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Aliases for DDX28 Gene

Aliases for DDX28 Gene

  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 28 2 3
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 28 2 3
  • Mitochondrial DEAD Box Protein 28 3 4
  • MDDX28 3 4
  • Mitochondrial DEAD-Box Polypeptide 28 3
  • EC 3.6.4.13 4
  • EC 3.6.1 63

External Ids for DDX28 Gene

Previous GeneCards Identifiers for DDX28 Gene

  • GC16M058750
  • GC16M068432
  • GC16M067790
  • GC16M067831
  • GC16M066612
  • GC16M068055
  • GC16M053928

Summaries for DDX28 Gene

Entrez Gene Summary for DDX28 Gene

  • 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 the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene is intronless. It encodes an RNA-dependent ATPase. The encoded protein is localized in the mitochondria and the nucleus, and can be transported between the mitochondria and the nucleus. [provided by RefSeq, Jul 2008]

GeneCards Summary for DDX28 Gene

DDX28 (DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 28) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and helicase activity. An important paralog of this gene is DDX47.

UniProtKB/Swiss-Prot for DDX28 Gene

  • Plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function (PubMed:25683708, PubMed:25683715). May be involved in RNA processing or transport. Has RNA and Mg(2+)-dependent ATPase activity (PubMed:11350955).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX28 Gene

Genomics for DDX28 Gene

Regulatory Elements for DDX28 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for DDX28 Gene

Chromosome:
16
Start:
68,021,274 bp from pter
End:
68,023,867 bp from pter
Size:
2,594 bases
Orientation:
Minus strand

Genomic View for DDX28 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for DDX28 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX28 Gene

Proteins for DDX28 Gene

  • Protein details for DDX28 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NUL7-DDX28_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase DDX28
    Protein Accession:
    Q9NUL7

    Protein attributes for DDX28 Gene

    Size:
    540 amino acids
    Molecular mass:
    59581 Da
    Quaternary structure:
    • Monomer. Found in a complex with GRSF1, DHX30, FASTKD2 and FASTKD5. Associates with the 16S mitochondrial rRNA (16S mt-rRNA) and with the mitochondrial ribosome large subunit (39S).

neXtProt entry for DDX28 Gene

Proteomics data for DDX28 Gene at MOPED

Selected DME Specific Peptides for DDX28 Gene

Post-translational modifications for DDX28 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DDX28 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

Domains & Families for DDX28 Gene

Gene Families for DDX28 Gene

Suggested Antigen Peptide Sequences for DDX28 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NUL7

UniProtKB/Swiss-Prot:

DDX28_HUMAN :
  • Contains 1 helicase ATP-binding domain.
  • Belongs to the DEAD box helicase family.
Domain:
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the DEAD box helicase family.
genes like me logo Genes that share domains with DDX28: view

Function for DDX28 Gene

Molecular function for DDX28 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + H(2)O = ADP + phosphate
UniProtKB/Swiss-Prot Function:
Plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function (PubMed:25683708, PubMed:25683715). May be involved in RNA processing or transport. Has RNA and Mg(2+)-dependent ATPase activity (PubMed:11350955).

Enzyme Numbers (IUBMB) for DDX28 Gene

Gene Ontology (GO) - Molecular Function for DDX28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding --
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0005524 ATP binding IEA --
GO:0019843 rRNA binding IDA 25683715
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with DDX28: view

Phenotypes for DDX28 Gene

GenomeRNAi human phenotypes for DDX28:
genes like me logo Genes that share phenotypes with DDX28: view

Animal Model Products

miRNA for DDX28 Gene

miRTarBase miRNAs that target DDX28

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDX28

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for DDX28 Gene

Localization for DDX28 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX28 Gene

Nucleus. Mitochondrion. Mitochondrion matrix, mitochondrion nucleoid. Mitochondrion matrix. Note=Transported between these two compartments. Nuclear localization depends on active RNA polymerase II transcription. Localizes to mitochondrial RNA granules found in close proximity to the mitochondrial nucleoids. {ECO:0000269 PubMed:25683708, ECO:0000269 PubMed:25683715}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for DDX28 Gene COMPARTMENTS Subcellular localization image for DDX28 gene
Compartment Confidence
mitochondrion 4
nucleus 4
cytosol 2

Gene Ontology (GO) - Cellular Components for DDX28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IDA --
GO:0005739 mitochondrion IDA --
GO:0035770 ribonucleoprotein granule IDA 25683715
genes like me logo Genes that share ontologies with DDX28: view

Pathways & Interactions for DDX28 Gene

SuperPathways for DDX28 Gene

No Data Available

Gene Ontology (GO) - Biological Process for DDX28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010501 RNA secondary structure unwinding IBA --
GO:1902775 mitochondrial large ribosomal subunit assembly IMP 25683715
genes like me logo Genes that share ontologies with DDX28: view

No data available for Pathways by source and SIGNOR curated interactions for DDX28 Gene

Drugs & Compounds for DDX28 Gene

(1) Drugs for DDX28 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine triphosphate Approved Nutra 0

