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Aliases for DDX46 Gene

Aliases for DDX46 Gene

  • DEAD-Box Helicase 46 2 3 5
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 46 2 3
  • DEAD Box Protein 46 3 4
  • PRP5 Homolog 3 4
  • Probable ATP-Dependent RNA Helicase DDX46 3
  • Prp5-Like DEAD-Box Protein 3
  • RNA Helicase 3
  • EC 4
  • KIAA0801 4
  • PRPF5 3
  • Prp5 3

External Ids for DDX46 Gene

Previous GeneCards Identifiers for DDX46 Gene

  • GC05P134125
  • GC05P134170
  • GC05P134122
  • GC05P134094
  • GC05P129280

Summaries for DDX46 Gene

Entrez Gene Summary for DDX46 Gene

  • This gene encodes a member of the DEAD box protein family. 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. The protein encoded by this gene is a component of the 17S U2 snRNP complex; it plays an important role in pre-mRNA splicing. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2014]

GeneCards Summary for DDX46 Gene

DDX46 (DEAD-Box Helicase 46) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and ATP-dependent RNA helicase activity.

UniProtKB/Swiss-Prot for DDX46 Gene

  • Plays an essential role in splicing, either prior to, or during splicing A complex formation.

Gene Wiki entry for DDX46 Gene

Additional gene information for DDX46 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX46 Gene

Genomics for DDX46 Gene

GeneHancer (GH) Regulatory Elements for DDX46 Gene

Promoters and enhancers for DDX46 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J134757 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 711.8 +0.4 427 2.6 MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 SP3 DDX46 C5orf66 SEC24A CATSPER3 RPL34P13 GC05M134654
GH05J134369 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 56.4 -387.2 -387150 3.6 CLOCK MLX DMAP1 YY1 ZNF213 E2F8 ZNF143 ZNF548 SP3 NFYC UBE2B ENSG00000273345 CDKL3 C5orf15 DDX46 SKP1 JADE2 SEC24A ENSG00000248559 C5orf66
GH05J134630 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 50.8 -126.5 -126534 2.5 ZFP64 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC MEF2D SAR1B DDX46 JADE2 C5orf24 C5orf66 TXNDC15 SEC24A SKP1 C5orf66-AS1 CAMLG
GH05J134546 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 61.2 -206.7 -206675 10.1 HDGF PKNOX1 ARNT SIN3A YBX1 ZBTB7B ZNF207 ZNF143 FOS DEK DDX46 SEC24A C5orf66 CAMLG PPP2CA JADE2 CATSPER3 UBE2B TXNDC15 CDKL3
GH05J134844 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 45.7 +87.9 87889 3.5 SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 E2F8 ZNF207 C5orf24 DDX46 C5orf66 TXNDC15 CAMLG JADE2 SEC24A ENSG00000270021 GC05M134654
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DDX46 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DDX46 gene promoter:

Genomic Locations for DDX46 Gene

Genomic Locations for DDX46 Gene
96,400 bases
Plus strand

Genomic View for DDX46 Gene

Genes around DDX46 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX46 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX46 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX46 Gene

Proteins for DDX46 Gene

  • Protein details for DDX46 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Probable ATP-dependent RNA helicase DDX46
    Protein Accession:
    Secondary Accessions:
    • O94894
    • Q96EI0
    • Q9Y658

    Protein attributes for DDX46 Gene

    1031 amino acids
    Molecular mass:
    117362 Da
    Quaternary structure:
    • Integral component of the 17S U2 snRNP.
    • Sequence=BAA34521.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for DDX46 Gene

Post-translational modifications for DDX46 Gene

  • Ubiquitination at posLast=10251025, Lys907, posLast=894894, Lys716, posLast=686686, posLast=493493, and Lys422
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for DDX46 Gene

Domains & Families for DDX46 Gene

Gene Families for DDX46 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for DDX46 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the DEAD box helicase family. DDX46/PRP5 subfamily.
  • Belongs to the DEAD box helicase family. DDX46/PRP5 subfamily.
genes like me logo Genes that share domains with DDX46: view

Function for DDX46 Gene

Molecular function for DDX46 Gene

UniProtKB/Swiss-Prot Function:
Plays an essential role in splicing, either prior to, or during splicing A complex formation.
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.

Enzyme Numbers (IUBMB) for DDX46 Gene

Phenotypes From GWAS Catalog for DDX46 Gene

Gene Ontology (GO) - Molecular Function for DDX46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA 22681889
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0004386 helicase activity IEA --
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with DDX46: view
genes like me logo Genes that share phenotypes with DDX46: view

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DDX46 Gene

Localization for DDX46 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX46 Gene

Nucleus speckle. Nucleus, Cajal body. Membrane; Lipid-anchor. Note=Present in Cajal bodies (CBs) and nuclear speckles.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DDX46 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus HDA,IEA 16791210
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IBA --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with DDX46: view

