DDX1 (DEAD-box helicase 1)

Gene

• Entrez ID: 1653
• Gene name: DEAD-box helicase 1
• Gene symbol: DDX1
• Synonyms (NCBI Gene): DBP-RB, UKVH5d
• Chromosome: 2
• Chromosome location: 2p24.3
• 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 m

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT038224	hsa-miR-342-5p	CLASH	23622248
MIRT035849	hsa-miR-1260a	CLASH	23622248
MIRT929677	hsa-miR-129-5p	CLIP-seq
MIRT929678	hsa-miR-3185	CLIP-seq
MIRT929679	hsa-miR-409-3p	CLIP-seq
MIRT929680	hsa-miR-4432	CLIP-seq
MIRT929681	hsa-miR-450b-3p	CLIP-seq
MIRT929682	hsa-miR-4709-3p	CLIP-seq
MIRT929683	hsa-miR-489	CLIP-seq
MIRT929684	hsa-miR-499-5p	CLIP-seq
MIRT929685	hsa-miR-526b	CLIP-seq
MIRT929686	hsa-miR-578	CLIP-seq
MIRT929687	hsa-miR-769-3p	CLIP-seq
MIRT929677	hsa-miR-129-5p	CLIP-seq
MIRT929678	hsa-miR-3185	CLIP-seq
MIRT929681	hsa-miR-450b-3p	CLIP-seq
MIRT929682	hsa-miR-4709-3p	CLIP-seq
MIRT1975262	hsa-miR-671-5p	CLIP-seq
MIRT929687	hsa-miR-769-3p	CLIP-seq
MIRT929684	hsa-miR-499-5p	CLIP-seq
MIRT2514591	hsa-miR-1179	CLIP-seq
MIRT2514592	hsa-miR-1303	CLIP-seq
MIRT2514593	hsa-miR-200b	CLIP-seq
MIRT2514594	hsa-miR-200c	CLIP-seq
MIRT2514595	hsa-miR-208a	CLIP-seq
MIRT2514596	hsa-miR-208b	CLIP-seq
MIRT2514597	hsa-miR-21	CLIP-seq
MIRT2514598	hsa-miR-3658	CLIP-seq
MIRT2514599	hsa-miR-429	CLIP-seq
MIRT929680	hsa-miR-4432	CLIP-seq
MIRT2514600	hsa-miR-452	CLIP-seq
MIRT2514601	hsa-miR-4676-3p	CLIP-seq
MIRT2514602	hsa-miR-4696	CLIP-seq
MIRT2514603	hsa-miR-4762-5p	CLIP-seq
MIRT929684	hsa-miR-499-5p	CLIP-seq
MIRT2514604	hsa-miR-499a-5p	CLIP-seq
MIRT2514605	hsa-miR-590-5p	CLIP-seq
MIRT2514606	hsa-miR-633	CLIP-seq
MIRT1975262	hsa-miR-671-5p	CLIP-seq
MIRT2514607	hsa-miR-888	CLIP-seq
MIRT2514591	hsa-miR-1179	CLIP-seq
MIRT2514592	hsa-miR-1303	CLIP-seq
MIRT2514593	hsa-miR-200b	CLIP-seq
MIRT2514594	hsa-miR-200c	CLIP-seq
MIRT2514595	hsa-miR-208a	CLIP-seq
MIRT2514596	hsa-miR-208b	CLIP-seq
MIRT2514597	hsa-miR-21	CLIP-seq
MIRT2514598	hsa-miR-3658	CLIP-seq
MIRT2514599	hsa-miR-429	CLIP-seq
MIRT929680	hsa-miR-4432	CLIP-seq
MIRT2514600	hsa-miR-452	CLIP-seq
MIRT2514601	hsa-miR-4676-3p	CLIP-seq
MIRT2514602	hsa-miR-4696	CLIP-seq
MIRT2514603	hsa-miR-4762-5p	CLIP-seq
MIRT929684	hsa-miR-499-5p	CLIP-seq
MIRT2514604	hsa-miR-499a-5p	CLIP-seq
MIRT2514605	hsa-miR-590-5p	CLIP-seq
MIRT2514606	hsa-miR-633	CLIP-seq
MIRT1975262	hsa-miR-671-5p	CLIP-seq
MIRT2514607	hsa-miR-888	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000245	Process	Spliceosomal complex assembly	NAS	7689221
GO:0002376	Process	Immune system process	IEA
GO:0002735	Process	Positive regulation of myeloid dendritic cell cytokine production	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IDA	19058135
GO:0003712	Function	Transcription coregulator activity	IDA	19058135
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003724	Function	RNA helicase activity	IDA	12183465, 18710941
GO:0003724	Function	RNA helicase activity	IEA
GO:0003725	Function	Double-stranded RNA binding	IEA
GO:0004386	Function	Helicase activity	IEA
GO:0004518	Function	Nuclease activity	IDA	18710941
GO:0004518	Function	Nuclease activity	IEA
GO:0004527	Function	Exonuclease activity	IEA
GO:0005515	Function	Protein binding	IPI	11598190, 12183465, 15567440, 18335541, 18710941, 19058135, 20573827, 24608264, 26030138, 28040436, 29992460, 30021884, 33961781, 34232536, 35107372
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IDA	19058135, 24608264
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	21311021
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	24608264, 24965446
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	21311021
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	ISS
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	IEA
GO:0006302	Process	Double-strand break repair	IDA	18710941
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IMP	24870230
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	NAS	24870230
GO:0006397	Process	MRNA processing	IEA
GO:0006446	Process	Regulation of translational initiation	NAS	7689221
GO:0008033	Process	TRNA processing	IEA
GO:0008143	Function	Poly(A) binding	IDA	12183465
GO:0009615	Process	Response to virus	IEA
GO:0010494	Component	Cytoplasmic stress granule	IDA	18335541
GO:0010494	Component	Cytoplasmic stress granule	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0033677	Function	DNA/RNA helicase activity	IDA	18710941
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IEA
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	ISS
GO:0043330	Process	Response to exogenous dsRNA	IEA
GO:0045087	Process	Innate immune response	IEA
GO:0051607	Process	Defense response to virus	IEA
GO:0071920	Component	Cleavage body	IDA	11598190
GO:0072669	Component	TRNA-splicing ligase complex	IDA	21311021, 24870230
GO:0072669	Component	TRNA-splicing ligase complex	NAS	24870230
GO:1903608	Process	Protein localization to cytoplasmic stress granule	IMP	24965446
GO:1990904	Component	Ribonucleoprotein complex	IDA	18809582

