Human Gene DDX39B (uc011dnp.1)
  Description: Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B (DDX39B), transcript variant 3, non-coding RNA.
RefSeq Summary (NR_037852): This gene encodes a member of the DEAD box family of RNA-dependent ATPases that mediate ATP hydrolysis during pre-mRNA splicing. The encoded protein is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. This gene belongs to a cluster of genes localized in the vicinity of the genes encoding tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. Mutations in this gene may be associated with rheumatoid arthritis. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on both chromosomes 6 and 11. Read-through transcription also occurs between this gene and the upstream ATP6V1G2 (ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2) gene. [provided by RefSeq, Feb 2011].
Transcript (Including UTRs)
   Position: hg19 chr6:31,501,775-31,509,925 Size: 8,151 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr6:31,503,006-31,508,296 Size: 5,291 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:31,501,775-31,509,925)mRNA (may differ from genome)Protein (212 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsH-INVHGNC
LynxMalacardsMGIPubMedUniProtKBWikipedia

-  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: DDX39B
Diseases sorted by gene-association score: plasmodium vivax malaria (10)

-  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: 3.87 RPKM in Brain - Cerebellum
Total median expression: 87.44 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 -77.70214-0.363 Picture PostScript Text
3' UTR -479.691231-0.390 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

Pfam Domains:
PF00270 - DEAD/DEAH box helicase

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

ModBase Predicted Comparative 3D Structure on B4DIZ8
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0004386 helicase activity
GO:0005524 ATP binding


-  Descriptions from all associated GenBank mRNAs
  BC004350 - Homo sapiens cDNA clone IMAGE:3536103.
AK222912 - Homo sapiens mRNA for HLA-B associated transcript 1 variant, clone: HRC02604.
BC013006 - Homo sapiens HLA-B associated transcript 1, mRNA (cDNA clone MGC:3991 IMAGE:3010263), complete cds.
Z37166 - H.sapiens BAT1 mRNA for nuclear RNA helicase (DEAD family).
BC000361 - Homo sapiens HLA-B associated transcript 1, mRNA (cDNA clone MGC:8674 IMAGE:2964517), complete cds.
AK298194 - Homo sapiens cDNA FLJ53073 complete cds, highly similar to Spliceosome RNA helicase Bat1 (EC 3.6.1.-).
AB209217 - Homo sapiens mRNA for HLA-B associated transcript 1 variant protein.
BT009909 - Homo sapiens HLA-B associated transcript 1 mRNA, complete cds.
DQ891881 - Synthetic construct clone IMAGE:100004511; FLH180891.01X; RZPDo839H02134D HLA-B associated transcript 1 (BAT1) gene, encodes complete protein.
KJ897793 - Synthetic construct Homo sapiens clone ccsbBroadEn_07187 hypothetical protein, encodes complete protein.
DQ895067 - Synthetic construct Homo sapiens clone IMAGE:100009527; FLH180887.01L; RZPDo839H02133D HLA-B associated transcript 1 (BAT1) gene, encodes complete protein.
AB528305 - Synthetic construct DNA, clone: pF1KE1035, Homo sapiens BAT1 gene for HLA-B associated transcript 1, without stop codon, in Flexi system.
AK127767 - Homo sapiens cDNA FLJ45868 fis, clone OCBBF3004487, highly similar to Probable ATP-dependent RNA helicase p47.
AK295854 - Homo sapiens cDNA FLJ54084 complete cds, moderately similar to Spliceosome RNA helicase Bat1 (EC 3.6.1.-).
AK316469 - Homo sapiens cDNA, FLJ79368 complete cds, highly similar to Spliceosome RNA helicase Bat1 (EC 3.6.1.-).
AK295634 - Homo sapiens cDNA FLJ54033 complete cds, highly similar to Spliceosome RNA helicase Bat1 (EC 3.6.1.-).
AK294939 - Homo sapiens cDNA FLJ53763 complete cds, highly similar to Spliceosome RNA helicase BAT1 (EC 3.6.1.-).
JD469310 - Sequence 450334 from Patent EP1572962.
JD211352 - Sequence 192376 from Patent EP1572962.
JD538060 - Sequence 519084 from Patent EP1572962.

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

-  Other Names for This Gene
  Alternate Gene Symbols: AK316469, B4DIZ8, B4DIZ8_HUMAN
UCSC ID: uc011dnp.1
RefSeq Accession: NR_037852
Protein: B4DIZ8

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK316469.1
exon count: 4CDS single in 3' UTR: no RNA size: 1176
ORF size: 639CDS single in intron: no Alignment % ID: 99.83
txCdsPredict score: 1465.00frame shift in genome: no % Coverage: 99.83
has start codon: yes stop codon in genome: no # of Alignments: 8
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 1369# 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.