Human Gene DDX46 (uc003kzw.3)
  Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 46 (DDX46), mRNA.
RefSeq Summary (NM_014829): 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].
Transcript (Including UTRs)
   Position: hg19 chr5:134,094,461-134,166,812 Size: 72,352 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr5:134,094,629-134,164,396 Size: 69,768 Coding Exon Count: 23 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:134,094,461-134,166,812)mRNA (may differ from genome)Protein (1031 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX46_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX46; EC=3.6.4.13; AltName: Full=DEAD box protein 46; AltName: Full=PRP5 homolog;
FUNCTION: Plays an essential role in splicing, either prior to, or during splicing A complex formation.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Integral component of the 17S U2 snRNP.
SUBCELLULAR LOCATION: Nucleus speckle. Nucleus, Cajal body. Note=Present in Cajal bodies (CBs) and nuclear speckles.
SIMILARITY: Belongs to the DEAD box helicase family. DDX46/PRP5 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SEQUENCE CAUTION: Sequence=BAA34521.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DDX46
CDC HuGE Published Literature: DDX46
Positive Disease Associations: height
Related Studies:
  1. height
    Gudbjartsson ,et al. 2008, Many sequence variants affecting diversity of adult human height, Nature genetics 2008 40- 5 : 609-15. [PubMed 18391951]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.61 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 532.67 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -66.51168-0.396 Picture PostScript Text
3' UTR -580.202416-0.240 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011545 - DNA/RNA_helicase_DEAD/DEAH_N
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000629 - RNA-helicase_DEAD-box_CS
IPR014014 - RNA_helicase_DEAD_Q_motif

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

ModBase Predicted Comparative 3D Structure on Q7L014
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
 Gene Details Gene DetailsGene Details 
 Gene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005524 ATP binding
GO:0016787 hydrolase activity

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0010468 regulation of gene expression
GO:0010501 RNA secondary structure unwinding

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0015030 Cajal body
GO:0016020 membrane
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AK126011 - Homo sapiens cDNA FLJ44023 fis, clone TESTI4026510, highly similar to Homo sapiens RNA helicase.
BC105598 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 46, mRNA (cDNA clone IMAGE:4714593), partial cds.
AK291788 - Homo sapiens cDNA FLJ78679 complete cds, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 46 (DDX46), mRNA.
AF106680 - Homo sapiens RNA helicase mRNA, complete cds.
AB018344 - Homo sapiens KIAA0801 mRNA for KIAA0801 protein.
BC012304 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 46, mRNA (cDNA clone MGC:9936 IMAGE:3873814), complete cds.
JD514166 - Sequence 495190 from Patent EP1572962.
CU680282 - Synthetic construct Homo sapiens gateway clone IMAGE:100020513 5' read DDX46 mRNA.
BX647426 - Homo sapiens mRNA; cDNA DKFZp686J23144 (from clone DKFZp686J23144).
AK058058 - Homo sapiens cDNA FLJ25329 fis, clone TST00542.
JD146756 - Sequence 127780 from Patent EP1572962.
JD490645 - Sequence 471669 from Patent EP1572962.
JD431377 - Sequence 412401 from Patent EP1572962.
JD286873 - Sequence 267897 from Patent EP1572962.
JD286874 - Sequence 267898 from Patent EP1572962.
JD511652 - Sequence 492676 from Patent EP1572962.
BC030755 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 46, mRNA (cDNA clone IMAGE:4797178).
JD020421 - Sequence 1445 from Patent EP1572962.
JD035572 - Sequence 16596 from Patent EP1572962.
JD035395 - Sequence 16419 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein Q7L014 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: DDX46_HUMAN, KIAA0801, NM_014829, NP_055644, O94894, Q7L014, Q96EI0, Q9Y658
UCSC ID: uc003kzw.3
RefSeq Accession: NM_014829
Protein: Q7L014 (aka DDX46_HUMAN)
CCDS: CCDS34240.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014829.2
exon count: 23CDS single in 3' UTR: no RNA size: 5695
ORF size: 3096CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6356.00frame shift in genome: no % Coverage: 99.74
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.