(3) Additional Compounds for DDX28 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Antagonist, Gating inhibitor 58-64-0
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
7664-38-2
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
genes like me logo Genes that share compounds with DDX28: view

Transcripts for DDX28 Gene

mRNA/cDNA for DDX28 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(165) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for DDX28 Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 28:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for DDX28

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for DDX28 Gene

No ASD Table

Relevant External Links for DDX28 Gene

GeneLoc Exon Structure for
DDX28
ECgene alternative splicing isoforms for
DDX28

Expression for DDX28 Gene

mRNA expression in normal human tissues for DDX28 Gene

Protein differential expression in normal tissues from HIPED for DDX28 Gene

This gene is overexpressed in Lung (59.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for DDX28 Gene



SOURCE GeneReport for Unigene cluster for DDX28 Gene Hs.458313

mRNA Expression by UniProt/SwissProt for DDX28 Gene

Q9NUL7-DDX28_HUMAN
Tissue specificity: Expressed in all tissues tested, including brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, leukocytes, colon, small intestine, ovary and prostate.
genes like me logo Genes that share expression patterns with DDX28: view

Protein tissue co-expression partners for DDX28 Gene

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for DDX28 Gene

Orthologs for DDX28 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX28 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia DDX28 35
  • 85.68 (n)
  • 85.19 (a)
DDX28 36
  • 84 (a)
OneToOne
dog
(Canis familiaris)
Mammalia DDX28 35
  • 84.89 (n)
  • 84 (a)
DDX28 36
  • 83 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx28 35
  • 79.68 (n)
  • 80.86 (a)
Ddx28 16
Ddx28 36
  • 81 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia DDX28 35
  • 99.07 (n)
  • 98.7 (a)
DDX28 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ddx28 35
  • 78.81 (n)
  • 78.62 (a)
oppossum
(Monodelphis domestica)
Mammalia DDX28 36
  • 68 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX28 36
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves DDX28 35
  • 60.18 (n)
  • 56.42 (a)
DDX28 36
  • 50 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX28 36
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx28 35
  • 51.87 (n)
  • 50.2 (a)
zebrafish
(Danio rerio)
Actinopterygii ddx28 35
  • 54.32 (n)
  • 51 (a)
Dr.15079 35
ddx28 36
  • 45 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG3561 37
  • 36 (a)
KH1 35
  • 47.03 (n)
  • 37.58 (a)
KH1 36
  • 29 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP013035 35
  • 50.88 (n)
  • 40.91 (a)
worm
(Caenorhabditis elegans)
Secernentea T26G10.1 36
  • 27 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RRP3 36
  • 25 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons RH39 35
  • 43.99 (n)
  • 36.34 (a)
rice
(Oryza sativa)
Liliopsida Os01g0184500 35
  • 46.55 (n)
  • 34.09 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 37 (a)
OneToOne
Species with no ortholog for DDX28:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for DDX28 Gene

ENSEMBL:
Gene Tree for DDX28 (if available)
TreeFam:
Gene Tree for DDX28 (if available)

Paralogs for DDX28 Gene

Paralogs for DDX28 Gene

(4) SIMAP similar genes for DDX28 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with DDX28: view

Variants for DDX28 Gene

Sequence variations from dbSNP and Humsavar for DDX28 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type MAF
rs182952 -- 68,020,831(-) atata(C/T)acata downstream-variant-500B
rs192107 -- 68,020,878(-) tacgt(A/G)tatat downstream-variant-500B
rs10641000 -- 68,020,801(+) TATAC(-/AT/CG)ATATA downstream-variant-500B
rs57021292 -- 68,020,810(+) ATATA(-/TATA)CGTAT downstream-variant-500B
rs57481882 -- 68,020,895(+) ATATA(-/TA)AAGAA downstream-variant-500B

Structural Variations from Database of Genomic Variants (DGV) for DDX28 Gene

Variant ID Type Subtype PubMed ID
nsv524363 CNV Loss 19592680
nsv522852 CNV Gain 19592680
esv2666619 CNV Deletion 23128226

Variation tolerance for DDX28 Gene

Residual Variation Intolerance Score: 42.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.20; 39.75% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for DDX28 Gene

HapMap Linkage Disequilibrium report
DDX28

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX28 Gene

Disorders for DDX28 Gene

Relevant External Links for DDX28

Genetic Association Database (GAD)
DDX28
Human Genome Epidemiology (HuGE) Navigator
DDX28
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
DDX28
genes like me logo Genes that share disorders with DDX28: view

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for DDX28 Gene

Publications for DDX28 Gene

  1. Cloning and characterization of MDDX28, a putative dead-box helicase with mitochondrial and nuclear localization. (PMID: 11350955) Valgardsdottir R. … Prydz H. (J. Biol. Chem. 2001) 2 23 67
  2. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PMID: 10493829) Loftus B.J. … Adams M.D. (Genomics 1999) 2 67
  3. Mitochondrial RNA granules are centers for posttranscriptional RNA processing and ribosome biogenesis. (PMID: 25683715) Antonicka H. … Shoubridge E.A. (Cell Rep. 2015) 67
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 67
  5. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 67

Products for DDX28 Gene

Sources for DDX28 Gene

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