Human Gene DDX6 (ENST00000534980.7_8) from GENCODE V47lift37
  Description: DEAD-box helicase 6, transcript variant 1 (from RefSeq NM_004397.6)
Gencode Transcript: ENST00000534980.7_8
Gencode Gene: ENSG00000110367.14_11
Transcript (Including UTRs)
   Position: hg19 chr11:118,618,472-118,661,873 Size: 43,402 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr11:118,625,421-118,656,960 Size: 31,540 Coding Exon Count: 12 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:118,618,472-118,661,873)mRNA (may differ from genome)Protein (483 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX6_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX6; EC=3.6.4.13; AltName: Full=ATP-dependent RNA helicase p54; AltName: Full=DEAD box protein 6; AltName: Full=Oncogene RCK;
FUNCTION: In the process of mRNA degradation, may play a role in mRNA decapping.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Forms a complex with DCP1A, DCP2, EDC3 and EDC4/HEDLS. Interacts with LIMD1, WTIP and AJUBA.
INTERACTION: Q9NPI6:DCP1A; NbExp=4; IntAct=EBI-351257, EBI-374238; Q96F86:EDC3; NbExp=2; IntAct=EBI-351257, EBI-997311;
SUBCELLULAR LOCATION: Cytoplasm, P-body. Note=Processing bodies (PB).
TISSUE SPECIFICITY: Abundantly expressed in most tissues.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Note=A chromosomal aberration involving DDX6 may be a cause of hematopoietic tumors such as B-cell lymphomas. Translocation t(11;14)(q23;q32).
SIMILARITY: Belongs to the DEAD box helicase family. DDX6/DHH1 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: DDX6
Diseases sorted by gene-association score: b-cell lymphomas (4)

-  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: 27.67 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 587.77 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 -84.70334-0.254 Picture PostScript Text
3' UTR -1231.904342-0.284 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:
51735 - NAD(P)-binding Rossmann-fold domains
52540 - P-loop containing nucleoside triphosphate hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1VEC - X-ray MuPIT 2WAX - X-ray MuPIT 2WAY - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P26196
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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    
 RGD    
      
      

-  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: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:0045296 cadherin binding

Biological Process:
GO:0006417 regulation of translation
GO:0007283 spermatogenesis
GO:0010501 RNA secondary structure unwinding
GO:0019074 viral RNA genome packaging
GO:0019827 stem cell population maintenance
GO:0033962 cytoplasmic mRNA processing body assembly
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:0045665 negative regulation of neuron differentiation

Cellular Component:
GO:0000792 heterochromatin
GO:0000932 P-body
GO:0001520 outer dense fiber
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0010494 cytoplasmic stress granule
GO:0016020 membrane
GO:0016442 RISC complex
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0043186 P granule
GO:0097227 sperm annulus


