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DDX1 Gene

protein-coding   GIFtS: 63

GC02P015682
DEAD (Asp-Glu-Ala-Asp) box polypeptide 1
(Previous name: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
DBP-RB 1, 2, 3
EC 3.6.1.- 3
OTTHUMP00000115711 2
UKVH5d 2
Descriptions
DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 2
DEAD box polypeptide 1 2
DEAD box protein 1 3
DEAD box protein retinoblastoma 3
DEAD box-1 2
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1 1, 2
External Ids
HGNC: 27341
Entrez Gene: 16532
UniProtKB: Q924993
Ensembl: ENSG000000797857
Search outside databases for aliases for DDX1 gene

Previous GC identifers: GC02P015736 GC02P015753

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for DDX1:
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]

Gene Wiki entry for DDX1
(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the DDX1 gene  

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)

GeneLoc gene densities for chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P015682:     (about GC identifiers)

Start:
15,648,753 bp from pter
End:
15,688,676 bp from pter
Size:
39,924 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000002.10  NT_005334.15  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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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

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_004930.1  

    ENSEMBL proteins: 
    ENSP00000233084 ENSP00000370745 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
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    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (DDX1)
    Human Recombinant Proteins from Abnova (DDX1)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    1 Gene Ontology (GO) cellular component term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575 cellular_component ND--
    About this table

    Antibodies for DDX1: 
    Browse Antibodies Central at Invitrogen
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    Sigma-Aldrich Antibodies for DDX1
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (DDX1), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (DDX1)
    Novus Biologicals Antibodies for DDX1

    Assays for DDX1: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

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

    5/9 InterPro domains/families (see all 9 ):
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR000629 RNA-helicase_DEAD-box_CS
     IPR001870 B302
     IPR003877 SPRY_rcpt
     IPR014014 RNA_helicase_DEAD_Q_motif


       GeneDecks  DDX1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q92499

    ProtoNet protein and cluster: Q92499

    1 Blocks protein family: IPB000629 ATP-dependent helicase

    UniProtKB/Swiss-Prot: DDX1_HUMAN, Q92499
    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

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (DDX1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (DDX1)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004939

                  Applied Biosystems Silencer® siRNAs for DDX1

                  Sigma-Aldrich siRNA for DDX1  
                         Sigma-Aldrich shRNA Panels and shRNA for DDX1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for DDX1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_004939
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_004939
                                     untagged cDNA clone in CMV expression vector: NM_004939 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_004939

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

    5/7 Gene Ontology (GO) molecular function terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166 nucleotide binding IEA--
    GO:0003723 RNA binding IEA--
    GO:0003724 RNA helicase activity TAS7689221
    GO:0005515 protein binding IPI17220478
    GO:0005524 ATP binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


    1 Sigma-Aldrich "Your Favorite Gene" Pathway for  DDX1  (Your Favorite Gene powered by Ingenuity) 
     Purine Metabolism

       GeneDecks  DDX1 for the pathways selected above  
    About GeneDecksing


    5/11 Interacting proteins for DDX1 (ENSP000003707453 Q924991, 2) via UniProtKB, MINT, and/or STRING (see all 11 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NDRG1Q925971EBI-358474, EBI-716486
    RELBQ012012MINT-49034
    YWHAZP631042MINT-3296956
    U2AF1ENSP000003696293STRING (score=.883)
    RELAENSP000003115083STRING (score=.873)
    About this table

    3 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000245 spliceosome assembly NAS7689221
    GO:0006446 regulation of translational initiation NAS7689221
    GO:0007275 multicellular organismal development IEP7689221
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for DDX1
    1 Novoseek chemical compound relationship for DDX1 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    ornithine 31.57 3 8622876 (2), 9516849 (1)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (DDX1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (DDX1)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_004939

                  Sigma-Aldrich siRNA for DDX1  
                         Sigma-Aldrich shRNA Panels and shRNA for DDX1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_004939  

    REFSEQ mRNAs for DDX1 gene: 

    NM_004939.1   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_004939  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_004939
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_004939
                                     untagged cDNA clone in CMV expression vector: NM_004939 

    Additional cDNA sequence: 

    AB073360.1 AK297432.1 AK298212.1 AK298426.1 AK313933.1 BC012132.1 BC012739.2 BC053673.1 
    CR598216.1 EF418570.1 EF418571.1 X70649.1 

    19 DOTS entries:

    DT.216759  DT.97781891  DT.216760  DT.121033032  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 

    24/613 AceView cDNA sequences (see all 613 ):

    BQ887887 BQ068757 BF221694 BE778011 BQ431462 BQ900532 BQ071989 AU119158 
    CR598216 BM564810 BQ012281 AW239481 BM667077 N86125 BQ938706 BM459532 
    BQ926996 BQ892053 CF129875 CA951149 BM451829 BF001359 BI492047 BG434386 

    highest scoring ESTs for DDX1:

