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Aliases for DDX1 Gene

Aliases for DDX1 Gene

  • DEAD (Asp-Glu-Ala-Asp) Box Helicase 1 2 3
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 1 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 1 2 3
  • DEAD Box Protein Retinoblastoma 3 4
  • DEAD Box Protein 1 3 4
  • DBP-RB 3 4
  • ATP-Dependent RNA Helicase DDX1 3
  • DEAD Box Polypeptide 1 3
  • EC 3.6.1.10 63
  • EC 3.6.4.13 4
  • DEAD Box-1 3
  • EC 3.6.1 63
  • UKVH5d 3

External Ids for DDX1 Gene

Previous GeneCards Identifiers for DDX1 Gene

  • GC02P015736
  • GC02P015753
  • GC02P015731

Summaries for DDX1 Gene

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. Among its related pathways are mRNA Splicing - Major Pathway. GO annotations related to this gene include chromatin binding and transcription cofactor activity. An important paralog of this gene is DDX4.

UniProtKB/Swiss-Prot for DDX1 Gene

  • 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. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease (ZBTB8OS), acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation (PubMed:24870230). 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX1 Gene

Genomics for DDX1 Gene

Regulatory Elements for DDX1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for DDX1 Gene

Start:
15,591,178 bp from pter
End:
15,631,111 bp from pter
Size:
39,934 bases
Orientation:
Plus strand

Genomic View for DDX1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DDX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX1 Gene

Proteins for DDX1 Gene

  • Protein details for DDX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92499-DDX1_HUMAN
    Recommended name:
    ATP-dependent RNA helicase DDX1
    Protein Accession:
    Q92499
    Secondary Accessions:
    • B4DME8
    • B4DPN6

    Protein attributes for DDX1 Gene

    Size:
    740 amino acids
    Molecular mass:
    82432 Da
    Quaternary structure:
    • 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.

    Alternative splice isoforms for DDX1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX1 Gene

Proteomics data for DDX1 Gene at MOPED

Post-translational modifications for DDX1 Gene

  • Phosphorylated. Phosphorylated by ATM kinase; phosphorylation is increased in response to ionizing radiation (IR).
  • Ubiquitination at Lys90, Lys132, Lys281, Lys288, Lys307, and Lys358
  • Modification sites at PhosphoSitePlus

Other Protein References for DDX1 Gene

Domains for DDX1 Gene

Gene Families for DDX1 Gene

HGNC:
  • DDX :DEAD-boxes

Graphical View of Domain Structure for InterPro Entry

Q92499

UniProtKB/Swiss-Prot:

DDX1_HUMAN :
  • Q92499
Domain:
  • The helicase domain is involved in the stimulation of RELA transcriptional activity
  • Contains 1 B30.2/SPRY domain.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the DEAD box helicase family. DDX1 subfamily.
genes like me logo Genes that share domains with DDX1: view

Function for DDX1 Gene

Molecular function for DDX1 Gene

GENATLAS Biochemistry: DEAD/H box protein 1,frequently amplified in retinoblastoma,neuroblastoma,small cell carcinoma of the lung,with poor prognosis
UniProtKB/Swiss-Prot CatalyticActivity: ATP + H(2)O = ADP + phosphate
UniProtKB/Swiss-Prot 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. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease (ZBTB8OS), acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation (PubMed:24870230). Required for HIV-1 Rev function as well as for HIV-1 replication. Binds to the RRE sequence of HIV-1 mRNAs.

Enzyme Numbers (IUBMB) for DDX1 Gene

Gene Ontology (GO) - Molecular Function for DDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IDA 19058135
GO:0003712 transcription cofactor activity IDA 19058135
GO:0003724 RNA helicase activity TAS 7689221
genes like me logo Genes that share ontologies with DDX1: view

Phenotypes for DDX1 Gene

genes like me logo Genes that share phenotypes with DDX1: view

Animal Model Products

CRISPR Products

miRNA for DDX1 Gene

miRTarBase miRNAs that target DDX1

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDX1

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for DDX1 Gene

Localization for DDX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX1 Gene

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. Enters into the nucleus in case of active transcription while it accumulates in cytosol when transcription level is low (PubMed:24608264). {ECO:0000269 PubMed:24608264}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DDX1 Gene COMPARTMENTS Subcellular localization image for DDX1 gene
Compartment Confidence
nucleus 5
cytosol 3

Gene Ontology (GO) - Cellular Components for DDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 19058135
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IBA --
GO:0005737 cytoplasm IDA --
GO:0010494 cytoplasmic stress granule IDA 18335541
genes like me logo Genes that share ontologies with DDX1: view

Pathways for DDX1 Gene

SuperPathways for DDX1 Gene

Superpath Contained pathways
1 mRNA Splicing - Major Pathway
genes like me logo Genes that share pathways with DDX1: view

Pathways by source for DDX1 Gene

1 BioSystems pathway for DDX1 Gene

Gene Ontology (GO) - Biological Process for DDX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly NAS 7689221
GO:0006200 obsolete ATP catabolic process --
GO:0006302 double-strand break repair IDA 18710941
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with DDX1: view

Compounds for DDX1 Gene

(1) Novoseek inferred chemical compound relationships for DDX1 Gene

Compound -log(P) Hits PubMed IDs
ornithine 29.7 3
genes like me logo Genes that share compounds with DDX1: view

Transcripts for DDX1 Gene

Unigene Clusters for DDX1 Gene

DEAD (Asp-Glu-Ala-Asp) box helicase 1:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDX1

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX1 Gene

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: -
SP6: -
SP7: -

ExUns: 22 ^ 23a · 23b · 23c ^ 24 ^ 25 ^ 26 ^ 27a · 27b
SP1: - -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:

