Human Gene DDX5 (uc002jek.2) Description and Page Index
  Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box helicase 5 (DDX5), mRNA.
RefSeq Summary (NM_004396): This gene encodes a member of the DEAD box family of RNA helicases that are involved in a variety of cellular processes as a result of its role as an adaptor molecule, promoting interactions with a large number of other factors. This protein is involved in pathways that include the alteration of RNA structures, plays a role as a coregulator of transcription, a regulator of splicing, and in the processing of small noncoding RNAs. Members of this family contain nine conserved motifs, including the conserved Asp-Glu-Ala-Asp (DEAD) motif, important to ATP binding and hydrolysis as well as RNA binding and unwinding activities. Dysregulation of this gene may play a role in cancer development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2017].
Transcript (Including UTRs)
   Position: hg19 chr17:62,494,374-62,502,484 Size: 8,111 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr17:62,496,041-62,502,237 Size: 6,197 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:62,494,374-62,502,484)mRNA (may differ from genome)Protein (614 aa)
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: DDX5_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX5; EC=3.6.4.13; AltName: Full=DEAD box protein 5; AltName: Full=RNA helicase p68;
FUNCTION: Involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner. Binds to the tau pre-mRNA in the stem-loop region downstream of exon 10. The rate of ATP hydrolysis is highly stimulated by single-stranded RNA. Involved in transcriptional regulation; the function is independent of the RNA helicase activity. Transcriptional coactivator for estrogen receptor ESR1 and androgen receptor AR. Increases ESR1 AF-1 domain-mediated transactivation and ESR1 AF-1 and AF-2 domains transcriptional synergistic activity. Synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and involved in skeletal muscle differentiation. Transcriptional coactivator for p53/TP53 and involved in p53/TP53 transcriptional response to DNA damage and p53/TP53-dependent apoptosis. Transcriptional coactivator for RUNX2 and involved in regulation of osteoblast differentiation. Acts as transcriptional repressor in a promoter-specicic manner; the function probbaly involves association with histone deacetylases, such as HDAC1.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Interacts with BRDT (By similarity). Identified in the spliceosome C complex. Interacts with RBM4; the interaction occurs in a RNA-independent manner. Interacts with EIF2C1 and EIF2C2. Interacts with ESR1; the interaction is enhanced by phosphorylation of ESR1 AF-1 domain. Interacts with AR, NCOA1, NCOA2, NCOA3, EP300, CREBBP, POLR2A, TP53, RUNX2 and HDAC1. Self- associates. Interacts with DDX17.
INTERACTION: Q12873:CHD3; NbExp=4; IntAct=EBI-351962, EBI-523590; P45481:Crebbp (xeno); NbExp=3; IntAct=EBI-351962, EBI-296306; Q09472:EP300; NbExp=4; IntAct=EBI-351962, EBI-447295; P03372:ESR1; NbExp=8; IntAct=EBI-351962, EBI-78473; P22087:FBL; NbExp=6; IntAct=EBI-351962, EBI-358318; Q13547:HDAC1; NbExp=4; IntAct=EBI-351962, EBI-301834; O95983:MBD3; NbExp=4; IntAct=EBI-351962, EBI-1783068; P10085:Myod1 (xeno); NbExp=3; IntAct=EBI-351962, EBI-4405734; P24928:POLR2A; NbExp=3; IntAct=EBI-351962, EBI-295301; Q08775-3:Runx2 (xeno); NbExp=2; IntAct=EBI-351962, EBI-6119991; P04637:TP53; NbExp=3; IntAct=EBI-351962, EBI-366083; P04637-1:TP53; NbExp=2; IntAct=EBI-351962, EBI-3895849; P04637-7:TP53; NbExp=2; IntAct=EBI-351962, EBI-3895873;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
PTM: Arg-502 is dimethylated, probably to asymmetric dimethylarginine.
PTM: Sumoylated; sumoylation, promoted by PIAS1, promotes interaction with HDAC1 and transcriptional repression activity. Sumoylation also significantly increases stability, and reduces polyubiquitination.
PTM: Polyubiquitinated, leading to proteasomal degradation.
SIMILARITY: Belongs to the DEAD box helicase family. DDX5/DBP2 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DDX5
CDC HuGE Published Literature: DDX5
Positive Disease Associations: hepatitis C, chronic
Related Studies:
  1. hepatitis C, chronic
    Huang, H. et al. 2006, Identification of two gene variants associated with risk of advanced fibrosis in patients with chronic hepatitis C, Gastroenterology 2006 130(6) 1679-87. [PubMed 16697732]
    Subjects with CHC carrying DDX5 minor allele or DDX5-POLG2 haplotypes are at an increased risk of developing advanced fibrosis, whereas those carrying the CPT1A minor allele are at a decreased risk.

