Free for academic non-profit institutions. Other users need a Commercial license

Aliases for DDX42 Gene

Aliases for DDX42 Gene

  • DEAD-Box Helicase 42 2 3 5
  • Splicing Factor 3B-Associated 125 KDa Protein 3 4
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 42 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Helicase 42 2 3
  • Splicing Factor 3b, Subunit 8 2 3
  • SF3b DEAD Box Protein 3 4
  • SF3b125 3 4
  • RHELP 3 4
  • RNAHP 3 4
  • ATP-Dependent RNA Helicase DDX42 3
  • RNA Helicase-Related Protein 4
  • RNA Helicase-Like Protein 4
  • DEAD Box Protein 42 4
  • EC 3.6.4.13 4
  • EC 3.6.1 61
  • DDX42P 3
  • SF3B8 3

External Ids for DDX42 Gene

Previous GeneCards Identifiers for DDX42 Gene

  • GC17P062192
  • GC17P062337
  • GC17P059205
  • GC17P061851
  • GC17P057219

Summaries for DDX42 Gene

Entrez Gene Summary for DDX42 Gene

  • This gene encodes a member of the Asp-Glu-Ala-Asp (DEAD) box protein family. Members of this protein family are putative RNA helicases, and 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. Members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for DDX42 Gene

DDX42 (DEAD-Box Helicase 42) 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 DDX46.

UniProtKB/Swiss-Prot for DDX42 Gene

  • ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.

Gene Wiki entry for DDX42 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX42 Gene

Genomics for DDX42 Gene

Regulatory Elements for DDX42 Gene

Enhancers for DDX42 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
GH17G063760 1.4 Ensembl ENCODE dbSUPER 77.7 -11.9 -11876 1.5 ZNF493 ZFP64 NFXL1 ZNF155 ZNF121 ZNF366 ZNF138 EGR1 ZNF302 ZNF354C CEP95 DDX42 DDX5 POLG2 FTSJ3 PSMC5 LIMD2 SMARCD2 GC17P063754
GH17G063837 1.8 FANTOM5 ENCODE dbSUPER 42.5 +67.4 67369 7.4 CREB3L1 ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 FTSJ3 CEP95 DDX42 POLG2 CSH2 DDX5 PLEKHM1P1 EEF1DP7 ENSG00000265982 MAP3K3
GH17G063621 1.4 ENCODE dbSUPER 49.1 -151.0 -151004 3.1 HDGF PKNOX1 CREB3L1 AGO1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B DDX42 CEP95 DDX5 POLG2 EEF1DP7 MAP3K3 FTSJ3 GC17M063634
GH17G062789 1.9 FANTOM5 Ensembl ENCODE dbSUPER 36.1 -981.4 -981446 5.9 HDGF PKNOX1 FOXA2 SIN3A YBX1 FEZF1 ZBTB7B ZNF207 FOS SP3 DDX42 INTS2 MED13 MIR633 STRADA MARCH10 GC17M062789 GC17M062752
GH17G064607 0.9 dbSUPER 68.7 +834.9 834908 1.5 ZFP64 ZNF121 ZNF138 ZNF366 ZNF354C ZNF207 RCOR1 FOS ZNF202 ZNF654 CEP95 DDX42 SLC16A6P1 ENSG00000265912 ENSG00000265218 DDX5 AMZ2P1 POLG2 AXIN2 PLEKHM1P1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DDX42 on UCSC Golden Path with GeneCards custom track

Promoters for DDX42 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000096841 397 3601 MLX CREB3L1 AGO1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3

Genomic Location for DDX42 Gene

Chromosome:
17
Start:
63,773,603 bp from pter
End:
63,819,317 bp from pter
Size:
45,715 bases
Orientation:
Plus strand

Genomic View for DDX42 Gene

Genes around DDX42 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX42 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX42 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX42 Gene

Proteins for DDX42 Gene

  • Protein details for DDX42 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86XP3-DDX42_HUMAN
    Recommended name:
    ATP-dependent RNA helicase DDX42
    Protein Accession:
    Q86XP3
    Secondary Accessions:
    • A6NML1
    • A8KA43
    • O75619
    • Q68G51
    • Q96BK1
    • Q96HR7
    • Q9Y3V8

