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Aliases for DDX54 Gene

Aliases for DDX54 Gene

  • DEAD-Box Helicase 54 2 3 5
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 54 2 3
  • ATP-Dependent RNA Helicase DDX54 3 4
  • ATP-Dependent RNA Helicase DP97 3 4
  • DEAD Box RNA Helicase 97 KDa 3 4
  • DEAD Box Protein 54 3 4
  • DEAD Box Helicase 97 KDa 3
  • EC 3.6.4.13 4
  • EC 3.6.1 56
  • DP97 3

External Ids for DDX54 Gene

Previous GeneCards Identifiers for DDX54 Gene

  • GC12M113377
  • GC12M112006
  • GC12M112057
  • GC12M113595
  • GC12M110607
  • GC12M113596
  • GC12M113598

Summaries for DDX54 Gene

Entrez Gene Summary for DDX54 Gene

  • This gene encodes a member of the DEAD box protein family. 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 this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The nucleolar protein encoded by this gene interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. Alternative splice variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for DDX54 Gene

DDX54 (DEAD-Box Helicase 54) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA binding. An important paralog of this gene is DDX46.

UniProtKB/Swiss-Prot for DDX54 Gene

  • Has RNA-dependent ATPase activity. Represses the transcriptional activity of nuclear receptors.

Additional gene information for DDX54 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for DDX54 Gene

Genomics for DDX54 Gene

GeneHancer (GH) Regulatory Elements for DDX54 Gene

Promoters and enhancers for DDX54 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
GH12J113183 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 610.7 -0.2 -175 3.7 CC2D1A SP1 ZFX MNT CBFA2T2 NKRF ZNF121 RERE POLR2A GTF2F1 RITA1 DDX54 RBM19 HECTD4 RPL6 SLC8B1 CFAP73 DYNLL1P4 GC12M113186 ENSG00000257286
GH12J113356 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 21.6 -173.4 -173417 4.6 ZNF652 SP1 ZFX CTCF ELF3 MNT CBFA2T2 NKRF POLR2A ZNF384 PLBD2 SLC8B1 LOC105369989 RBM19 DDX54 SDSL RITA1 ENSG00000201208 RPL6 SDS
GH12J113220 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.6 -36.9 -36940 4.4 HDGF ZFX SP1 ELF3 MNT NKRF POLR2A CSDE1 ZNF687 ZSCAN21 TPCN1 IQCD RITA1 RBM19 RASAL1 DDX54 ENSG00000201208 ENSG00000277566
GH12J113226 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 11.6 -44.8 -44777 8.1 SP1 CC2D1A CBFA2T2 ZNF148 NKRF ZNF121 CEBPG RERE ZNF687 ZSCAN21 RBM19 RITA1 DDX54 ENSG00000201208 IQCD TPCN1 DTX1 ENSG00000277566
GH12J112407 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.9 +776.7 776746 3 ELF3 ZFX SIX5 NKRF POLR2A MLLT1 ZNF121 GTF2F1 CSDE1 ZNF384 RPL6 ADAM1A MAPKAPK5 DDX54 SLC8B1 ERP29 RPS2P41 TMEM116 PTPN11 GC12M112409
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DDX54 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DDX54 gene promoter:
  • AML1a
  • GCNF
  • GCNF-1
  • GCNF-2
  • HNF-4alpha1
  • HTF
  • LCR-F1
  • Lmo2
  • Pax-5
  • Sp1

Genomic Locations for DDX54 Gene

Genomic Locations for DDX54 Gene
chr12:113,157,173-113,185,479
(GRCh38/hg38)
Size:
28,307 bases
Orientation:
Minus strand
chr12:113,594,978-113,623,284
(GRCh37/hg19)
Size:
28,307 bases
Orientation:
Minus strand

Genomic View for DDX54 Gene

Genes around DDX54 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX54 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX54 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX54 Gene

Proteins for DDX54 Gene

  • Protein details for DDX54 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TDD1-DDX54_HUMAN
    Recommended name:
    ATP-dependent RNA helicase DDX54
    Protein Accession:
    Q8TDD1
    Secondary Accessions:
    • Q86YT8
    • Q9BRZ1

    Protein attributes for DDX54 Gene

    Size:
    881 amino acids
    Molecular mass:
    98595 Da
    Quaternary structure:
    • Interacts in a hormone-dependent manner with nuclear receptors.
    SequenceCaution:
    • Sequence=AAN59978.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the N-terminal part.; Evidence={ECO:0000305};

    Alternative splice isoforms for DDX54 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX54 Gene

Selected DME Specific Peptides for DDX54 Gene

Q8TDD1:
  • ARTGSGKT
  • PTPIQRK
  • AARGLDIP
  • IIATPGR
  • LVEFARAGL
  • DEADRLFEMGF
  • SPTRELA
  • ALILSPTR
  • YVVFDEAD
  • QTVLFSA
  • TDLAARGLD
  • IATPGRL
  • PTRELALQ

