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    DDX1 DEAD-box helicase 1 [ Homo sapiens (human) ]

    Gene ID: 1653, updated on 7-Apr-2024

    Summary

    Official Symbol
    DDX1provided by HGNC
    Official Full Name
    DEAD-box helicase 1provided by HGNC
    Primary source
    HGNC:HGNC:2734
    See related
    Ensembl:ENSG00000079785 MIM:601257; AllianceGenome:HGNC:2734
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DBP-RB; UKVH5d
    Summary
    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 that acts as an ATP-dependent RNA helicase that has been found to promote coronaviruses replication. [provided by RefSeq, Aug 2021]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in SARS-CoV-2 infection.
    Expression
    Ubiquitous expression in thyroid (RPKM 36.4), brain (RPKM 36.1) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    Location:
    2p24.3
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (15591868..15631101)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (15623489..15662692)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (15731992..15771225)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373440 Neighboring gene uncharacterized LOC124905975 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15347 Neighboring gene MPRA-validated peak3608 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:15833968-15834468 Neighboring gene long intergenic non-protein coding RNA 1804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11185 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:15886207-15886368 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:15900134-15900634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:15900635-15901135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:15909490-15910388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:15921105-15922052 Neighboring gene uncharacterized LOC124905976

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies susceptibility loci for Wilms tumor.
    EBI GWAS Catalog
    Common genes underlying asthma and COPD? Genome-wide analysis on the Dutch hypothesis.
    EBI GWAS Catalog
    Genome-wide association and functional follow-up reveals new loci for kidney function.
    EBI GWAS Catalog
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of DDX1 by siRNA inhibits HIV-1 replication in HIV-1-infected HeLa cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box helicase 1 (DDX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box helicase 1 (DDX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Nef nef Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box helicase 1 (DDX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box helicase 1 (DDX1), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
    Rev rev Overexpression of DDX1 can compensate for the inhibitory effect of HIV-1 Tat mutant Nullbasic on HIV-1 Rev function PubMed
    rev HIV-1 Tat mutant Nullbasic can compete with HIV-1 Rev for binding to DDX1 and the interaction of Nullbasic with DDX1 is not through Tat's basic domain PubMed
    rev DDX1 co-localizes with HIV-1 Rev in the nucleolus. DDX1 interacts with DDX3 or DDX5 and synergistically enhances the Rev function PubMed
    rev The RNA helicase DDX1 interacts with HIV-1 Rev through yeast two-hybrid screening and co-immunoprecipitation assays, and DDX1 is required for proper subcellular localization of Rev PubMed
    rev DDX1 interacts with HIV-1 Rev and promotes oligomerization of Rev on the RRE. The location of the DDX1 binding region in Rev is amino acids 10 to 24 PubMed
    rev HIV-1 Rev interacting protein, DEAD (Asp-Glu-Ala-Asp) box polypeptide 1 (DDX1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with DDX1 is increased by RRE PubMed
    rev The HIV-1 Rev V16D, I55N, and V16D/I55N mutants abolish the interaction between Rev and DDX1 PubMed
    rev Overexpression of exogenous DDX1 significantly alters both Rev sub-cellular localization from cytoplasmic to nuclear predominance and concomitantly increases HIV-1 viral production in human astrocytes PubMed
    rev Endogenous DDX1 expression in human astrocytes leads to a shift of Rev sub-cellular distribution dominance from nuclear and/or nucleolar to cytoplasmic PubMed
    rev DDX1 is capable of binding to HIV-1 RRE RNA in vivo, suggesting an interaction with HIV-1 Rev, however DDX1 alone cannot rescue HIV-1 virion production from a Rev-negative provirus in the absence of Rev PubMed
    Tat tat DEAD (Asp-Glu-Ala-Asp) box helicase 1 (DDX1) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS PubMed
    tat HIV-1 Tat mutant Nullbasic can compete with HIV-1 Rev for binding to DDX1 and the interaction of Nullbasic with DDX1 is not through Tat's basic domain PubMed
    tat HIV-1 Tat mutant Nullbasic significantly enhances the level of DDX1 in the cytoplasm compared with in its absence PubMed
    tat Overexpression of DDX1 can compensate for the inhibitory effect of HIV-1 Tat mutant Nullbasic on HIV-1 Rev function PubMed
    capsid gag Coexpression of HIV-1 Rev with DDX1 greatly downregulate the expression of HIV-1 CA in HeLa cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA/RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables double-stranded RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables exonuclease activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables nuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables poly(A) binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription coregulator activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cleavage body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytoplasmic stress granule IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in membrane HDA PubMed 
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of tRNA-splicing ligase complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of tRNA-splicing ligase complex NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    ATP-dependent RNA helicase DDX1
    Names
    DEAD (Asp-Glu-Ala-Asp) box helicase 1
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 1
    DEAD box polypeptide 1
    DEAD box protein 1
    DEAD box protein retinoblastoma
    DEAD box-1
    DEAD-box RNA helicase DDX1
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1
    DEAD/H-box helicase 1
    NP_004930.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_004939.3NP_004930.1  ATP-dependent RNA helicase DDX1

      See identical proteins and their annotated locations for NP_004930.1

      Status: REVIEWED

      Source sequence(s)
      BC053673, X70649
      Consensus CDS
      CCDS1686.1
      UniProtKB/Swiss-Prot
      B4DME8, B4DPN6, Q92499
      UniProtKB/TrEMBL
      A0A7I2V4F0, A3RJH1
      Related
      ENSP00000233084.3, ENST00000233084.8
      Conserved Domains (4) summary
      COG0513
      Location:284624
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd12873
      Location:93245
      SPRY_DDX1; SPRY domain associated with DEAD box gene DDX1
      cd17938
      Location:288430
      DEADc_DDX1; DEAD-box helicase domain of DEAD box protein 1
      cl28899
      Location:464
      DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      15591868..15631101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      15623489..15662692
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)