX1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for DDX1

    1 Novoseek inferred chemical compound relationship for DDX1 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    ornithine 29.7 3 8622876 (2), 9516849 (1)



    Find genes that share compounds with DDX1           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for DDX1 gene: 
    NM_004939.2  

    Unigene Cluster for DDX1:

    DEAD (Asp-Glu-Ala-Asp) box helicase 1
    Hs.440599  [show with all ESTs]
    Unigene Representative Sequence: NM_004939
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000381341 ENST00000434671 ENST00000459706 ENST00000470674 ENST00000478695
    ENST00000233084(uc010yjq.1 uc002rce.3 uc021vee.1)
    miRNA
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    4 qRT-PCR Assays for microRNAs that regulate DDX1:
    hsa-miR-200c hsa-miR-499-5p hsa-miR-429 hsa-miR-200b
    SwitchGear 3'UTR luciferase reporter plasmidDDX1 3' UTR sequence
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      QuantiTect SYBR Green Assays in human, mouse, rat DDX1
      QuantiFast Probe-based Assays in human, mouse, rat DDX1

    Additional mRNA sequence: 

    AB073360.1 AB593031.1 AB593032.1 AB593033.1 AB593034.1 AK297432.1 AK298212.1 AK298426.1 
    AK313933.1 BC012132.1 BC012739.2 BC053673.1 EF418570.1 EF418571.1 X70649.1 

    19 DOTS entries:

    DT.216759  DT.97781891  DT.121033032  DT.216760  DT.121033071  DT.121032940  DT.92456116  DT.95370517 
    DT.100836226  DT.121032951  DT.92456115  DT.100661145  DT.100782941  DT.121032866  DT.121032966  DT.121032987 
    DT.86845309  DT.95283542  DT.97857850 

    Selected AceView cDNA sequences (see all 613):

    NM_004939 BM451829 BX457707 CA951149 BQ926996 BF001359 BM667077 AW239481 
    BE794719 BQ071940 BQ887887 AU119158 BU189274 BQ900596 BQ881484 BQ938706 
    BQ956967 BQ069191 BF221694 BM458194 CF129875 AW673942 CA397223 BU150380 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for DDX1 (see all 7)    About this scheme

    ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^ 21a · 21b ^
    SP1:                                                                                                                                      -                 -   
    SP2:                                                                                                                                                            
    SP3:        -                                                                                                                                                   
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                      -                     

    ExUns: 22 ^ 23a · 23b · 23c ^ 24 ^ 25 ^ 26 ^ 27a · 27b
    SP1:        -           -                                 
    SP2:                    -                                 
    SP3:                                                      
    SP4:                                                      
    SP5:                                                      


    ECgene alternative splicing isoforms for DDX1

    (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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    DDX1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TCAAGAAACA
    DDX1 Expression
    About this image


    DDX1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 14) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 3 entries
             Primary Oocyte Primary Follicle
             Oviduct
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Gonad
             Primary Oocyte Primary Follicle
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
    DDX1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DDX1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.440599

    UniProtKB/Swiss-Prot: DDX1_HUMAN, Q92499
    Tissue specificity: Highest levels of transcription in 2 retinoblastoma cell lines and in tissues of
    neuroectodermal origin including the retina, brain, and spinal cord

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

    Orthologs for DDX1 gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ddx11 , 5 DEAD (Asp-Glu-Ala-Asp) box polypeptide 11, 5 90.23(n)1
    97.57(a)1
      12 (6.40 cM)5
    1047211  NM_134040.11  NP_598801.11 
     132193075 
    chicken
    (Gallus gallus)
    Aves DDX11 DEAD (Asp-Glu-Ala-Asp) box helicase 1 83.06(n)
    93.24(a)
      395249  NM_204563.1  NP_989894.1 
    lizard
    (Anolis carolinensis)
    Reptilia DDX16
    DEAD (Asp-Glu-Ala-Asp) box helicase 1
    91(a)
    1 ↔ 1
    1(144534119-144561341)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.15452 Xenopus laevis transcribed sequence with moderate similarity more 78.77(n)    CA973691.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.194662 Transcribed sequence with moderate similarity to protein more 76.87(n)    CB357242.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Ddx11 , 3 regulation of translational initiation
    helicase3
    Dead-box-11
    58(a)3
    57.89(n)1
    60.86(a)1
      3 79D33
    404571  NM_079488.41  NP_524212.21 
    worm
    (Caenorhabditis elegans)
    Secernentea Y55F3BR.11 , 3 Y55F3BR.11 47(a)
    (best of 2)3
    53.38(n)1
    50.35(a)1
      IV(874988-881841)3
    1769131  NM_067603.61  NP_500004.21 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes DED16
    ATP-dependent DEAD (Asp-Glu-Ala-Asp)-box RNA helic...
    23(a)
    1 → many
    XV(722911-724725) YOR204W