Other IDs

• MIM: 601257
• HGNC: 2734
• e!Ensembl: ENSG00000079785

Protein

• UniProt ID: Q92499
• Protein name: ATP-dependent RNA helicase DDX1 (EC 3.6.4.13) (DEAD box protein 1) (DEAD box protein retinoblastoma) (DBP-RB)
• Protein 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 c
• PDB: 4XW3, 8TBX
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00270	DEAD	26 → 418	DEAD/DEAH box helicase	Domain
  PF00622	SPRY	132 → 245	SPRY domain	Family
  PF00271	Helicase_C	488 → 610	Helicase conserved C-terminal domain	Family

• Tissue specificity: TISSUE SPECIFICITY: Highest levels of transcription in 2 retinoblastoma cell lines and in tissues of neuroectodermal origin including the retina, brain, and spinal cord. {ECO:0000269|PubMed:7689221}.
• Sequence:

  MAAFSEMGVMPEIAQAVEEMDWLLPTDIQAESIPLILGGGDVLMAAETGSGKTGAFSIPV
  IQIVYETLKDQQEGKKGKTTIKTGASVLNKWQMNPYDRGSAFAIGSDGLCCQSREVKEWH
  GCRATKGLMKGKHYYEVSCHDQGLCRVGWSTMQASLDLGTDKFGFGFGGTGKKSHNKQFD
  NYGEEFTMHDTIGCYLDIDKGHVKFSKNGKDLGLAFEIPPHMKNQALFPACVLKNAELKF
  NFGEEEFKFPPKDGFVALSKAPDGYIVKSQHSGNAQVTQTKFLPNAPKALIVEPSRELAE
  QTLNNIKQFKKYIDNPKLRELLIIGGVAARDQLSVLENGVDIVVGTPGRLDDLVSTGKLN
  LSQVRFLVLDEADGLLSQGYSDFINRMHNQIPQVTSDGKRLQVIVCSATLHSFDVKKLSE
  KIMHFPTWVDLKGEDSVPDTVHHVVVPVNPKTDRLWERLGKSHIRTDDVHAKDNTRPGAN
  SPEMWSEAIKILKGEYAVRAIKEHKMDQAIIFCRTKIDCDNLEQYFIQQGGGPDKKGHQF
  SCVCLHGDRKPHERKQNLERFKKGDVRFLICTDVAARGIDIHGVPYVINVTLPDEKQNYV
  HRIGRVGRAERMGLAISLVATEKEKVWYHVCSSRGKGCYNTRLKEDGGCTIWYNEMQLLS
  EIEEHLNCTISQVEPDIKVPVDEFDGKVTYGQKRAAGGGSYKGHVDILAPTVQELAALEK
  EAQTSFLHLGYLPNQLFRTF

• Sequence length: 740

Pathways

Reactome:

tRNA processing in the nucleus

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATYPICAL ENDOMETRIAL HYPERPLASIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMPLEX ENDOMETRIAL HYPERPLASIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ENDOMETRIAL HYPERPLASIA	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HIV INFECTIONS	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TREATMENT-RESISTANT HYPERTENSION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Alzheimer Disease	Associate	40194700	★☆☆☆☆ Found in Text Mining only
Asthma	Associate	24993907	★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Associate	21761397	★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Associate	36054300	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Associate	36451087	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Associate	36478716	★☆☆☆☆ Found in Text Mining only
Immune System Diseases	Associate	36250618	★☆☆☆☆ Found in Text Mining only
Inflammation	Associate	24993907	★☆☆☆☆ Found in Text Mining only
Influenza Human	Associate	37556111	★☆☆☆☆ Found in Text Mining only
Melanoma	Associate	31573152	★☆☆☆☆ Found in Text Mining only
Microcephaly	Associate	30842647	★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	18710941, 21761397, 25690890	★☆☆☆☆ Found in Text Mining only
Neoplasms	Inhibit	32626994	★☆☆☆☆ Found in Text Mining only
Neoplasms Radiation Induced	Associate	18710941	★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Associate	11464910, 18710941, 21761397, 9694872	★☆☆☆☆ Found in Text Mining only
Neurologic Manifestations	Associate	38096740	★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Inhibit	32626994	★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Associate	24993907	★☆☆☆☆ Found in Text Mining only
Retinoblastoma	Associate	18710941, 21761397, 9694872	★☆☆☆☆ Found in Text Mining only
Rhabdomyosarcoma	Associate	10935481	★☆☆☆☆ Found in Text Mining only
Testicular Neoplasms	Associate	21761397	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Associate	21761397	★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Associate	36054300	★☆☆☆☆ Found in Text Mining only
Virus Diseases	Associate	37556111	★☆☆☆☆ Found in Text Mining only
Wilms Tumor	Associate	21761397, 22544364	★☆☆☆☆ Found in Text Mining only