Pathways & Interactions for DDX46 Gene

genes like me logo Genes that share pathways with DDX46: view

Pathways by source for DDX46 Gene

Gene Ontology (GO) - Biological Process for DDX46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0010468 regulation of gene expression IBA --
GO:0010501 RNA secondary structure unwinding IBA --
genes like me logo Genes that share ontologies with DDX46: view

No data available for SIGNOR curated interactions for DDX46 Gene

Drugs & Compounds for DDX46 Gene

(3) Drugs for DDX46 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist, Activator, Full agonist, Antagonist, Potentiation, Pore Blocker 0

(1) Additional Compounds for DDX46 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with DDX46: view

Transcripts for DDX46 Gene

mRNA/cDNA for DDX46 Gene

Unigene Clusters for DDX46 Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 46:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX46 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19 ^
SP1: - - - - -
SP2: -
SP3: - - - - -
SP4: - - -
SP6: - -
SP8: - - -

ExUns: 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b
SP5: -

Relevant External Links for DDX46 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for DDX46 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX46 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDX46 Gene

This gene is overexpressed in Nasal epithelium (10.3), Lymph node (10.2), and Peripheral blood mononuclear cells (9.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DDX46 Gene

Protein tissue co-expression partners for DDX46 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DDX46 Gene:


SOURCE GeneReport for Unigene cluster for DDX46 Gene:


Evidence on tissue expression from TISSUES for DDX46 Gene

  • Nervous system(4.6)
  • Eye(4.4)
  • Liver(4.4)
genes like me logo Genes that share expression patterns with DDX46: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX46 Gene

Orthologs for DDX46 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX46 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia DDX46 34
  • 100 (a)
(Pan troglodytes)
Mammalia DDX46 34 33
  • 99.74 (n)
(Monodelphis domestica)
Mammalia DDX46 34
  • 97 (a)
(Canis familiaris)
Mammalia DDX46 34 33
  • 94.15 (n)
(Ornithorhynchus anatinus)
Mammalia DDX46 34
  • 94 (a)
(Mus musculus)
Mammalia Ddx46 16 34 33
  • 89.48 (n)
(Rattus norvegicus)
Mammalia Ddx46 33
  • 88.47 (n)
(Gallus gallus)
Aves DDX46 34 33
  • 82.99 (n)
(Anolis carolinensis)
Reptilia DDX46 34
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx46 33
  • 78.82 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13242 33
(Danio rerio)
Actinopterygii ddx46 34 33
  • 72.5 (n)
Dr.25491 33
fruit fly
(Drosophila melanogaster)
Insecta CG6227 34 33
  • 60.08 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010656 33
  • 46.33 (n)
(Caenorhabditis elegans)
Secernentea CELE_F53H1.1 33
  • 56.34 (n)
F53H1.1 34
  • 50 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DBP2 34
  • 38 (a)
PRP5 36
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G20920 33
  • 56.23 (n)
(Oryza sativa)
Liliopsida Os08g0159900 33
  • 55.43 (n)
Os.24620 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4221 34
  • 62 (a)
Cin.5602 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp11 33
  • 56.49 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02696 33
  • 53.46 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5602 33
Species where no ortholog for DDX46 was found in the sources mined by GeneCards:
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DDX46 Gene

Gene Tree for DDX46 (if available)
Gene Tree for DDX46 (if available)
Evolutionary constrained regions (ECRs) for DDX46: view image

Paralogs for DDX46 Gene

(24) SIMAP similar genes for DDX46 Gene using alignment to 6 proteins:

  • H0Y9U3_HUMAN
genes like me logo Genes that share paralogs with DDX46: view

No data available for Paralogs for DDX46 Gene

Variants for DDX46 Gene

Sequence variations from dbSNP and Humsavar for DDX46 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000000691 -- 134,816,818(+) A/G genic_downstream_transcript_variant, intron_variant
rs1000019324 -- 134,817,147(+) T/C genic_downstream_transcript_variant, intron_variant
rs1000060014 -- 134,813,093(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000072917 -- 134,780,050(+) T/C intron_variant
rs1000112139 -- 134,765,823(+) T/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for DDX46 Gene

Variant ID Type Subtype PubMed ID
dgv5810n100 CNV gain 25217958
esv3400590 CNV duplication 20981092
esv3575882 CNV gain 25503493
nsv1109727 CNV deletion 24896259
nsv512860 CNV insertion 21212237
nsv523937 CNV gain 19592680
nsv830493 CNV loss 17160897
nsv830494 CNV gain+loss 17160897

Variation tolerance for DDX46 Gene

Residual Variation Intolerance Score: 5.06% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.47; 10.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX46 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX46 Gene

Disorders for DDX46 Gene

Additional Disease Information for DDX46

No disorders were found for DDX46 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for DDX46 Gene

Publications for DDX46 Gene

  1. Many sequence variants affecting diversity of adult human height. (PMID: 18391951) Gudbjartsson DF … Stefansson K (Nature genetics 2008) 3 44 58
  2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein. (PMID: 12234937) Will CL … Lührmann R (The EMBO journal 2002) 3 4 58
  5. Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9872452) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 3 4 58

Products for DDX46 Gene

Sources for DDX46 Gene

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