    Protein attributes for DDX42 Gene

    Size:
    938 amino acids
    Molecular mass:
    102975 Da
    Quaternary structure:
    • Component of splicing factor SF3B complex which is composed of at least eight subunits; SF3B1, SF3B2, SF3B3, SF3B4, SF3B5, SF3B6, PHF5A/SF3B14B, and DDX42/SF3B125. Interacts (via the C-terminus) with TP53BP2; the interaction is not inhibitied by TP53BP2 ubiquitination and is independent of p53/TP53.
    SequenceCaution:
    • Sequence=AAC32396.1; Type=Frameshift; Positions=818; Evidence={ECO:0000305};

    Alternative splice isoforms for DDX42 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX42 Gene

Selected DME Specific Peptides for DDX42 Gene

Q86XP3:
  • VAARGLDI
  • DPIRVVQGDIGEANED
  • FVTKKANAEELA
  • QSERNKV
  • SGRDMIGIA
  • WTSAGSL
  • AARGLDIP
  • AKTGSGKT
  • VSKELLDLAMQN
  • AFQSQYK
  • SNFAGDLVRNLEGANQ
  • HRIGRTGR
  • DGPIAVIVCPTRELCQQIH
  • DEEEDSSNVDLPYIPAENSPTRQQ
  • DPLEAFMAEVEDQAA
  • LVATDVAARGL
  • TGSGKTAAF
  • QLPSFYKIGSKRANFDEEN
  • GAMGDRL
  • YLVFDEADRMFDMGFEYQVRSIA
  • TPGRLID
  • GRTGRAG
  • LRHKLNLRVSGAAPPR
  • RQTLLFSAT
  • GKKEEPKL
  • WFRKSRFK
  • WLTRRLVEFTS
  • HQIRKSEYTQPTPIQCQG
  • GKGKKLNIGGGGLGYRERPGLG
  • TDVAARGLD

Post-translational modifications for DDX42 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for DDX42 Gene

Gene Families for DDX42 Gene

Suggested Antigen Peptide Sequences for DDX42 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q86XP3

UniProtKB/Swiss-Prot:

DDX42_HUMAN :
  • Belongs to the DEAD box helicase family. DDX42 subfamily.
Family:
  • Belongs to the DEAD box helicase family. DDX42 subfamily.
genes like me logo Genes that share domains with DDX42: view

Function for DDX42 Gene

Molecular function for DDX42 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
ATP-dependent RNA helicase. Binds to partially double-stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.

Enzyme Numbers (IUBMB) for DDX42 Gene

Gene Ontology (GO) - Molecular Function for DDX42 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,IDA 22681889
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0004386 helicase activity IEA --
GO:0005515 protein binding IPI 19377511
genes like me logo Genes that share ontologies with DDX42: view
genes like me logo Genes that share phenotypes with DDX42: view

Animal Models for DDX42 Gene

MGI Knock Outs for DDX42:

Animal Model Products

  • Taconic Biosciences Mouse Models for DDX42

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DDX42 Gene

Localization for DDX42 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX42 Gene

Cytoplasm. Nucleus speckle. Nucleus, Cajal body. Note=Isoform 2 is present in Cajal bodies (CBs) and nuclear speckles.

Subcellular locations from

COMPARTMENTS
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 DDX42 gene
Compartment Confidence
nucleus 5
cytosol 5

Gene Ontology (GO) - Cellular Components for DDX42 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 19377511
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA,IEA 19377511
GO:0005829 cytosol IDA --
GO:0015030 Cajal body IEA --
genes like me logo Genes that share ontologies with DDX42: view

Pathways & Interactions for DDX42 Gene

genes like me logo Genes that share pathways with DDX42: view

Pathways by source for DDX42 Gene

Gene Ontology (GO) - Biological Process for DDX42 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0008104 protein localization IDA 19377511
GO:0010501 RNA secondary structure unwinding IBA --
genes like me logo Genes that share ontologies with DDX42: view

No data available for SIGNOR curated interactions for DDX42 Gene

Drugs & Compounds for DDX42 Gene

(3) Drugs for DDX42 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 DDX42 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 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 DDX42: view

Transcripts for DDX42 Gene

Unigene Clusters for DDX42 Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 42:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX42 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b ^ 18a · 18b ^
SP1: - - - -
SP2: - - - -
SP3: - - -
SP4: - -
SP5: - -
SP6: - - -
SP7:
SP8:
SP9: - -
SP10:
SP11:
SP12:

ExUns: 19 ^ 20a · 20b ^ 21a · 21b ^ 22a · 22b · 22c · 22d · 22e
SP1: - -
SP2: - -
SP3: - -
SP4:
SP5:
SP6:
SP7: - -
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for DDX42 Gene

GeneLoc Exon Structure for
DDX42
ECgene alternative splicing isoforms for
DDX42

Expression for DDX42 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX42 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDX42 Gene

This gene is overexpressed in Lymph node (12.5) and Peripheral blood mononuclear cells (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for DDX42 Gene



Protein tissue co-expression partners for DDX42 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DDX42 Gene:

DDX42

SOURCE GeneReport for Unigene cluster for DDX42 Gene:

Hs.702010

mRNA Expression by UniProt/SwissProt for DDX42 Gene:

Q86XP3-DDX42_HUMAN
Tissue specificity: Expressed in several cell lines (at protein level). Expressed in liver, lung, tonsil, thymus, muscle and pancreatic islets.

