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

Gene ID: 1653, updated on 4-Nov-2018

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; Vega:OTTHUMG00000090593
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 of unknown function. It shows high transcription levels in 2 retinoblastoma cell lines and in tissues of neuroectodermal origin. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 36.4), brain (RPKM 36.1) and 25 other tissues See more
Orthologs

Genomic context

See DDX1 in Genome Data Viewer
Location:
2p24.3
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (15591621..15631111)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (15731745..15771235)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene neuroblastoma amplified sequence Neighboring gene ribosomal protein S26 pseudogene 18 Neighboring gene uncharacterized LOC105373440 Neighboring gene long intergenic non-protein coding RNA 1804 Neighboring gene RNA, U5E small nuclear 7, pseudogene

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

  • DDX1 as a regulatory component of the Drosha microprocessor, organism-specific biosystem (from WikiPathways)
    DDX1 as a regulatory component of the Drosha microprocessor, organism-specific biosystemPosttranscriptional maturation is a critical step in microRNA (miRNA) biogenesis that determines mature miRNA levels. In addition to core components (Drosha and DGCR8 [DiGeorge syndrome critical regi...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • tRNA processing, organism-specific biosystem (from REACTOME)
    tRNA processing, organism-specific biosystemGenes encoding transfer RNAs (tRNAs) are transcribed by RNA polymerase III in the nucleus and by mitochondrial RNA polymerase in the mitochondrion.In the nucleus transcription reactions produce precu...
  • tRNA processing in the nucleus, organism-specific biosystem (from REACTOME)
    tRNA processing in the nucleus, organism-specific biosystemGenes encoding transfer RNAs are transcribed in the nucleus by RNA polymerase III. (Distinct processes of transcription and processing also occur in mitochondria.) The initial transcripts, pre-tRNAs,...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATP-dependent helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA/RNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
RNA helicase activity TAS
Traceable Author Statement
more info
PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded RNA binding IEA
Inferred from Electronic Annotation
more info
 
exonuclease activity IEA
Inferred from Electronic Annotation
more info
 
nuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
poly(A) binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription coregulator activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
DNA duplex unwinding IDA
Inferred from Direct Assay
more info
PubMed 
double-strand break repair IDA
Inferred from Direct Assay
more info
PubMed 
multicellular organism development IEP
Inferred from Expression Pattern
more info
PubMed 
nucleic acid phosphodiester bond hydrolysis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of I-kappaB kinase/NF-kappaB signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of myeloid dendritic cell cytokine production IEA
Inferred from Electronic Annotation
more info
 
protein localization to cytoplasmic stress granule IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of nucleic acid-templated transcription IEA
Inferred from Electronic Annotation
more info
 
regulation of translational initiation NAS
Non-traceable Author Statement
more info
PubMed 
response to exogenous dsRNA IEA
Inferred from Electronic Annotation
more info
 
response to virus IEA
Inferred from Electronic Annotation
more info
 
spliceosomal complex assembly NAS
Non-traceable Author Statement
more info
PubMed 
tRNA splicing, via endonucleolytic cleavage and ligation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cleavage body IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic stress granule IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
membrane HDA PubMed 
mitochondrion ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
tRNA-splicing ligase complex IDA
Inferred from Direct Assay
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/H (Asp-Glu-Ala-Asp/His) box polypeptide 1
DEAD/H-box helicase 1
NP_004930.1

NCBI Reference Sequences (RefSeq)

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_004939.2NP_004930.1  ATP-dependent RNA helicase DDX1

    See identical proteins and their annotated locations for NP_004930.1

    Status: REVIEWED

    Source sequence(s)
    BC053673, DC360930, X70649
    Consensus CDS
    CCDS1686.1
    UniProtKB/Swiss-Prot
    Q92499
    UniProtKB/TrEMBL
    A3RJH1
    Related
    ENSP00000233084.3, ENST00000233084.7
    Conserved Domains (3) 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
    cl25401
    Location:472
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    15591621..15631111
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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