DDX28 Gene
protein-coding GIFtS: 50
GCID: GC16M068055
|
|
DEAD (Asp-Glu-Ala-Asp) box polypeptide 28(Previous name: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 28 )
| |
Aliases
for DDX28 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 281 2 | | Mitochondrial DEAD-Box Polypeptide 282 | | MDDX281 2 3 | | Probable ATP-Dependent RNA Helicase DDX282 | | DEAD/H (Asp-Glu-Ala-Asp/His) Box Polypeptide 281 2 | | EC 3.6.4.133 | | Mitochondrial DEAD Box Protein 282 3 | | M5 | | FLJ112821 | | EC 3.6.18 |
Export aliases for DDX28 gene to outside databasesPrevious GC identifers: GC16M058750 GC16M068432 GC16M067790 GC16M067831 GC16M066612 GC16M053928 |
Summaries
for DDX28 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for DDX28:
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They areimplicated in a number of cellular processes involving alteration of RNA secondary structure, such as translationinitiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distributionpatterns, 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 islocalized in the mitochondria and the nucleus, and can be transported between the mitochondria and the nucleus.(provided by RefSeq, Jul 2008)
UniProtKB/Swiss-Prot: DDX28_HUMAN, Q9NUL7Function: May be involved in RNA processing or transport. Has RNA and Mg(2+)-dependent ATPase activity
|
Genomic Views
for DDX28 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000016.9 NC_018927.1 NT_010498.15
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the DDX28 gene promoter:
AML1a SREBP-1c MyoD FOXD1 SREBP-1b CREB POU2F1 SREBP-1a POU2F1a
Other transcription factors
Search SABiosciences Chromatin IP Primers for DDX28
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat DDX28 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 16q22.1 Ensembl cytogenetic band: 16q22.1 HGNC cytogenetic band: 16q22.1-q22.3DDX28 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 16 GeneLoc Exon Structure GeneLoc location for GC16M068055: view genomic region
(about GC identifiers)
Start:
|
68,055,177 bp from pter |
End:
|
68,057,770 bp from pter |
Size:
|
2,594 bases |
Orientation:
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minus strand |
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Proteins
for DDX28 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: DDX28_HUMAN, Q9NUL7 (See
protein sequence)Recommended Name: Probable ATP-dependent RNA helicase DDX28 Size: 540 amino acids; 59581 Da
Subcellular location: Nucleus. Mitochondrion. Note=Transported between these two compartments. Nuclear localizationdepends on active RNA polymerase II transcriptionExplore the universe of human proteins at neXtProt for DDX28: NX_Q9NUL7
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9NUL7
2 DME Specific Peptides for DDX28 (Q9NUL7)
DDX28 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_060850.2
ENSEMBL proteins: ENSP00000332340
Human Recombinant Protein Products:
Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view): About this table
DDX28 for ontologies About GeneDecksing
DDX28 Antibody Products:
Assay Products for DDX28: |
Protein
Domains /
Families
for DDX28 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
DDX28 for domains About GeneDecksing
4 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9NUL7ProtoNet protein and cluster: Q9NUL7 1 Blocks protein family: IPB000629 ATP-dependent helicase
UniProtKB/Swiss-Prot: DDX28_HUMAN, Q9NUL7Similarity: Belongs to the DEAD box helicase familySimilarity: Contains 1 helicase ATP-binding domainSimilarity: Contains 1 helicase C-terminal domain |
Function
for DDX28 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Function Summary:
UniProtKB/Swiss-Prot: DDX28_HUMAN, Q9NUL7Function: May be involved in RNA processing or transport. Has RNA and Mg(2+)-dependent ATPase activityCatalytic activity: ATP + H(2)O = ADP + phosphateEnzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.131
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for DDX28 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for DDX28 (see all 2)
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DDX28 |
Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table
DDX28 for ontologies About GeneDecksing
|
Pathways & Interactions
for DDX28 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for DDX28
STRING Interaction
Network Preview (showing 3 interactants - click image to see more details)
5/232 Interacting proteins for DDX28 (Q9NUL72, 3 ENSP000003323404) via UniProtKB, MINT, STRING, and/or I2D (see all 232)About this table
|
Drugs & Compounds
for DDX28 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for DDX28
Search CenterWatch for drugs/clinical trials and news about DDX28
|
Transcripts
for DDX28 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for DDX28 gene: NM_018380.3 Unigene Cluster for DDX28: DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 Hs.458313 [show with all ESTs]Unigene Representative Sequence: NM_0183801 Ensembl transcript including schematic representation, and UCSC links where relevant: ENST00000332395(uc002evh.2)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for DDX28 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for DDX28 (see all 2)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: DDX28 (NM_018380) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for DDX28 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DDX28 |
Additional cDNA sequence: AK002144.1 BC014517.2 BC024273.1 7 DOTS entries: DT.120665140 DT.444077 DT.101958141 DT.120665024 DT.120664978 DT.120665109 DT.95294833 24/165 AceView cDNA sequences (see all 165): BM794854 AI688630 BM910625 BM710170 AI380816 Z25077 CB159878 AW194721 BU528728 BM128887 BM129155 BM839735 AI087964 AI199039 BQ687952 AI869985 BQ009574 BE273939 BM563666 NM_018380 BM832061 AI867482 BM822377 AI494294
GeneLoc Exon Structure
|
Expression
for DDX28 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| DDX28 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ATTTCTAACA
About this image
See DDX28 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for DDX28
SOURCE GeneReport for Unigene cluster: Hs.458313
UniProtKB/Swiss-Prot: DDX28_HUMAN, Q9NUL7Tissue specificity: Expressed in all tissues tested, including brain, placenta, lung, liver, skeletal muscle, kidney,pancreas, leukocytes, colon, small intestine, ovary and prostate
SABiosciences Custom PCR Arrays for DDX28
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for DDX28
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DDX28 |
Orthologs
for DDX28 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of eukaryotes.