-  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: 347.02 RPKM in Spleen
Total median expression: 8825.72 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 -79.90247-0.323 Picture PostScript Text
3' UTR -429.051667-0.257 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
IPR012587 - P68HR
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
PF08061 - P68HR (NUC004) repeat

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

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

3FE2
- X-ray MuPIT

4A4D
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P17844
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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 BrowserNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsemblFlyBase SGD
 Protein SequenceProtein SequenceProtein Sequence Protein Sequence
 AlignmentAlignmentAlignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0003730 mRNA 3'-UTR binding
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005516 calmodulin binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0019899 enzyme binding
GO:0035500 MH2 domain binding
GO:0036002 pre-mRNA binding
GO:0043021 ribonucleoprotein complex binding
GO:0046332 SMAD binding
GO:0048306 calcium-dependent protein binding
GO:0050681 androgen receptor binding
GO:0070412 R-SMAD binding
GO:0070878 primary miRNA binding
GO:1990841 promoter-specific chromatin binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000380 alternative mRNA splicing, via spliceosome
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
GO:0000398 mRNA splicing, via spliceosome
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0001837 epithelial to mesenchymal transition
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0009299 mRNA transcription
GO:0010501 RNA secondary structure unwinding
GO:0016049 cell growth
GO:0030509 BMP signaling pathway
GO:0030520 intracellular estrogen receptor signaling pathway
GO:0030521 androgen receptor signaling pathway
GO:0043517 positive regulation of DNA damage response, signal transduction by p53 class mediator
GO:0045069 regulation of viral genome replication
GO:0045445 myoblast differentiation
GO:0045667 regulation of osteoblast differentiation
GO:0048511 rhythmic process
GO:0060765 regulation of androgen receptor signaling pathway
GO:0061614 pri-miRNA transcription from RNA polymerase II promoter
GO:0072332 intrinsic apoptotic signaling pathway by p53 class mediator
GO:1903800 positive regulation of production of miRNAs involved in gene silencing by miRNA
GO:2001014 regulation of skeletal muscle cell differentiation
GO:1902893 regulation of pri-miRNA transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0016020 membrane
GO:0070062 extracellular exosome
GO:0071013 catalytic step 2 spliceosome
GO:1990904 ribonucleoprotein complex
GO:0071141 SMAD protein complex


