Human Gene DDX10 (uc001pkm.3) Description and Page Index
  Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 (DDX10), mRNA.
RefSeq Summary (NM_004398): DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, and it may be involved in ribosome assembly. Fusion of this gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1803615.195133.1, BC091521.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000322536.8/ ENSP00000314348.3 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:108,535,816-108,811,648 Size: 275,833 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr11:108,535,881-108,811,150 Size: 275,270 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:108,535,816-108,811,648)mRNA (may differ from genome)Protein (875 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DDX10_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX10; EC=3.6.4.13; AltName: Full=DEAD box protein 10;
FUNCTION: Putative ATP-dependent RNA helicase.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
TISSUE SPECIFICITY: High in testis but widely expressed.
DOMAIN: The Q motif is unique to and characteristic of the DEAD box family of RNA helicases and controls ATP binding and hydrolysis.
SIMILARITY: Belongs to the DEAD box helicase family. DDX10/DBP4 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/DDX10.html";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DDX10
CDC HuGE Published Literature: DDX10
Positive Disease Associations: Electrocardiography
Related Studies:
  1. Electrocardiography
    Christopher Newton-Cheh et al. BMC medical genetics 2007, Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study., BMC medical genetics. [PubMed 17903306]
    In the community-based Framingham Heart Study none of the ECG and HRV results individually attained genomewide significance. However, the presence of bona fide QT-associated SNPs among the top 117 results for QT duration supports the importance of efforts to validate top results from the reported scans. Finding genetic variants associated with ECG and HRV quantitative traits may identify novel genes and pathways implicated in arrhythmogenesis and allow for improved recognition of individuals at high risk for arrhythmias in the general population.

-  MalaCards Disease Associations
  MalaCards Gene Search: DDX10
Diseases sorted by gene-association score: myelodysplastic syndrome (3), leukemia, acute myeloid (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: 6.02 RPKM in Testis
Total median expression: 125.96 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 -20.2065-0.311 Picture PostScript Text
3' UTR -125.32498-0.252 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
IPR025313 - DUF4217
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
PF13959 - Domain of unknown function (DUF4217)

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

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

2PL3
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q13206
FrontTopSide
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  EnsemblFlyBaseWormBaseSGD
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence
  AlignmentAlignmentAlignmentAlignment

-  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:0005524 ATP binding
GO:0016787 hydrolase activity

Biological Process:
GO:0010501 RNA secondary structure unwinding
GO:0097065 anterior head development

Cellular Component:
GO:0005730 nucleolus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK296752 - Homo sapiens cDNA FLJ51228 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX10 (EC 3.6.1.-).
BC091521 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 10, mRNA (cDNA clone MGC:111510 IMAGE:30388370), complete cds.
AB040537 - Homo sapiens DDX10 mRNA for RNA helicase, complete cds.
LF384549 - JP 2014500723-A/192052: Polycomb-Associated Non-Coding RNAs.
U28042 - Human DEAD box RNA helicase-like protein mRNA, complete cds.
AK315216 - Homo sapiens cDNA, FLJ96210, Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 (DDX10),mRNA.
BC093654 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 10, mRNA (cDNA clone MGC:120689 IMAGE:7939499), complete cds.
BC093656 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 10, mRNA (cDNA clone MGC:120691 IMAGE:7939501), complete cds.
AB209884 - Homo sapiens mRNA for DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 variant protein.
BC064921 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 10, mRNA (cDNA clone IMAGE:6141012), partial cds.
BC049217 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 10, mRNA (cDNA clone IMAGE:5500425), partial cds.
MA620126 - JP 2018138019-A/192052: Polycomb-Associated Non-Coding RNAs.
LF377020 - JP 2014500723-A/184523: Polycomb-Associated Non-Coding RNAs.
AB001343 - Homo sapiens mRNA for DDX10-NUP98 fusion protein type 2, partial cds.
AB000267 - Homo sapiens mRNA for NUP98-DDX10 fusion protein type 1, partial cds.
LF377016 - JP 2014500723-A/184519: Polycomb-Associated Non-Coding RNAs.
LF377011 - JP 2014500723-A/184514: Polycomb-Associated Non-Coding RNAs.
JD353481 - Sequence 334505 from Patent EP1572962.
JD268151 - Sequence 249175 from Patent EP1572962.
LF377009 - JP 2014500723-A/184512: Polycomb-Associated Non-Coding RNAs.
LF377008 - JP 2014500723-A/184511: Polycomb-Associated Non-Coding RNAs.
MA612597 - JP 2018138019-A/184523: Polycomb-Associated Non-Coding RNAs.
MA612593 - JP 2018138019-A/184519: Polycomb-Associated Non-Coding RNAs.
MA612588 - JP 2018138019-A/184514: Polycomb-Associated Non-Coding RNAs.
MA612586 - JP 2018138019-A/184512: Polycomb-Associated Non-Coding RNAs.
MA612585 - JP 2018138019-A/184511: Polycomb-Associated Non-Coding RNAs.
LF377002 - JP 2014500723-A/184505: Polycomb-Associated Non-Coding RNAs.
LF377000 - JP 2014500723-A/184503: Polycomb-Associated Non-Coding RNAs.
LF376999 - JP 2014500723-A/184502: Polycomb-Associated Non-Coding RNAs.
LF376998 - JP 2014500723-A/184501: Polycomb-Associated Non-Coding RNAs.
LF376993 - JP 2014500723-A/184496: Polycomb-Associated Non-Coding RNAs.
MA612579 - JP 2018138019-A/184505: Polycomb-Associated Non-Coding RNAs.
MA612577 - JP 2018138019-A/184503: Polycomb-Associated Non-Coding RNAs.
MA612576 - JP 2018138019-A/184502: Polycomb-Associated Non-Coding RNAs.
MA612575 - JP 2018138019-A/184501: Polycomb-Associated Non-Coding RNAs.
MA612570 - JP 2018138019-A/184496: Polycomb-Associated Non-Coding RNAs.
JD326606 - Sequence 307630 from Patent EP1572962.
JD164146 - Sequence 145170 from Patent EP1572962.
JD351973 - Sequence 332997 from Patent EP1572962.
JD220454 - Sequence 201478 from Patent EP1572962.
JD126277 - Sequence 107301 from Patent EP1572962.
JD240361 - Sequence 221385 from Patent EP1572962.
JD290915 - Sequence 271939 from Patent EP1572962.
JD553932 - Sequence 534956 from Patent EP1572962.
JD173916 - Sequence 154940 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RCQ3, DDX10_HUMAN, NM_004398, NP_004389, Q13206, Q5BJD8
UCSC ID: uc001pkm.3
RefSeq Accession: NM_004398
Protein: Q13206 (aka DDX10_HUMAN or DD10_HUMAN)
CCDS: CCDS8342.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004398.2
exon count: 18CDS single in 3' UTR: no RNA size: 3204
ORF size: 2628CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 4631.00frame shift in genome: no % Coverage: 99.59
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # 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.