Orthologs for DDX28 gene from 6/23 species (see all 23) About this table
| Organism |
Taxonomic
classification |
Gene |
Description |
Human
Similarity |
Orthology
Type |
Details |
chicken
(Gallus gallus) |
Aves |
DDX281 |
DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 |
60.48(n)
55.43(a) |
|
427544 XM_425116.3 XP_425116.3 |
lizard
(Anolis carolinensis) |
Reptilia |
DDX286 |
-- |
51(a) |
1 ↔ 1 |
LGc(6238828-6240441) |
zebrafish
(Danio rerio) |
Actinopterygii |
Dr.150792 |
Transcribed sequence with weak similarity to protein more |
75.89(n) |
|
BM181654.1 |
fruit fly
(Drosophila melanogaster) |
Insecta |
CG35613
KH11 |
helicase3
CG3561-PA1 |
36(a)3
47.26(n)1
37.78(a)1 |
|
21D33
332541 NM_134700.31 NP_608544.11 |
thale cress
(Arabidopsis thaliana) |
eudicotyledons |
RH391 |
DEAD-box ATP-dependent RNA helicase 39 |
44.85(n)
36.86(a) |
|
826559 NM_179017.2 NP_849348.1 |
rice
(Oryza sativa) |
Liliopsida |
Os01g01845001 |
hypothetical protein |
46.8(n)
34.34(a) |
|
4325344 NM_001048769.1 NP_001042234.1 |
ENSEMBL Gene Tree for DDX28 (if available)
TreeFam Gene Tree for DDX28 (if available) |
Paralogs
for DDX28 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for DDX28 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 16 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for DDX28 (68055177 - 68057770 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for DDX28: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing DDX28 |
|
Disorders
/ Diseases
for DDX28 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
DDX28 for disorders About GeneDecksing
OMIM gene information: 607618
OMIM disorders: --
1  disease for DDX28: About MalaCardsprostatitis
Human Genome Epidemiology (HuGE) Navigator: DDX28 (1 document)
Export disorders for DDX28 gene to outside databases
|
Publications
for DDX28 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for DDX28 gene, integrated from 9 sources (see all 20):
(articles sorted by number of sources associating them with DDX28) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Cloning and characterization of MDDX28, a putative dead-box helicase with mitochondrial and nuclear localization. (PubMed id 11350955)1, 2, 3, 9 Valgardsdottir R.... Prydz H. (2001)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PubMed id 10493829)1, 3 Loftus B.J.... Adams M.D. (1999)
- DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. (PubMed id 22446626)1 Close P.... Svejstrup J.Q. (2012)
- A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
- Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
- A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome. (PubMed id 20186120)1 Richter R....Chrzanowska-Lightowlers Z.M. (2010)
- Systematic analysis of human protein complexes identi fies chromosome segregation proteins. (PubMed id 20360068)1 Hutchins J.R....Peters J.M. (2010)
- Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1 Hendrickson S.L....O'Brien S.J. (2010)
|
External Searches for DDX28 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing DDX28 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing DDX28 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing DDX28 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for DDX28 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for DDX28 gene:
Search GeneIP for patents involving DDX28
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for DDX28 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
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| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat DDX28 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing DDX28 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat DDX28 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat DDX28 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat DDX28 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat DDX28 |
| |
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| |  |  |  |  | | | | |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DDX28 |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DDX28 |
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