-  Descriptions from all associated GenBank mRNAs
  LF208456 - JP 2014500723-A/15959: Polycomb-Associated Non-Coding RNAs.
LF384543 - JP 2014500723-A/192046: Polycomb-Associated Non-Coding RNAs.
DL492438 - Novel nucleic acids.
MA620120 - JP 2018138019-A/192046: Polycomb-Associated Non-Coding RNAs.
MA444033 - JP 2018138019-A/15959: Polycomb-Associated Non-Coding RNAs.
AK021715 - Homo sapiens cDNA FLJ11653 fis, clone HEMBA1004538.
LF376430 - JP 2014500723-A/183933: Polycomb-Associated Non-Coding RNAs.
LF376429 - JP 2014500723-A/183932: Polycomb-Associated Non-Coding RNAs.
JD500030 - Sequence 481054 from Patent EP1572962.
JD021652 - Sequence 2676 from Patent EP1572962.
JD148150 - Sequence 129174 from Patent EP1572962.
JD328172 - Sequence 309196 from Patent EP1572962.
LF376428 - JP 2014500723-A/183931: Polycomb-Associated Non-Coding RNAs.
JD097843 - Sequence 78867 from Patent EP1572962.
JD446182 - Sequence 427206 from Patent EP1572962.
JD343318 - Sequence 324342 from Patent EP1572962.
JD445558 - Sequence 426582 from Patent EP1572962.
JD536844 - Sequence 517868 from Patent EP1572962.
JD551495 - Sequence 532519 from Patent EP1572962.
LF376427 - JP 2014500723-A/183930: Polycomb-Associated Non-Coding RNAs.
MA612007 - JP 2018138019-A/183933: Polycomb-Associated Non-Coding RNAs.
MA612006 - JP 2018138019-A/183932: Polycomb-Associated Non-Coding RNAs.
MA612005 - JP 2018138019-A/183931: Polycomb-Associated Non-Coding RNAs.
MA612004 - JP 2018138019-A/183930: Polycomb-Associated Non-Coding RNAs.
DL490917 - Novel nucleic acids.
D17532 - Homo sapiens mRNA for RCK, complete cds.
JD566593 - Sequence 547617 from Patent EP1572962.
BC039826 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 6, mRNA (cDNA clone IMAGE:5582799), complete cds.
JD531901 - Sequence 512925 from Patent EP1572962.
JD127367 - Sequence 108391 from Patent EP1572962.
LF376426 - JP 2014500723-A/183929: Polycomb-Associated Non-Coding RNAs.
JD250721 - Sequence 231745 from Patent EP1572962.
JD538584 - Sequence 519608 from Patent EP1572962.
JD238620 - Sequence 219644 from Patent EP1572962.
DL491269 - Novel nucleic acids.
DL489909 - Novel nucleic acids.
JD081895 - Sequence 62919 from Patent EP1572962.
JD044141 - Sequence 25165 from Patent EP1572962.
JD224558 - Sequence 205582 from Patent EP1572962.
JD224783 - Sequence 205807 from Patent EP1572962.
JD445952 - Sequence 426976 from Patent EP1572962.
DQ596593 - Homo sapiens piRNA piR-34659, complete sequence.
JD215815 - Sequence 196839 from Patent EP1572962.
JD484303 - Sequence 465327 from Patent EP1572962.
LF376425 - JP 2014500723-A/183928: Polycomb-Associated Non-Coding RNAs.
JD465125 - Sequence 446149 from Patent EP1572962.
BC065007 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 6, mRNA (cDNA clone MGC:74611 IMAGE:6163439), complete cds.
AK093657 - Homo sapiens cDNA FLJ36338 fis, clone THYMU2006357, highly similar to PROBABLE ATP-DEPENDENT RNA HELICASE P54.
Z11685 - H.sapiens mRNA for RNA helicase.
JD457611 - Sequence 438635 from Patent EP1572962.
JD153935 - Sequence 134959 from Patent EP1572962.
LF376424 - JP 2014500723-A/183927: Polycomb-Associated Non-Coding RNAs.
JD359129 - Sequence 340153 from Patent EP1572962.
LF376423 - JP 2014500723-A/183926: Polycomb-Associated Non-Coding RNAs.
JD049680 - Sequence 30704 from Patent EP1572962.
JD202978 - Sequence 184002 from Patent EP1572962.
LF376422 - JP 2014500723-A/183925: Polycomb-Associated Non-Coding RNAs.
JD045578 - Sequence 26602 from Patent EP1572962.
JD043432 - Sequence 24456 from Patent EP1572962.
JD284503 - Sequence 265527 from Patent EP1572962.
JD562789 - Sequence 543813 from Patent EP1572962.
LF376421 - JP 2014500723-A/183924: Polycomb-Associated Non-Coding RNAs.
LF205569 - JP 2014500723-A/13072: Polycomb-Associated Non-Coding RNAs.
AK313244 - Homo sapiens cDNA, FLJ93750, Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 (DDX6), mRNA.
HQ448157 - Synthetic construct Homo sapiens clone IMAGE:100071544; CCSB012339_01 DEAD (Asp-Glu-Ala-Asp) box polypeptide 6 (DDX6) gene, encodes complete protein.
KJ891037 - Synthetic construct Homo sapiens clone ccsbBroadEn_00431 DDX6 gene, encodes complete protein.
AB527511 - Synthetic construct DNA, clone: pF1KB5842, Homo sapiens DDX6 gene for DEAD (Asp-Glu-Ala-Asp) box polypeptide 6, without stop codon, in Flexi system.
LF376420 - JP 2014500723-A/183923: Polycomb-Associated Non-Coding RNAs.
LF346285 - JP 2014500723-A/153788: Polycomb-Associated Non-Coding RNAs.
CU687996 - Synthetic construct Homo sapiens gateway clone IMAGE:100023194 5' read DDX6 mRNA.
LF376419 - JP 2014500723-A/183922: Polycomb-Associated Non-Coding RNAs.
BC026228 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 6, mRNA (cDNA clone IMAGE:4701626), with apparent retained intron.
LF346283 - JP 2014500723-A/153786: Polycomb-Associated Non-Coding RNAs.
LF376417 - JP 2014500723-A/183920: Polycomb-Associated Non-Coding RNAs.
LF346281 - JP 2014500723-A/153784: Polycomb-Associated Non-Coding RNAs.
JD409742 - Sequence 390766 from Patent EP1572962.
MA581862 - JP 2018138019-A/153788: Polycomb-Associated Non-Coding RNAs.
MA581860 - JP 2018138019-A/153786: Polycomb-Associated Non-Coding RNAs.
MA581858 - JP 2018138019-A/153784: Polycomb-Associated Non-Coding RNAs.
MA612003 - JP 2018138019-A/183929: Polycomb-Associated Non-Coding RNAs.
MA612002 - JP 2018138019-A/183928: Polycomb-Associated Non-Coding RNAs.
MA612001 - JP 2018138019-A/183927: Polycomb-Associated Non-Coding RNAs.
MA612000 - JP 2018138019-A/183926: Polycomb-Associated Non-Coding RNAs.
MA611999 - JP 2018138019-A/183925: Polycomb-Associated Non-Coding RNAs.
MA611998 - JP 2018138019-A/183924: Polycomb-Associated Non-Coding RNAs.
MA441146 - JP 2018138019-A/13072: Polycomb-Associated Non-Coding RNAs.
MA611997 - JP 2018138019-A/183923: Polycomb-Associated Non-Coding RNAs.
MA611996 - JP 2018138019-A/183922: Polycomb-Associated Non-Coding RNAs.
MA611994 - JP 2018138019-A/183920: Polycomb-Associated Non-Coding RNAs.

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

Protein P26196 (Reactome details) participates in the following event(s):

R-HSA-429860 DCP1-DCP2 complex decaps mRNA
R-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: DDX6_HUMAN, ENST00000534980.1, ENST00000534980.2, ENST00000534980.3, ENST00000534980.4, ENST00000534980.5, ENST00000534980.6, HLR2, NM_004397, P26196, Q5D048, RCK, uc324nnr.1, uc324nnr.2
UCSC ID: ENST00000534980.7_8
RefSeq Accession: NM_004397.6
Protein: P26196 (aka DDX6_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.