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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
  • EC 3.6.1 61
  • 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. GO annotations related to this gene include nucleic acid binding and ATP-dependent RNA helicase activity. An important paralog of this gene is DDX42.

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

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

Genomics for DDX46 Gene

Regulatory Elements for DDX46 Gene

Enhancers for DDX46 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G134590 1.4 Ensembl ENCODE dbSUPER 10.4 -166.7 -166696 2.7 HDGF PKNOX1 ATF1 WRNIP1 ARID4B SIN3A RFX5 TCF12 SCRT2 ETV6 TXNDC15 RNU6-1311P SAR1B ENSG00000248559 DDX46 GC05M134578 GC05M134635
GH05G134623 1.3 ENCODE dbSUPER 10.4 -133.1 -133088 4.3 PKNOX1 ATF1 ARNT MLX ZFP64 YY1 ZNF263 TSHZ1 ZNF623 ZNF518A JADE2 ENSG00000248559 DDX46 GC05M134635 RNU6-1311P GC05M134578
GH05G134844 1.1 ENCODE 11.4 +87.9 87889 3.5 HNRNPUL1 ARNT CREB3L1 AGO1 WRNIP1 ARID4B SIN3A DMAP1 YY1 ZNF766 CAMLG C5orf24 TXNDC15 DDX46 ENSG00000270021 GC05M134654
GH05G134607 1.1 ENCODE dbSUPER 10.2 -149.4 -149385 4.4 HDAC1 HDGF ZNF2 RAD21 YY1 ZNF121 ZNF766 ZNF654 ZNF362 JUNB CAMLG RNU6-1311P SAR1B JADE2 ENSG00000248559 DDX46 GC05M134635 GC05M134578
GH05G134842 0.9 ENCODE 10.7 +84.2 84179 1.8 FOXA2 ZFP64 INSM2 KLF17 DMAP1 RAD21 GATA2 SCRT2 FOS DEK CAMLG DDX46 C5orf24 RPL34P13
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DDX46 on UCSC Golden Path with GeneCards custom track

Promoters for DDX46 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187115 266 1601 MLX CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3

Genomic Location for DDX46 Gene

134,758,734 bp from pter
134,855,133 bp from pter
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

Selected DME Specific Peptides for DDX46 Gene


Post-translational modifications for DDX46 Gene

  • Ubiquitination at isoforms=422, isoforms=493, isoforms=686, Lys716, Lys894, isoforms=907, and Lys1025
  • Modification sites at PhosphoSitePlus

Domains & Families for DDX46 Gene

Gene Families for DDX46 Gene

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

Enzyme Numbers (IUBMB) 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 IDA,IEA 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

CRISPR Products

miRNA for DDX46 Gene

Inhibitory RNA 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

Gene Ontology (GO) - Cellular Components for DDX46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IDA,IEA 16791210
GO:0005654 nucleoplasm TAS --
GO:0015030 Cajal body IEA --
GO:0016020 membrane IEA --
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
Adenosine triphosphate Approved Nutra 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with DDX46: view

Transcripts for DDX46 Gene

Unigene Clusters for DDX46 Gene

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

CRISPR Products

Inhibitory RNA 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, PaxDb, 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

Primer Products

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 35
  • 100 (a)
(Pan troglodytes)
Mammalia DDX46 34 35
  • 99.74 (n)
(Monodelphis domestica)
Mammalia DDX46 35
  • 97 (a)
(Canis familiaris)
Mammalia DDX46 34 35
  • 94.15 (n)
(Ornithorhynchus anatinus)
Mammalia DDX46 35
  • 94 (a)
(Mus musculus)
Mammalia Ddx46 34 16 35
  • 89.48 (n)
(Rattus norvegicus)
Mammalia Ddx46 34
  • 88.47 (n)
(Gallus gallus)
Aves DDX46 34 35
  • 82.99 (n)
(Anolis carolinensis)
Reptilia DDX46 35
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx46 34
  • 78.82 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.13242 34
(Danio rerio)
Actinopterygii ddx46 34 35
  • 72.5 (n)
Dr.25491 34
fruit fly
(Drosophila melanogaster)
Insecta CG6227 34 35
  • 60.08 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010656 34
  • 46.33 (n)
(Caenorhabditis elegans)
Secernentea CELE_F53H1.1 34
  • 56.34 (n)
F53H1.1 35
  • 50 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DBP2 35
  • 38 (a)
PRP5 37
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G20920 34
  • 56.23 (n)
(Oryza sativa)
Liliopsida Os08g0159900 34
  • 55.43 (n)
Os.24620 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4221 35
  • 62 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp11 34
  • 56.49 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU02696 34
  • 53.46 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5602 34
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)

Paralogs for DDX46 Gene

Paralogs for DDX46 Gene

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

Variants for DDX46 Gene

Sequence variations from dbSNP and Humsavar for DDX46 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000000691 -- 134,816,818(+) TTTCT(A/G)ACTGT intron-variant
rs1000019324 -- 134,817,147(+) AACAT(C/T)CAAAT intron-variant
rs1000060014 -- 134,813,093(+) CGCGC(C/T)ACCAT intron-variant
rs1000072917 -- 134,780,050(+) ACCAC(C/T)GTACT intron-variant
rs1000112139 -- 134,765,823(+) AATAT(A/T)CACCC 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)

Relevant External Links for DDX46 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for DDX46 Gene

Relevant External Links for DDX46

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

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 D.F. … Stefansson K. (Nat. Genet. 2008) 3 46 64
  2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein. (PMID: 12234937) Will C.L. … Luehrmann R. (EMBO J. 2002) 3 4 64
  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 Res. 1998) 3 4 64

Products for DDX46 Gene

Sources for DDX46 Gene

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