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Aliases for DDX28 Gene

Aliases for DDX28 Gene

  • DEAD-Box Helicase 28 2 3 5
  • DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 28 2 3
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 28 2 3
  • Mitochondrial DEAD Box Protein 28 3 4
  • MDDX28 3 4
  • Probable ATP-Dependent RNA Helicase DDX28 3
  • Mitochondrial DEAD-Box Polypeptide 28 3
  • EC 3.6.4.13 4
  • EC 3.6.1 56

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-Box Helicase 28) is a Protein Coding gene. Gene Ontology (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).

Additional gene information for DDX28 Gene

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

Genomics for DDX28 Gene

GeneHancer (GH) Regulatory Elements for DDX28 Gene

Promoters and enhancers for DDX28 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16I068021 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 550.8 +0.8 762 3 SMAD1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SLC30A9 DDX28 GC16M068022 PIR37774 DUS2 EDC4 NFATC3 CTCF PRMT7 CENPT FHOD1
GH16I067992 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 18.3 +29.0 28988 4.1 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF213 E2F8 PRMT7 EDC4 ACD DDX28 E2F4 CENPT KIAA0895L RNU6-359P SLC12A4 LCAT
GH16I067997 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 12.1 +24.1 24067 4.4 FOXA2 ZSCAN9 ZNF335 POLR2B PAF1 SMAD5 NFYC KAT8 SREBF1 KLF16 DPEP2 LCAT DDX28 SLC12A4 PRMT7 ENSG00000263276 HSD11B2 DUS2
GH16I067892 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10 +130.2 130161 2.6 PKNOX1 ATF1 FOXA2 ARID4B SIN3A DMAP1 BRCA1 ZNF48 YY1 POLR2B PSKH1 DUS2 EDC4 PRMT7 C16orf86 ENKD1 DDX28 DPEP3 ACD PARD6A
GH16I068061 Enhancer 1.3 Ensembl ENCODE dbSUPER 10.9 -40.1 -40052 5.3 PKNOX1 ARNT ZNF143 FOS ATF7 REST KAT8 SSRP1 SMARCA4 CTCF PRMT7 EDC4 E2F4 ENSG00000263276 CTCF FBXL8 NFATC3 ENSG00000270165 THAP11 DDX28
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DDX28 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DDX28 gene promoter:

Genomic Locations for DDX28 Gene

Genomic Locations for DDX28 Gene
chr16:68,021,274-68,023,867
(GRCh38/hg38)
Size:
2,594 bases
Orientation:
Minus strand
chr16:68,055,177-68,057,770
(GRCh37/hg19)

Genomic View for DDX28 Gene

Genes around DDX28 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX28 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Selected DME Specific Peptides for DDX28 Gene

Q9NUL7:
  • AETGSGKT
  • TGSGKTLS

Post-translational modifications for DDX28 Gene

No Post-translational modifications

Other Protein References for DDX28 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for DDX28 Gene

Gene Families for DDX28 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted secreted proteins

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 :
  • Belongs to the DEAD box helicase family.
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

Phenotypes From GWAS Catalog for DDX28 Gene

Gene Ontology (GO) - Molecular Function for DDX28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA,IEA 22658674
GO:0004004 ATP-dependent RNA helicase activity IBA --
GO:0004386 helicase activity IEA --
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with DDX28: view
genes like me logo Genes that share phenotypes with DDX28: view

Animal Model Products

CRISPR Products

miRNA for DDX28 Gene

miRTarBase miRNAs that target DDX28

Inhibitory RNA Products

No data available for Human Phenotype Ontology , 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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DDX28 gene
Compartment Confidence
mitochondrion 5
nucleus 5
cytosol 5
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Mitochondria (3)
  • Nucleoli (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005730 nucleolus IBA,IDA --
GO:0005739 mitochondrion IEA,IDA --
GO:0005759 mitochondrial matrix IEA --
GO:0005829 cytosol IDA --
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:0042254 ribosome biogenesis IEA --
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

(3) Drugs for DDX28 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist 0

(1) 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
Full agonist, Agonist 58-64-0
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:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for DDX28 Gene



Protein tissue co-expression partners for DDX28 Gene

NURSA nuclear receptor signaling pathways regulating expression of DDX28 Gene:

DDX28

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.

Evidence on tissue expression from TISSUES for DDX28 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with DDX28: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
Mammalia DDX28 33 34
  • 99.07 (n)
cow
(Bos Taurus)
Mammalia DDX28 33 34
  • 85.68 (n)
dog
(Canis familiaris)
Mammalia DDX28 33 34
  • 84.89 (n)
mouse
(Mus musculus)
Mammalia Ddx28 33 16 34
  • 79.68 (n)
rat
(Rattus norvegicus)
Mammalia Ddx28 33
  • 78.81 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX28 34
  • 68 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX28 34
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves DDX28 33 34
  • 60.18 (n)
lizard
(Anolis carolinensis)
Reptilia DDX28 34
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx28 33
  • 51.87 (n)
zebrafish
(Danio rerio)
Actinopterygii ddx28 33 34
  • 54.32 (n)
Dr.15079 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP013035 33
  • 50.88 (n)
fruit fly
(Drosophila melanogaster)
Insecta KH1 33 34
  • 47.03 (n)
CG3561 35
  • 36 (a)
worm
(Caenorhabditis elegans)
Secernentea T26G10.1 34
  • 27 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RRP3 34
  • 25 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons RH39 33
  • 43.99 (n)
rice
(Oryza sativa)
Liliopsida Os01g0184500 33
  • 46.55 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 37 (a)
OneToOne
Species where no ortholog for DDX28 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs1001226438 -- 68,024,708(-) G/A upstream_transcript_variant
rs1001294787 -- 68,023,348(-) C/T 5_prime_UTR_variant
rs1001410260 -- 68,023,215(-) G/A 5_prime_UTR_variant
rs1003636025 -- 68,024,980(-) C/T upstream_transcript_variant
rs1005554272 -- 68,022,754(-) T/C/G coding_sequence_variant, missense_variant

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

Variant ID Type Subtype PubMed ID
esv2666619 CNV deletion 23128226
esv3638897 CNV loss 21293372
esv3638899 CNV loss 21293372
esv3638900 CNV gain 21293372
nsv522852 CNV gain 19592680
nsv524363 CNV loss 19592680

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)

Additional Variant Information for DDX28 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX28

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

Disorders for DDX28 Gene

Additional Disease Information for DDX28

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for DDX28 Gene.

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 (The Journal of biological chemistry 2001) 2 3 4 22 58
  2. Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis. (PMID: 25683715) Antonicka H … Shoubridge EA (Cell reports 2015) 3 4 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for DDX28 Gene

Sources for DDX28 Gene

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