-  Descriptions from all associated GenBank mRNAs
  LF213995 - JP 2014500723-A/21498: Polycomb-Associated Non-Coding RNAs.
AL133585 - Homo sapiens mRNA; cDNA DKFZp434E109 (from clone DKFZp434E109).
AB209919 - Homo sapiens mRNA for Hypothetical protein DKFZp686J01190 variant protein.
BC016027 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 5, mRNA (cDNA clone MGC:1516 IMAGE:3528578), complete cds.
X15729 - Human mRNA for nuclear p68 protein.
LP895359 - Sequence 223 from Patent EP3253886.
X52104 - Human mRNA for p68 protein.
AK055995 - Homo sapiens cDNA FLJ31433 fis, clone NT2NE2000575, highly similar to PROBABLE RNA-DEPENDENT HELICASE P68.
AK297192 - Homo sapiens cDNA FLJ59339 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX5 (EC 3.6.1.-).
BX571764 - Homo sapiens mRNA; cDNA DKFZp686J01190 (from clone DKFZp686J01190).
AK297905 - Homo sapiens cDNA FLJ59357 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX5 (EC 3.6.1.-).
JD237659 - Sequence 218683 from Patent EP1572962.
AK297753 - Homo sapiens cDNA FLJ53366 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX5 (EC 3.6.1.-).
AK310318 - Homo sapiens cDNA, FLJ17360.
DQ890687 - Synthetic construct clone IMAGE:100003317; FLH165134.01X; RZPDo839G05158D DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5) gene, encodes complete protein.
AB451257 - Homo sapiens DDX5 mRNA for ATP-dependent RNA helicase DDX5, complete cds, clone: FLJ08070AAAN.
BT006943 - Homo sapiens DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kDa) mRNA, complete cds.
DQ893774 - Synthetic construct Homo sapiens clone IMAGE:100008234; FLH165130.01L; RZPDo839G05157D DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5) gene, encodes complete protein.
AB451382 - Homo sapiens DDX5 mRNA for ATP-dependent RNA helicase DDX5, partial cds, clone: FLJ08070AAAF.
AB384902 - Synthetic construct DNA, clone: pF1KB4122, Homo sapiens DDX5 gene for ATP-dependent RNA helicase DDX5, complete cds, without stop codon, in Flexi system.
JD019308 - Sequence 332 from Patent EP1572962.
JD030780 - Sequence 11804 from Patent EP1572962.
DL492053 - Novel nucleic acids.
JD022026 - Sequence 3050 from Patent EP1572962.
JD020172 - Sequence 1196 from Patent EP1572962.
JD021250 - Sequence 2274 from Patent EP1572962.
JD027775 - Sequence 8799 from Patent EP1572962.
JD028556 - Sequence 9580 from Patent EP1572962.
JD035561 - Sequence 16585 from Patent EP1572962.
JD035431 - Sequence 16455 from Patent EP1572962.
JD020160 - Sequence 1184 from Patent EP1572962.
JD019006 - Sequence 30 from Patent EP1572962.
JD021339 - Sequence 2363 from Patent EP1572962.
JD035257 - Sequence 16281 from Patent EP1572962.
JD433220 - Sequence 414244 from Patent EP1572962.
MA449572 - JP 2018138019-A/21498: Polycomb-Associated Non-Coding RNAs.

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

BioCarta from NCI Cancer Genome Anatomy Project
h_akap95Pathway - AKAP95 role in mitosis and chromosome dynamics

Reactome (by CSHL, EBI, and GO)

Protein P17844 (Reactome details) participates in the following event(s):

R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-9009536 DDX5 binds ESR1:estrogen:TFF1 gene promoter
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-9009533 TBP and TFIIA bind TATA box on ESR1:estrogen bound TFF1 gene promoter
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-9009526 CARM1 binds TBP:TFIIA:DDX5:ESR1:estrogen:TFF1 gene
R-HSA-9023861 PRMT1 binds TBP:TFIIA:DDX5:ESR1:estrogen:TFF1 gene
R-HSA-9023860 Histone acetyltransferases are recruited to the TFF1 gene
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-72172 mRNA Splicing
R-HSA-8939211 ESR-mediated signaling
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-8953854 Metabolism of RNA
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B5BU21, D3DU32, DDX5_HUMAN, G17P1, HELR, HLR1, NM_004396, NP_004387, O75681, P17844, Q53Y61
UCSC ID: uc002jek.2
RefSeq Accession: NM_004396
Protein: P17844 (aka DDX5_HUMAN)
CCDS: CCDS11659.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004396.3
exon count: 13CDS single in 3' UTR: no RNA size: 3769
ORF size: 1845CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3890.00frame shift in genome: no % Coverage: 99.73
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.