Human Gene DDX47 (ENST00000358007.7_4) from GENCODE V47lift37
  Description: DEAD-box helicase 47, transcript variant 1 (from RefSeq NM_016355.4)
Gencode Transcript: ENST00000358007.7_4
Gencode Gene: ENSG00000213782.7_10
Transcript (Including UTRs)
   Position: hg19 chr12:12,966,280-12,982,915 Size: 16,636 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr12:12,966,302-12,982,488 Size: 16,187 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:12,966,280-12,982,915)mRNA (may differ from genome)Protein (455 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX47_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX47; EC=3.6.4.13; AltName: Full=DEAD box protein 47;
FUNCTION: Involved in apoptosis. May have a role in rRNA processing and mRNA splicing. Associates with pre-rRNA precursors.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Interacts with EIF2C1 and EIF2C2. Interacts with GABARAP. Interacts with NOL8; the interaction is RNA-dependent.
INTERACTION: O95166:GABARAP; NbExp=3; IntAct=EBI-2515241, EBI-712001;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Note=Localizes in the nucleolar-organizing region during ribosome biogenesis.
SIMILARITY: Belongs to the DEAD box helicase family. DDX47/RRP3 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 0.79 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 11.41 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 0.00220.000 Picture PostScript Text
3' UTR -100.20427-0.235 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
PF04851 - Type III restriction enzyme, res subunit

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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3BER - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9H0S4
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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 orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  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:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity

Biological Process:
GO:0006364 rRNA processing
GO:0006397 mRNA processing
GO:0006915 apoptotic process
GO:0008380 RNA splicing
GO:0008625 extrinsic apoptotic signaling pathway via death domain receptors
GO:0010501 RNA secondary structure unwinding

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK127712 - Homo sapiens cDNA FLJ45812 fis, clone NT2RP7016508, highly similar to Probable ATP-dependent RNA helicase DDX47 (EC 3.6.1.-).
AK310501 - Homo sapiens cDNA, FLJ17543.
AL136666 - Homo sapiens mRNA; cDNA DKFZp564O176 (from clone DKFZp564O176); complete cds.
AL833469 - Homo sapiens mRNA; cDNA DKFZp686J1317 (from clone DKFZp686J1317).
AK054574 - Homo sapiens cDNA FLJ30012 fis, clone 3NB692000281, moderately similar to PUTATIVE ATP-DEPENDENT RNA HELICASE T26G10.1 IN CHROMOSOME III.
BC068009 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 47, mRNA (cDNA clone MGC:74686 IMAGE:6142837), complete cds.
AB462951 - Synthetic construct DNA, clone: pF1KB8694, Homo sapiens APOLD1 gene for apolipoprotein L domain containing 1, without stop codon, in Flexi system.
AM393320 - Synthetic construct Homo sapiens clone IMAGE:100001978 for hypothetical protein (DDX47 gene).
AM393714 - Synthetic construct Homo sapiens clone IMAGE:100001972 for hypothetical protein (DDX47 gene).
AJ276704 - Homo sapiens mRNA for DEAD box protein (E4-DBP gene).
AK225144 - Homo sapiens mRNA for DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 isoform 1 variant, clone: CBL05864.
AF190165 - Homo sapiens MSTP162 (MST162) mRNA, complete cds.
BC009379 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 47, mRNA (cDNA clone IMAGE:4125275), partial cds.
AK222940 - Homo sapiens mRNA for DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 isoform 1 variant, clone: HRC11936.
AF078843 - Homo sapiens hqp0256 protein mRNA, complete cds.
CU679339 - Synthetic construct Homo sapiens gateway clone IMAGE:100018919 5' read DDX47 mRNA.
KJ902568 - Synthetic construct Homo sapiens clone ccsbBroadEn_11962 DDX47 gene, encodes complete protein.
AK302536 - Homo sapiens cDNA FLJ57094 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX47 (EC3.6.1.-).
EF036507 - Homo sapiens DEAD box polypeptide 47 isoform 1 variant mRNA, partial cds.
JD328198 - Sequence 309222 from Patent EP1572962.
JD540149 - Sequence 521173 from Patent EP1572962.
JD094757 - Sequence 75781 from Patent EP1572962.
JD092813 - Sequence 73837 from Patent EP1572962.
JD354204 - Sequence 335228 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H0S4 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B3KXP4, DDX47_HUMAN, ENST00000358007.1, ENST00000358007.2, ENST00000358007.3, ENST00000358007.4, ENST00000358007.5, ENST00000358007.6, G5E955, NM_016355, Q96GM0, Q96NV8, Q9H0S4, Q9UI98, uc318aif.1, uc318aif.2
UCSC ID: ENST00000358007.7_4
RefSeq Accession: NM_016355.4
Protein: Q9H0S4 (aka DDX47_HUMAN or DX47_HUMAN)

-  Gene Model Information
  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.