    ENSEMBL Gene Tree for DDX1 (if available)
    TreeFam Gene Tree for DDX1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DDX1 gene
    DDX3X2  DDX42  DDX3Y2  
    1 SIMAP similar gene for DDX1 using alignment to 4 protein entries:     DDX1_HUMAN (see all proteins):
    DDX59

    Find genes that share paralogs with DDX1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, 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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for DDX1 (see all 990)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs120533441,2
    C,F--15729762(+) GGGACG/AGCTTC 1 -- us2k11Minor allele frequency- A:0.22EA 120
    rs37551321,2
    C,F,H--15729820(+) GAGTAT/GTTCCC 1 -- us2k118Minor allele frequency- G:0.34NS EA WA NA 2338
    rs58295151,2
    C--15730045(+) TTTTT-/TAATTT 1 -- us2k1 tfbs30--------
    rs1421380511,2
    --15730169(+) GCCATC/GATGCC 1 -- us2k10--------
    rs1148082741,2
    F--15730202(+) AGGTGG/AGCATT 1 -- us2k11Minor allele frequency- A:0.02WA 118
    rs1511404691,2
    --15730326(+) ACACTA/GCATAA 1 -- us2k10--------
    rs749739781,2
    C,F--15730332(+) CATAAC/TTCTCA 1 -- us2k11Minor allele frequency- T:0.03WA 118
    rs1889447711,2
    --15730359(+) AAATAC/TAACAA 1 -- us2k10--------
    rs1140040691,2
    F--15730451(+) TTCAGG/ATGAAT 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs727808501,2
    C,F--15730503(+) CACCAT/CGTGCT 1 -- us2k14Minor allele frequency- C:0.16NA WA EA 360

    HapMap Linkage Disequilibrium report for DDX1 (15731302 - 15771235 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for DDX1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv515567CNV Gain+Loss19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing DDX1
    DNA2.0 Custom Variant and Variant Library Synthesis for DDX1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 601257    OMIM disorders: --

    2 diseases for DDX1:    
    About MalaCards
    heavy chain disease    retinoblastoma

    1 disease from the University of Copenhagen DISEASES database for DDX1:
    Neuroblastoma

    Find genes that share disorders with DDX1           About GenesLikeMe

    3 Novoseek inferred disease relationships for DDX1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoblastoma 65.2 8 9694872 (2), 17927523 (1), 8125309 (1), 8666277 (1) (see all 7)
    tumors 12.5 13 15226335 (2), 9694872 (2), 17927523 (1), 8834177 (1) (see all 10)
    leukemia 0 1 11598190 (1)

    Genetic Association Database (GAD): DDX1
    Human Genome Epidemiology (HuGE) Navigator: DDX1 (2 documents)

    Export disorders for DDX1 gene to outside databases

    (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)
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    PubMed articles for DDX1 gene, integrated from 10 sources (see all 105):
    (articles sorted by number of sources associating them with DDX1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DEAD-box RNA helicase DDX1 interacts with RelA and enhances nuclear factor kappaB-mediated transcription. (PubMed id 19058135)1, 2, 3, 9 Ishaq M.... Guo D. (J. Cell. Biochem. 2009)
    2. Association of human DEAD box protein DDX1 with a cleavage stimulation factor involved in 3'-end processing of pre-MRNA. (PubMed id 11598190)1, 2, 9 Bleoo S.... Godbout R. (Mol. Biol. Cell 2001)
    3. MBNL1 associates with YB-1 in cytoplasmic stress granules. (PubMed id 18335541)1, 2, 9 Onishi H.... Ishiura S. (J. Neurosci. Res. 2008)
    4. Genome-wide association and functional follow-up reveals new loci for kidney function. (PubMed id 22479191)1, 4 Pattaro C....Fox C.S. (PLoS Genet. 2012)
    5. Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function. (PubMed id 21946350)1, 4 Soler Artigas M....Tobin M.D. (Nat. Genet. 2011)
    6. The cellular RNA helicase DDX1 interacts with coronavirus nonstructural protein 14 and enhances viral replication. (PubMed id 20573827)1, 2 Xu L.... Liu D.X. (J. Virol. 2010)
    7. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PubMed id 19240061)1, 4 Trynka G....Wijmenga C. (Gut 2009)
    8. A role for DEAD box 1 at DNA double-strand breaks. (PubMed id 18710941)1, 2 Li L.... Godbout R. (Mol. Cell. Biol. 2008)
    9. A DEAD box protein facilitates HIV-1 replication as a cellular co- factor of Rev. (PubMed id 15567440)1, 2 Fang J....Pomerantz R.J. (Virology 2004)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1653 HGNC: 2734 AceView: DDX1 Ensembl:ENSG00000079785 euGenes: HUgn1653
    ECgene: DDX1 H-InvDB: DDX1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for DDX1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for DDX1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for DDX1 gene:
    Search GeneIP for patents involving DDX1

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



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