Human Gene DDX28 (ENST00000332395.7_6) from GENCODE V47lift37
  Description: DEAD-box helicase 28 (from RefSeq NM_018380.4)
Gencode Transcript: ENST00000332395.7_6
Gencode Gene: ENSG00000182810.7_8
Transcript (Including UTRs)
   Position: hg19 chr16:68,054,819-68,057,135 Size: 2,317 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr16:68,055,483-68,057,105 Size: 1,623 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:68,054,819-68,057,135)mRNA (may differ from genome)Protein (540 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DDX28_HUMAN
DESCRIPTION: RecName: Full=Probable ATP-dependent RNA helicase DDX28; EC=3.6.4.13; AltName: Full=Mitochondrial DEAD box protein 28;
FUNCTION: May be involved in RNA processing or transport. Has RNA and Mg(2+)-dependent ATPase activity.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBCELLULAR LOCATION: Nucleus. Mitochondrion. Note=Transported between these two compartments. Nuclear localization depends on active RNA polymerase II transcription.
TISSUE SPECIFICITY: Expressed in all tissues tested, including brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, leukocytes, colon, small intestine, ovary and prostate.
SIMILARITY: Belongs to the DEAD box helicase family.
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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -6.0030-0.200 Picture PostScript Text
3' UTR -176.50664-0.266 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
IPR014014 - RNA_helicase_DEAD_Q_motif

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain

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

ModBase Predicted Comparative 3D Structure on Q9NUL7
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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 Details  
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-  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:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0019843 rRNA binding

Biological Process:
GO:0010501 RNA secondary structure unwinding
GO:0042254 ribosome biogenesis
GO:1902775 mitochondrial large ribosomal subunit assembly

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0035770 ribonucleoprotein granule
GO:0042645 mitochondrial nucleoid


-  Descriptions from all associated GenBank mRNAs
  JD039433 - Sequence 20457 from Patent EP1572962.
BC014517 - Homo sapiens cDNA clone IMAGE:3939244, containing frame-shift errors.
AK002144 - Homo sapiens cDNA FLJ11282 fis, clone PLACE1009476, weakly similar to PUTATIVE ATP-DEPENDENT RNA HELICASE T26G10.1 IN CHROMOSOME III.
BC024273 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 28, mRNA (cDNA clone MGC:39160 IMAGE:4130937), complete cds.
LF208291 - JP 2014500723-A/15794: Polycomb-Associated Non-Coding RNAs.
JD355785 - Sequence 336809 from Patent EP1572962.
JD190250 - Sequence 171274 from Patent EP1572962.
LF374173 - JP 2014500723-A/181676: Polycomb-Associated Non-Coding RNAs.
JD067172 - Sequence 48196 from Patent EP1572962.
KJ899194 - Synthetic construct Homo sapiens clone ccsbBroadEn_08588 DDX28 gene, encodes complete protein.
DQ576663 - Homo sapiens piRNA piR-44775, complete sequence.
JD268162 - Sequence 249186 from Patent EP1572962.
MA443868 - JP 2018138019-A/15794: Polycomb-Associated Non-Coding RNAs.
MA609750 - JP 2018138019-A/181676: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: DDX28_HUMAN, ENST00000332395.1, ENST00000332395.2, ENST00000332395.3, ENST00000332395.4, ENST00000332395.5, ENST00000332395.6, MDDX28, NM_018380, Q9NUL7, uc317tkv.1, uc317tkv.2
UCSC ID: ENST00000332395.7_6
RefSeq Accession: NM_018380.4
Protein: Q9NUL7 (aka DDX28_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.