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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 58

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. 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

Regulatory Elements for DDX28 Gene

Enhancers for DDX28 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16H067992 1.6 FANTOM5 ENCODE dbSUPER 18.3 +29.0 28989 4 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF143 ZNF207 SP3 PRMT7 EDC4 ACD CENPT CTCF ENSG00000263276 DDX28 E2F4 KIAA0895L SLC7A6OS
GH16H067997 1.3 Ensembl ENCODE dbSUPER 12 +24.1 24067 4 TBP FOXA2 ZSCAN9 PAF1 SMAD5 NFYC KAT8 SREBF1 KLF16 CEBPA LCAT DDX28 SLC12A4 PRMT7 ENSG00000263276 HSD11B2 DPEP2 DUS2
GH16H068061 1.4 Ensembl ENCODE dbSUPER 10.9 -40.1 -40052 5 HDAC1 PKNOX1 RB1 TBL1XR1 ARNT RAD21 GATA2 ZNF143 FOS ATF7 PRMT7 NFATC3 THAP11 DDX28 DUS2 RNU6-359P DPEP3 CENPT EDC4 PLA2G15
GH16H068068 1.4 FANTOM5 ENCODE dbSUPER 10.9 -47.2 -47157 4 HDGF CTCF ZIC2 ZNF121 ZNF316 CTBP1 GATA3 POLR2A GATA2 NCOR1 DUS2 PRMT7 DPEP3 THAP11 DDX28 RNU6-359P EDC4 CENPT DPEP2 RANBP10
GH16H068074 1.4 Ensembl ENCODE dbSUPER 10.8 -51.6 -51607 2 HDGF TBL1XR1 RAD21 RARA YY1 SCRT2 ZNF143 ATF7 ETV6 RUNX3 DUS2 DDX28 ENSG00000261864
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around DDX28 on UCSC Golden Path with GeneCards custom track

Promoters for DDX28 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000087220 567 1801 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 ZNF207 DEK

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

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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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 IEA,IDA 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

Clone Products

  • Applied Biological Materials Clones for DDX28
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 IDA,IBA --
GO:0005739 mitochondrion IDA,IEA --
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 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

Clone Products

  • Applied Biological Materials Clones for DDX28
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 Sequence Context AA Info Type
rs1001226438 -- 68,024,708(+) ATCTG(A/G)AAGTA intron-variant, upstream-variant-2KB
rs1001294787 -- 68,023,348(+) AGCTG(C/T)GAGGT utr-variant-5-prime
rs1001410260 -- 68,023,215(+) TTAGT(A/G)CGGGA utr-variant-5-prime
rs1003636025 -- 68,024,980(+) GTGTG(C/T)GCTAC intron-variant, upstream-variant-2KB
rs1005554272 -- 68,022,754(+) TGGGC(C/T)GAACG upstream-variant-2KB, reference, missense

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)

Relevant External Links 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

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

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 60
  2. Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis. (PMID: 25683715) Antonicka H … Shoubridge EA (Cell reports 2015) 3 4 60
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  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 60

Products for DDX28 Gene

Sources for DDX28 Gene

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