Human Gene DDX50 (ENST00000373585.8_4) from GENCODE V47lift37
  Description: DExD-box helicase 50 (from RefSeq NM_024045.2)
Gencode Transcript: ENST00000373585.8_4
Gencode Gene: ENSG00000107625.14_8
Transcript (Including UTRs)
   Position: hg19 chr10:70,661,071-70,706,603 Size: 45,533 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr10:70,661,141-70,706,386 Size: 45,246 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:70,661,071-70,706,603)mRNA (may differ from genome)Protein (737 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX50_HUMAN
DESCRIPTION: RecName: Full=ATP-dependent RNA helicase DDX50; EC=3.6.4.13; AltName: Full=DEAD box protein 50; AltName: Full=Gu-beta; AltName: Full=Nucleolar protein Gu2;
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Belongs to the DEAD box helicase family. DDX21/DDX50 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


-  MalaCards Disease Associations
  MalaCards Gene Search: DDX50
Diseases sorted by gene-association score: rectal disease (1)

-  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: 27.55 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 722.05 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 -29.6070-0.423 Picture PostScript Text
3' UTR -25.84217-0.119 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
IPR012562 - GUCT
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
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
PF08152 - GUCT (NUC152) domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2E29 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9BQ39
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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 orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  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:0010501 RNA secondary structure unwinding

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  BC000272 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 50, mRNA (cDNA clone MGC:3199 IMAGE:3357684), complete cds.
LF384641 - JP 2014500723-A/192144: Polycomb-Associated Non-Coding RNAs.
AK223297 - Homo sapiens mRNA for nucleolar protein GU2 variant, clone: SYN06332.
AB051075 - Homo sapiens mcdrh mRNA for malignant cell derived RNA helicase, complete cds.
AF334103 - Homo sapiens nucleolar protein GU2 mRNA, complete cds.
AK301431 - Homo sapiens cDNA FLJ61430 complete cds, highly similar to ATP-dependent RNA helicase DDX50 (EC 3.6.1.-).
AK293577 - Homo sapiens cDNA FLJ56545 complete cds, highly similar to ATP-dependent RNA helicase DDX50 (EC 3.6.1.-).
BC014263 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 50, mRNA (cDNA clone IMAGE:4810686), partial cds.
JD141736 - Sequence 122760 from Patent EP1572962.
CU674120 - Synthetic construct Homo sapiens gateway clone IMAGE:100017793 5' read DDX50 mRNA.
DQ892547 - Synthetic construct clone IMAGE:100005177; FLH187369.01X; RZPDo839G0772D DEAD (Asp-Glu-Ala-Asp) box polypeptide 50 (DDX50) gene, encodes complete protein.
DQ895758 - Synthetic construct Homo sapiens clone IMAGE:100010218; FLH187365.01L; RZPDo839G0762D DEAD (Asp-Glu-Ala-Asp) box polypeptide 50 (DDX50) gene, encodes complete protein.
KJ894630 - Synthetic construct Homo sapiens clone ccsbBroadEn_04024 DDX50 gene, encodes complete protein.
LF322649 - JP 2014500723-A/130152: Polycomb-Associated Non-Coding RNAs.
LF322643 - JP 2014500723-A/130146: Polycomb-Associated Non-Coding RNAs.
BC000210 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 50, mRNA (cDNA clone IMAGE:3351405), partial cds.
LF322640 - JP 2014500723-A/130143: Polycomb-Associated Non-Coding RNAs.
BC018637 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 50, mRNA (cDNA clone IMAGE:3614635), partial cds.
LF322638 - JP 2014500723-A/130141: Polycomb-Associated Non-Coding RNAs.
AL137423 - Homo sapiens mRNA; cDNA DKFZp761E0323 (from clone DKFZp761E0323); partial cds.
LF322636 - JP 2014500723-A/130139: Polycomb-Associated Non-Coding RNAs.
LF322635 - JP 2014500723-A/130138: Polycomb-Associated Non-Coding RNAs.
LF322633 - JP 2014500723-A/130136: Polycomb-Associated Non-Coding RNAs.
LF322631 - JP 2014500723-A/130134: Polycomb-Associated Non-Coding RNAs.
MA620218 - JP 2018138019-A/192144: Polycomb-Associated Non-Coding RNAs.
MA558226 - JP 2018138019-A/130152: Polycomb-Associated Non-Coding RNAs.
MA558220 - JP 2018138019-A/130146: Polycomb-Associated Non-Coding RNAs.
MA558217 - JP 2018138019-A/130143: Polycomb-Associated Non-Coding RNAs.
MA558215 - JP 2018138019-A/130141: Polycomb-Associated Non-Coding RNAs.
MA558213 - JP 2018138019-A/130139: Polycomb-Associated Non-Coding RNAs.
MA558212 - JP 2018138019-A/130138: Polycomb-Associated Non-Coding RNAs.
MA558210 - JP 2018138019-A/130136: Polycomb-Associated Non-Coding RNAs.
MA558208 - JP 2018138019-A/130134: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: DDX50_HUMAN, ENST00000373585.1, ENST00000373585.2, ENST00000373585.3, ENST00000373585.4, ENST00000373585.5, ENST00000373585.6, ENST00000373585.7, NM_024045, Q5VX37, Q8WV76, Q9BQ39, Q9BWI8, uc318kwx.1, uc318kwx.2
UCSC ID: ENST00000373585.8_4
RefSeq Accession: NM_024045.2
Protein: Q9BQ39 (aka DDX50_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.