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Aliases for DDX42 Gene

Aliases for DDX42 Gene

  • DEAD (Asp-Glu-Ala-Asp) Box Helicase 42 2 3
  • RHELP 3 4 6
  • Splicing Factor 3B-Associated 125 KDa Protein 3 4
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 42 2 3
  • SF3b DEAD Box Protein 3 4
  • SF3b125 3 4
  • RNAHP 3 4
  • ATP-Dependent RNA Helicase DDX42 3
  • Splicing Factor 3b, Subunit 8 3
  • RNA Helicase-Related Protein 4
  • RNA Helicase-Like Protein 4
  • DEAD Box Protein 42 4
  • Splicing Factor 3b 2
  • EC 3.6.4.13 4
  • Subunit 8 2
  • EC 3.6.1 64
  • DDX42P 3
  • SF3B8 3

External Ids for DDX42 Gene

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 (Asp-Glu-Ala-Asp) Box Helicase 42) is a Protein Coding gene. Among its related pathways are Spliceosome. GO annotations related to this gene include RNA binding and ATP-dependent helicase activity. An important paralog of this gene is DDX53.

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 Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX42 Gene

Genomics for DDX42 Gene

Genomic Location for DDX42 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DDX42 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX42 Gene

Regulatory Elements 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

Proteomics data for DDX42 Gene at MOPED

Post-translational modifications for DDX42 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains for DDX42 Gene

Gene Families for DDX42 Gene

HGNC:
  • DDX :DEAD-boxes

UniProtKB/Swiss-Prot:

DDX42_HUMAN
Domain:
  • Contains 1 helicase ATP-binding domain.:
    • Q86XP3
  • Contains 1 helicase C-terminal domain.:
    • Q86XP3
Family:
  • Belongs to the DEAD box helicase family. DDX42 subfamily.:
    • Q86XP3
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 --
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0005515 protein binding IPI 19377511
GO:0005524 ATP binding IEA --
GO:0008026 ATP-dependent helicase activity --
genes like me logo Genes that share ontologies with DDX42: view

Phenotypes for DDX42 Gene

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

No data available for Animal Models , Transcription Factor Targeting 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
Jensen Localization Image for DDX42 Gene COMPARTMENTS Subcellular localization image for DDX42 gene
Compartment Confidence
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for DDX42 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 19377511
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IBA --
GO:0005737 cytoplasm IDA --
GO:0015030 Cajal body IEA --
genes like me logo Genes that share ontologies with DDX42: view

Pathways for DDX42 Gene

SuperPathways for DDX42 Gene

Superpath Contained pathways
1 Spliceosome
genes like me logo Genes that share pathways with DDX42: view

Pathways by source for DDX42 Gene

1 KEGG pathway for DDX42 Gene

Gene Ontology (GO) - Biological Process for DDX42 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006200 obsolete ATP catabolic process --
GO:0008104 protein localization IDA 19377511
GO:0010501 RNA secondary structure unwinding IBA --
genes like me logo Genes that share ontologies with DDX42: view

Transcripts for DDX42 Gene

Unigene Clusters for DDX42 Gene

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

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 for DDX42 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for DDX42 Gene

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.
genes like me logo Genes that share expressions with DDX42: view

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 36
  • 99.79 (n)
  • 99.79 (a)
DDX42 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia DDX42 36
  • 91.11 (n)
  • 96.25 (a)
DDX42 37
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDX42 36
  • 92.53 (n)
  • 96.67 (a)
DDX42 37
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx42 36
  • 90.77 (n)
  • 96.44 (a)
Ddx42 16
Ddx42 37
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia DDX42 37
  • 96 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX42 37
  • 92 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ddx42 36
  • 90.09 (n)
  • 96.01 (a)
chicken
(Gallus gallus)
Aves DDX42 36
  • 77.54 (n)
  • 88.98 (a)
DDX42 37
  • 84 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX42 37
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx42 36
  • 70.92 (n)
  • 79.48 (a)
zebrafish
(Danio rerio)
Actinopterygii ddx42 36
  • 69.36 (n)
  • 75.96 (a)
ddx42 37
  • 72 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012523 36
  • 60.63 (n)
  • 60.28 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6418 36
  • 59.15 (n)
  • 58.06 (a)
CG6418 37
  • 53 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C46F11.4 36
  • 58.18 (n)
  • 57.39 (a)
C46F11.4 37
  • 46 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DBP2 37
  • 37 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G47330 36
  • 56.5 (n)
  • 53.67 (a)
rice
(Oryza sativa)
Liliopsida Os03g0308500 36
  • 54.06 (n)
  • 50.67 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2428 37
  • 72 (a)
OneToOne
Species with no ortholog for DDX42:
  • 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 MAF
rs896064 -- 63,783,572(+) AATTA(C/T)GTTGA intron-variant
rs972875 -- 63,794,650(-) ccAAA(A/T)ttttt intron-variant
rs1062787 -- 63,818,644(+) TCATG(C/T)GGGTA utr-variant-3-prime
rs1062788 -- 63,818,767(+) ATTGA(C/G)TTCTT utr-variant-3-prime
rs2016172 -- 63,783,923(+) GCTGA(G/T)CCTGG intron-variant

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

Variant ID Type Subtype PubMed ID
nsv833510 CNV Loss 17160897
esv2658528 CNV Deletion 23128226
esv2716097 CNV Deletion 23290073
nsv510720 CNV Loss 20534489
nsv517272 CNV Gain+Loss 19592680

Relevant External Links for DDX42 Gene

HapMap Linkage Disequilibrium report
DDX42

Disorders for DDX42 Gene

No disorders were found for DDX42 Gene.

No data available for UniProtKB/Swiss-Prot 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 23
  2. 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 23
  3. Ddx42p -- a human DEAD box protein with RNA chaperone activities. (PMID: 16397294) Uhlmann-Schiffler H. … Stahl H. (Nucleic Acids Res. 2006) 2 3 4
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4

Products for DDX42 Gene

Sources for DDX42 Gene

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