Human Gene DDX20 (ENST00000369702.5_5) from GENCODE V47lift37
  Description: DEAD-box helicase 20 (from RefSeq NM_007204.5)
Gencode Transcript: ENST00000369702.5_5
Gencode Gene: ENSG00000064703.13_8
Transcript (Including UTRs)
   Position: hg19 chr1:112,298,523-112,310,622 Size: 12,100 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr1:112,298,547-112,309,521 Size: 10,975 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq 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 (chr1:112,298,523-112,310,622)mRNA (may differ from genome)Protein (824 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX20_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX20; EC=3.6.4.13; AltName: Full=Component of gems 3; AltName: Full=DEAD box protein 20; AltName: Full=DEAD box protein DP 103; AltName: Full=Gemin-3;
FUNCTION: The SMN complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus. It may also play a role in the metabolism of snoRNPs.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Part of the core SMN complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8 and STRAP/UNRIP. Interacts directly with SMN1 and with several spliceosomal snRNP core Sm proteins, including SNUPN, SNRPB, SNRPD2 and SNRPD3. Interacts with PPP4R2. Interacts with EBV EBNA2 and EBNA3C. Interacts with FOXL2.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, gem. Note=Localized in subnuclear structures next to coiled bodies, called Gemini of Cajal bodies (Gems).
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the DEAD box helicase family. DDX20 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: DDX20
Diseases sorted by gene-association score: spinal muscular atrophy (16), muscular atrophy (9), blepharophimosis, epicanthus inversus, and ptosis, type 1 (5)

-  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: 50.35 RPKM in Testis
Total median expression: 208.96 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -2.2024-0.092 Picture PostScript Text
3' UTR -286.101101-0.260 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
2OXC - X-ray MuPIT 3B7G - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9UHI6
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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 DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGD  WormBase 
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0019904 protein domain specific binding
GO:0030674 protein binding, bridging
GO:0042826 histone deacetylase binding
GO:0070491 repressing transcription factor binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000387 spliceosomal snRNP assembly
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0008285 negative regulation of cell proliferation
GO:0008380 RNA splicing
GO:0010501 RNA secondary structure unwinding
GO:0043065 positive regulation of apoptotic process
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048477 oogenesis
GO:0050810 regulation of steroid biosynthetic process
GO:0051170 nuclear import

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016020 membrane
GO:0017053 transcriptional repressor complex
GO:0032797 SMN complex
GO:0034719 SMN-Sm protein complex
GO:0090571 RNA polymerase II transcription repressor complex
GO:0097504 Gemini of coiled bodies


-  Descriptions from all associated GenBank mRNAs
  KJ906070 - Synthetic construct Homo sapiens clone ccsbBroadEn_15740 DDX20 gene, encodes complete protein.
KJ898379 - Synthetic construct Homo sapiens clone ccsbBroadEn_07773 DDX20 gene, encodes complete protein.
KR709543 - Synthetic construct Homo sapiens clone CCSBHm_00003314 DDX20 (DDX20) mRNA, encodes complete protein.
BC034953 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 20, mRNA (cDNA clone MGC:26212 IMAGE:4824324), complete cds.
LF206283 - JP 2014500723-A/13786: Polycomb-Associated Non-Coding RNAs.
AF171063 - Homo sapiens DEAD box RNA helicase Gemin3 mRNA, complete cds.
AK301697 - Homo sapiens cDNA FLJ50269 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX20 (EC 3.6.1.-).
BC031062 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 20, mRNA (cDNA clone MGC:33313 IMAGE:5273709), complete cds.
AK001506 - Homo sapiens cDNA FLJ10644 fis, clone NT2RP2005763, weakly similar to EUKARYOTIC INITIATION FACTOR 4A.
BC011556 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 20, mRNA (cDNA clone MGC:20004 IMAGE:4651697), complete cds.
AF106019 - Homo sapiens DEAD-box protein (DP103) mRNA, complete cds.
AF155803 - Homo sapiens DEAD-box corepressor DP103 (DDX20) mRNA, complete cds.
AK314312 - Homo sapiens cDNA, FLJ95070.
DQ892249 - Synthetic construct clone IMAGE:100004879; FLH184509.01X; RZPDo839G09144D DEAD (Asp-Glu-Ala-Asp) box polypeptide 20 (DDX20) gene, encodes complete protein.
DQ895449 - Synthetic construct Homo sapiens clone IMAGE:100009909; FLH184505.01L; RZPDo839G09143D DEAD (Asp-Glu-Ala-Asp) box polypeptide 20 (DDX20) gene, encodes complete protein.
CU679958 - Synthetic construct Homo sapiens gateway clone IMAGE:100020439 5' read DDX20 mRNA.
AL133598 - Homo sapiens mRNA; cDNA DKFZp434H052 (from clone DKFZp434H052).
LF352976 - JP 2014500723-A/160479: Polycomb-Associated Non-Coding RNAs.
LF352975 - JP 2014500723-A/160478: Polycomb-Associated Non-Coding RNAs.
LF352974 - JP 2014500723-A/160477: Polycomb-Associated Non-Coding RNAs.
AY007146 - Homo sapiens clone CDABP0082 mRNA sequence.
LF352973 - JP 2014500723-A/160476: Polycomb-Associated Non-Coding RNAs.
JD560317 - Sequence 541341 from Patent EP1572962.
JD509712 - Sequence 490736 from Patent EP1572962.
LF352972 - JP 2014500723-A/160475: Polycomb-Associated Non-Coding RNAs.
JD287743 - Sequence 268767 from Patent EP1572962.
JD299267 - Sequence 280291 from Patent EP1572962.
JD273242 - Sequence 254266 from Patent EP1572962.
MA588553 - JP 2018138019-A/160479: Polycomb-Associated Non-Coding RNAs.
MA588552 - JP 2018138019-A/160478: Polycomb-Associated Non-Coding RNAs.
MA588551 - JP 2018138019-A/160477: Polycomb-Associated Non-Coding RNAs.
MA588550 - JP 2018138019-A/160476: Polycomb-Associated Non-Coding RNAs.
MA588549 - JP 2018138019-A/160475: Polycomb-Associated Non-Coding RNAs.
MA441860 - JP 2018138019-A/13786: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_etsPathway - METS affect on Macrophage Differentiation

Reactome (by CSHL, EBI, and GO)

Protein Q9UHI6 (Reactome details) participates in the following event(s):

R-HSA-191790 Loading and methylation of Sm proteins onto SMN Complexes
R-HSA-191830 snRNP nuclear import and release
R-HSA-191786 snRNP complex assembly
R-HSA-191763 snRNP:Snurportin complex formation
R-HSA-191784 snRNA Cap hypermethylation
R-HSA-191859 snRNP Assembly
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B4DWV7, DDX20_HUMAN, DP103, ENST00000369702.1, ENST00000369702.2, ENST00000369702.3, ENST00000369702.4, GEMIN3, NM_007204, Q96F72, Q9NVM3, Q9UF59, Q9UHI6, Q9UIY0, Q9Y659, uc318htx.1, uc318htx.2
UCSC ID: ENST00000369702.5_5
RefSeq Accession: NM_007204.5
Protein: Q9UHI6 (aka DDX20_HUMAN or DD20_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.