Human Gene DDX31 (uc004cbq.1)
  Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 31 (DDX31), transcript variant 1, mRNA.
RefSeq Summary (NM_022779): 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 DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a member of this family. The function of this member has not been determined. Alternative splicing of this gene generates multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2016].
Transcript (Including UTRs)
   Position: hg19 chr9:135,469,676-135,545,788 Size: 76,113 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr9:135,470,253-135,545,636 Size: 75,384 Coding Exon Count: 20 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:135,469,676-135,545,788)mRNA (may differ from genome)Protein (851 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX31_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX31; EC=3.6.4.13; AltName: Full=DEAD box protein 31; AltName: Full=Helicain;
FUNCTION: Probable ATP-dependent RNA helicase (By similarity).
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Belongs to the DEAD box helicase family. DDX31/DBP7 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SEQUENCE CAUTION: Sequence=AAQ14889.1; Type=Frameshift; Positions=816, 825; Sequence=AAQ14890.1; Type=Frameshift; Positions=816; Sequence=BAB14644.1; Type=Erroneous initiation; Sequence=BAB15620.1; Type=Frameshift; Positions=141; Sequence=CAH70532.1; Type=Erroneous gene model prediction; Sequence=CAI16565.1; Type=Erroneous gene model prediction;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DDX31
CDC HuGE Published Literature: DDX31
Positive Disease Associations: Schizophrenia
Related Studies:
  1. Schizophrenia
    , , . [PubMed 0]

-  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: 6.93 RPKM in Thyroid
Total median expression: 132.52 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 -68.10152-0.448 Picture PostScript Text
3' UTR -207.60577-0.360 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

ModBase Predicted Comparative 3D Structure on Q9H8H2
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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 orthologGenome BrowserGenome BrowserNo orthologGenome Browser
Gene Details  Gene Details Gene Details
Gene Sorter  Gene Sorter Gene Sorter
  EnsemblFlyBase SGD
  Protein SequenceProtein Sequence Protein Sequence
  AlignmentAlignment Alignment

-  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:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity

Biological Process:
GO:0010501 RNA secondary structure unwinding
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AK225121 - Homo sapiens mRNA for DEAD (Asp-Glu-Ala-Asp) box polypeptide 31 isoform 1 variant, clone: CBL01338.
AK027002 - Homo sapiens cDNA: FLJ23349 fis, clone HEP13913.
AK225350 - Homo sapiens mRNA for DEAD (Asp-Glu-Ala-Asp) box polypeptide 31 isoform 1 variant, clone: HEP13913.
AF427339 - Homo sapiens DEAD/DEXH helicase DDX31 mRNA, complete cds.
AK023695 - Homo sapiens cDNA FLJ13633 fis, clone PLACE1011114, weakly similar to PROBABLE ATP-DEPENDENT RNA HELICASE HAS1.
AF335568 - Homo sapiens helicain B mRNA, complete cds, alternatively spliced.
AF335569 - Homo sapiens helicain C mRNA, complete cds, alternatively spliced.
BC012726 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 31, mRNA (cDNA clone IMAGE:3941452), partial cds.
AK302670 - Homo sapiens cDNA FLJ59786 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX31 (EC 3.6.1.-).
KJ903102 - Synthetic construct Homo sapiens clone ccsbBroadEn_12496 DDX31 gene, encodes complete protein.
AK027484 - Homo sapiens cDNA FLJ14578 fis, clone NT2RM4001178, weakly similar to PROBABLE ATP-DEPENDENT RNA HELICASE HAS1.
BC156832 - Synthetic construct Homo sapiens clone IMAGE:100062551, MGC:190556 DEAD (Asp-Glu-Ala-Asp) box polypeptide 31 (DDX31) mRNA, encodes complete protein.
CU680380 - Synthetic construct Homo sapiens gateway clone IMAGE:100018407 5' read DDX31 mRNA.
JD359825 - Sequence 340849 from Patent EP1572962.
JD530683 - Sequence 511707 from Patent EP1572962.
JD490972 - Sequence 471996 from Patent EP1572962.
JD219061 - Sequence 200085 from Patent EP1572962.
JD459159 - Sequence 440183 from Patent EP1572962.
JD280566 - Sequence 261590 from Patent EP1572962.
JD070869 - Sequence 51893 from Patent EP1572962.
JD209073 - Sequence 190097 from Patent EP1572962.
JD292108 - Sequence 273132 from Patent EP1572962.
JD125986 - Sequence 107010 from Patent EP1572962.
JD310193 - Sequence 291217 from Patent EP1572962.
JD522629 - Sequence 503653 from Patent EP1572962.
AF335567 - Homo sapiens helicain A mRNA, complete cds, alternatively spliced.
AK304715 - Homo sapiens cDNA FLJ56295 complete cds, highly similar to Probable ATP-dependent RNA helicase DDX31 (EC 3.6.1.-).

-  Other Names for This Gene
  Alternate Gene Symbols: DDX31_HUMAN, NM_022779, NP_073616, Q5K6N2, Q5K6N3, Q5K6N4, Q5VZJ4, Q5VZJ9, Q96E91, Q96NY2, Q96SX5, Q9H5K6, Q9H8H2
UCSC ID: uc004cbq.1
RefSeq Accession: NM_022779
Protein: Q9H8H2 (aka DDX31_HUMAN)
CCDS: CCDS6951.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022779.7
exon count: 20CDS single in 3' UTR: no RNA size: 3285
ORF size: 2556CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4775.00frame shift in genome: no % Coverage: 100.00
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.