Relevant External Links for DDX1 Gene

GeneLoc Exon Structure for
DDX1
ECgene alternative splicing isoforms for
DDX1

Expression for DDX1 Gene

mRNA expression in normal human tissues for DDX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for DDX1 Gene

SOURCE GeneReport for Unigene cluster for DDX1 Gene Hs.440599

mRNA Expression by UniProt/SwissProt for DDX1 Gene

Q92499-DDX1_HUMAN
Tissue specificity: Highest levels of transcription in 2 retinoblastoma cell lines and in tissues of neuroectodermal origin including the retina, brain, and spinal cord.
genes like me logo Genes that share expressions with DDX1: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for DDX1 Gene

Orthologs for DDX1 Gene

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

Orthologs for DDX1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DDX1 35
  • 99.55 (n)
  • 99.86 (a)
DDX1 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DDX1 35
  • 91.4 (n)
  • 97.3 (a)
DDX1 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDX1 35
  • 93.51 (n)
  • 97.7 (a)
DDX1 36
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx1 35
  • 90.23 (n)
  • 97.57 (a)
Ddx1 16
Ddx1 36
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia DDX1 36
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX1 36
  • 58 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ddx1 35
  • 89.95 (n)
  • 97.7 (a)
chicken
(Gallus gallus)
Aves DDX1 35
  • 83.06 (n)
  • 93.24 (a)
DDX1 36
  • 93 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX1 36
  • 91 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.1545 35
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx1 35
  • 79.1 (n)
  • 90.27 (a)
zebrafish
(Danio rerio)
Actinopterygii ddx1 35
  • 74.95 (n)
  • 84.86 (a)
ddx1 36
  • 85 (a)
OneToOne
Dr.19466 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004765 35
  • 60.85 (n)
  • 62.99 (a)
fruit fly
(Drosophila melanogaster)
Insecta Ddx1 35
  • 57.89 (n)
  • 60.86 (a)
Ddx1 36
  • 60 (a)
OneToOne
Ddx1 37
  • 58 (a)
worm
(Caenorhabditis elegans)
Secernentea F20A1.9 36
  • 33 (a)
OneToMany
glh-1 36
  • 16 (a)
OneToMany
glh-2 36
  • 13 (a)
OneToMany
glh-3 36
  • 15 (a)
OneToMany
glh-4 36
  • 11 (a)
OneToMany
mut-14 36
  • 15 (a)
OneToMany
smut-1 36
  • 15 (a)
OneToMany
Y55F3BR.1 35
  • 53.38 (n)
  • 50.35 (a)
Y55F3BR.1 36
  • 49 (a)
OneToMany
F20A1.9 37
  • 46 (a)
Y55F3BR.1 37
  • 47 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DED1 36
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 61 (a)
OneToOne
Species with no ortholog for DDX1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DDX1 Gene

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

Paralogs for DDX1 Gene

Paralogs for DDX1 Gene

Selected SIMAP similar genes for DDX1 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with DDX1: view

Variants for DDX1 Gene

Sequence variations from dbSNP and Humsavar for DDX1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs407277 -- 15,612,114(+) ccgga(C/G)ggggc intron-variant
rs807635 -- 15,629,483(-) TTATA(A/G)GTATG intron-variant
rs807636 -- 15,627,828(-) CATGC(A/G)ATGTG intron-variant
rs1544734 -- 15,618,321(+) TATGT(A/C)TAATG intron-variant
rs1972614 -- 15,624,481(+) aaaca(C/T)gtcct intron-variant

Structural Variations from Database of Genomic Variants (DGV) for DDX1 Gene

Variant ID Type Subtype PubMed ID
nsv515567 CNV Gain+Loss 19592680

Relevant External Links for DDX1 Gene

HapMap Linkage Disequilibrium report
DDX1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX1 Gene

Disorders for DDX1 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (2) Diseases for DDX1 Gene including...

Search for DDX1 Gene in MalaCards »

(1) University of Copenhagen DISEASES for DDX1 Gene

(3) Novoseek inferred disease relationships for DDX1 Gene

Disease -log(P) Hits PubMed IDs
retinoblastoma 65.2 8
tumors 12.5 12
leukemia 0 1

Relevant External Links for DDX1

Genetic Association Database (GAD)
DDX1
Human Genome Epidemiology (HuGE) Navigator
DDX1
genes like me logo Genes that share disorders with DDX1: view

No data available for UniProtKB/Swiss-Prot for DDX1 Gene

Publications for DDX1 Gene

  1. The DEAD-box RNA helicase DDX1 interacts with RelA and enhances nuclear factor kappaB-mediated transcription. (PMID: 19058135) Ishaq M. … Guo D. (J. Cell. Biochem. 2009) 2 3 4 23
  2. MBNL1 associates with YB-1 in cytoplasmic stress granules. (PMID: 18335541) Onishi H. … Ishiura S. (J. Neurosci. Res. 2008) 3 4 23
  3. Association of human DEAD box protein DDX1 with a cleavage stimulation factor involved in 3'-end processing of pre-MRNA. (PMID: 11598190) Bleoo S. … Godbout R. (Mol. Biol. Cell 2001) 3 4 23
  4. Expression of two dead box genes (DDX1 and DDX6) is independent of that of MYCN in human neuroblastoma cell lines. (PMID: 10319407) Akiyama K. … Nishi Y. (Biochem. Mol. Biol. Int. 1999) 3 23
  5. Alterations in the expression of DEAD-box and other RNA binding proteins during HIV-1 replication. (PMID: 15588285) Krishnan V. … Zeichner S.L. (Retrovirology 2004) 3 23

Products for DDX1 Gene

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