Evidence on tissue expression from TISSUES for DDX42 Gene

  • Liver(4.3)
  • Pancreas(4.3)
  • Eye(4.2)
  • Nervous system(3.6)
  • Skin(2.9)
  • Spleen(2.1)
  • Heart(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with DDX42: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX42 Gene

Orthologs for DDX42 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX42 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DDX42 34 35
  • 99.79 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX42 35
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDX42 34 35
  • 92.53 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia DDX42 35
  • 92 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DDX42 34 35
  • 91.11 (n)
mouse
(Mus musculus)
Mammalia Ddx42 34 16 35
  • 90.77 (n)
rat
(Rattus norvegicus)
Mammalia Ddx42 34
  • 90.09 (n)
chicken
(Gallus gallus)
Aves DDX42 34 35
  • 77.54 (n)
lizard
(Anolis carolinensis)
Reptilia DDX42 35
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx42 34
  • 70.92 (n)
zebrafish
(Danio rerio)
Actinopterygii ddx42 34 35
  • 69.36 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012523 34
  • 60.63 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6418 34 35
  • 59.15 (n)
worm
(Caenorhabditis elegans)
Secernentea C46F11.4 34 35
  • 58.18 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DBP2 35
  • 37 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G47330 34
  • 56.5 (n)
rice
(Oryza sativa)
Liliopsida Os03g0308500 34
  • 54.06 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2428 35
  • 72 (a)
OneToOne
Species where no ortholog for DDX42 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 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 DDX42 Gene

ENSEMBL:
Gene Tree for DDX42 (if available)
TreeFam:
Gene Tree for DDX42 (if available)

Paralogs for DDX42 Gene

Paralogs for DDX42 Gene

genes like me logo Genes that share paralogs with DDX42: view

Variants for DDX42 Gene

Sequence variations from dbSNP and Humsavar for DDX42 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1000066153 -- 63,790,186(+) ATGAA(C/T)GAATA intron-variant
rs1000096647 -- 63,789,931(+) GAGTC(A/G)AATAT intron-variant
rs1000097118 -- 63,806,207(+) TGGCA(A/G)AAGAA intron-variant
rs1000170405 -- 63,806,555(+) CCTCC(C/T)AGACC reference, synonymous-codon, utr-variant-5-prime
rs1000279054 -- 63,801,003(+) TTTTT(C/T)CCTCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for DDX42 Gene

Variant ID Type Subtype PubMed ID
esv2658528 CNV deletion 23128226
esv2716097 CNV deletion 23290073
esv3337816 CNV insertion 20981092
esv3641006 CNV loss 21293372
nsv1134666 CNV deletion 24896259
nsv510720 CNV deletion 20534489
nsv517272 CNV gain+loss 19592680
nsv833510 CNV loss 17160897

Variation tolerance for DDX42 Gene

Residual Variation Intolerance Score: 3.16% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.55; 29.99% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DDX42 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX42

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX42 Gene

Disorders for DDX42 Gene

Relevant External Links for DDX42

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DDX42

No disorders were found for DDX42 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for DDX42 Gene

Publications for DDX42 Gene

  1. Identification of a novel human member of the DEAD box protein family. (PMID: 10727850) Suk K. … Lee M.-S. (Biochim. Biophys. Acta 2000) 2 3 4 22 64
  2. Ddx42p -- a human DEAD box protein with RNA chaperone activities. (PMID: 16397294) Uhlmann-Schiffler H. … Stahl H. (Nucleic Acids Res. 2006) 2 3 4 64
  3. 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 22 64
  4. The DEAD box protein Ddx42p modulates the function of ASPP2, a stimulator of apoptosis. (PMID: 19377511) Uhlmann-Schiffler H. … Stahl H. (Oncogene 2009) 3 4 64
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64

Products for DDX42 Gene

Sources for DDX42 Gene

Content
Loading form....