    X70649 AA044422 AA137212 AA173161 AA211413 AA232235 AA316093 AA365029 AA425687 AA573220 

    Unigene Cluster for DDX1:

    DEAD (Asp-Glu-Ala-Asp) box polypeptide 1
    Hs.440599  [show with all ESTs]
    Unigene Representative Sequence: NM_004939


    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for DDX1 (see all 7 )

    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:                                                      

    About this scheme

    ECgene alternative splicing isoforms for DDX1

    2 Ensembl transcripts including schematic representations:
    ENST00000233084  ENST00000381341  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    DDX1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for DDX1

    1 / 2 / 3

    3 probe-sets matching DDX1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    37663_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 X70649 1.00 1.00 1.00 1

    201241_at2, 3 U133-A 1 1.00 1.00 -- -- NM_004939 0.60 1.00 0.82 1

    201241_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: TCAAGAAACA

    SOURCE GeneReport for Unigene cluster: Hs.440599

    Expression variation in blood from EXPOLDB for DDX1

    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

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for DDX1 gene from 5/15 species (see all 15 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    DDX11   -- DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 93.51(n)
    97.7(a)
    475671  XM_843772.1  XP_848865.1 
    chimpanzee
    (Pan troglodytes)
    DDX11   -- DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 99.55(n)
    99.86(a)
    459042  XM_001162182.1  XP_001162182.1 
    cow
    (Bos taurus)
    DDX11   -- DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 91.4(n)
    97.3(a)
    510816  NM_001075468.1  NP_001068936.1 
    rat
    (Rattus norvegicus)
    Ddx11   -- DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 89.95(n)
    97.7(a)
    84474  NM_053414.1  NP_445866.1 
    mouse
    (Mus musculus)
    Ddx11, 5 125
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 11, 5 90.23(n)1
    97.57(a)1
    1047211  NM_134040.11  NP_598801.11 
     AA4091855  AK0283415  (see all 15)
    About this table        Species with no ortholog for DDX1

    ENSEMBL Gene Tree for DDX1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for DDX1 gene
    DDX242  DDX512  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/290 NCBI SNPs in DDX1 are shown (see all 290 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 121)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 2 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs46689361,2
    A,C,F,H15649056(+) ACTCAT/CTGGCA 1 -- ng514Minor allele frequency- C:0.17EU EA WA 382
    rs46689491,2
    A,C,F,H15689066(+) CCCATC/TAAAGT 1 -- ng317Minor allele frequency- T:0.28EU EA WA NA 550
    rs101537291,2
    A,C,F,H15649310(+) CCCAGC/AGGTCC 1 -- ut51 ese38Minor allele frequency- A:0.34EU EA WA 828
    rs168628071,2
    C,F,H15688824(+) ATTCTA/GAAAGT 1 -- ng317Minor allele frequency- G:0.08NA EU EA WA 550
    rs37551331,2
    C,F,H15649034(+) AAATAC/TCTACT 1 -- ng519Minor allele frequency- T:0.25EU EA WA NA MN 1804
    rs46689481,2
    C,F,H15689037(+) TATGAA/CCCTTG 1 -- ng317Minor allele frequency- C:0.28EU EA WA NA 548
    rs37551321,2
    C,F,H15647271(+) GAGTAT/GTTCCC 1 -- ng514Minor allele frequency- G:0.31EU EA WA 418
    rs22779131,2
    C,F15649453(+) CACGCC/TGTGTC 1 -- ut51 ese32Minor allele frequency- T:0.13MN EA 1252
    rs102217701,2
    A,C15649449(+) CTGCCA/GCGCCG 1 -- ut51 ese30--------
    --
    rs129958391,2
    H15681147(+) ATACAA/CCAAGG 1 Q/H mis1 ese34Minor allele frequency- C:0.00EU EA WA 406
    About this table

    HapMap Linkage Disequilibrium images for DDX1 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 601257

    3 Novoseek disease relationships for DDX1 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinoblastoma 66.64 8 9694872 (2), 17927523 (1), 8125309 (1), 8666277 (1) (see all 7)
    tumors 11.99 12 15226335 (2), 9694872 (2), 17927523 (1), 8834177 (1) (see all 9)
    leukemia 0.00 1 11598190 (1)
    About this table

    Human Genome Epidemiology Navigator: DDX1 (1 document)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

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

    10/50 PubMed articles for DDX1 gene (see all 50 ):
    (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)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 1653 HGNC: 2734 AceView: DDX1 Ensembl:ENSG00000079785 euGenes: HUgn1653
    ECgene: DDX1 H-InvDB: DDX1
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for DDX1 Genetics and Cytogenetics in Oncology and Haematology
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for DDX1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for DDX1 Antibodies for DDX1
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for DDX1 Browse small molecules at Sigma-Aldrich
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     Antibodies for DDX1

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