Post-translational modifications for DDX54 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DDX54 Gene

Domains & Families for DDX54 Gene

Gene Families for DDX54 Gene

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

Suggested Antigen Peptide Sequences for DDX54 Gene

GenScript: Design optimal peptide antigens:
  • DEAD box protein 54 (DDX54_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TDD1

UniProtKB/Swiss-Prot:

DDX54_HUMAN :
  • Belongs to the DEAD box helicase family. DDX54/DBP10 subfamily.
Family:
  • Belongs to the DEAD box helicase family. DDX54/DBP10 subfamily.
genes like me logo Genes that share domains with DDX54: view

Function for DDX54 Gene

Molecular function for DDX54 Gene

UniProtKB/Swiss-Prot Function:
Has RNA-dependent ATPase activity. Represses the transcriptional activity of nuclear receptors.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;.

Enzyme Numbers (IUBMB) for DDX54 Gene

Phenotypes From GWAS Catalog for DDX54 Gene

Gene Ontology (GO) - Molecular Function for DDX54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003714 transcription corepressor activity IDA 12466272
GO:0003723 RNA binding IEA,HDA 22658674
GO:0004004 ATP-dependent RNA helicase activity IEA,IDA 12466272
GO:0004386 helicase activity IEA --
genes like me logo Genes that share ontologies with DDX54: view
genes like me logo Genes that share phenotypes with DDX54: view

Animal Models for DDX54 Gene

MGI Knock Outs for DDX54:
  • Ddx54 Ddx54<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX54

Clone Products

  • Applied Biological Materials (abm): Clones for DDX54 - Now 50% OFF >
  • * DDX54 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * DDX54 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
  • Addgene plasmids for DDX54

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for DDX54 Gene

Localization for DDX54 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX54 Gene

Nucleus, nucleolus.

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 DDX54 gene
Compartment Confidence
nucleus 5
golgi apparatus 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 12466272
GO:0005730 nucleolus IDA,IEA 12466272
GO:0005794 Golgi apparatus IDA --
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with DDX54: view

Pathways & Interactions for DDX54 Gene

PathCards logo

SuperPathways for DDX54 Gene

No Data Available

Gene Ontology (GO) - Biological Process for DDX54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IDA 12466272
GO:0016070 RNA metabolic process IDA 12466272
GO:0030520 intracellular estrogen receptor signaling pathway TAS 12466272
GO:1903507 negative regulation of nucleic acid-templated transcription IEA --
genes like me logo Genes that share ontologies with DDX54: view

No data available for Pathways by source and SIGNOR curated interactions for DDX54 Gene

Drugs & Compounds for DDX54 Gene

(3) Drugs for DDX54 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, Activator, Full agonist, Antagonist, Pore Blocker, Potentiation 0

(1) Additional Compounds for DDX54 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Full agonist, Agonist, Partial agonist, Antagonist, Gating inhibitor 58-64-0
genes like me logo Genes that share compounds with DDX54: view

Transcripts for DDX54 Gene

mRNA/cDNA for DDX54 Gene

Unigene Clusters for DDX54 Gene

DEAD (Asp-Glu-Ala-Asp) box polypeptide 54:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX54

Clone Products

  • Applied Biological Materials (abm): Clones for DDX54 - Now 50% OFF >
  • * DDX54 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * DDX54 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All
  • Addgene plasmids for DDX54

Alternative Splicing Database (ASD) splice patterns (SP) for DDX54 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18a · 18b ·
SP1: -
SP2:
SP3: - -
SP4: -
SP5: - -
SP6:
SP7: - - - - - - - - - - - - - - - - - - -
SP8:
SP9:
SP10:
SP11:
SP12: - -
SP13:
SP14: -
SP15:
SP16:
SP17:

ExUns: 18c ^ 19 ^ 20a · 20b · 20c · 20d ^ 21a · 21b ^ 22a · 22b · 22c ^ 23a · 23b · 23c · 23d · 23e
SP1:
SP2:
SP3: - - - - -
SP4:
SP5:
SP6:
SP7: - - - - - - -
SP8:
SP9:
SP10:
SP11: - - - -
SP12: -
SP13: -
SP14:
SP15:
SP16:
SP17:

Relevant External Links for DDX54 Gene

GeneLoc Exon Structure for
DDX54
ECgene alternative splicing isoforms for
DDX54

Expression for DDX54 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for DDX54 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDX54 Gene

This gene is overexpressed in CD8 Tcells (16.6), Peripheral blood mononuclear cells (14.9), and Lymph node (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DDX54 Gene



Protein tissue co-expression partners for DDX54 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of DDX54 Gene:

DDX54

SOURCE GeneReport for Unigene cluster for DDX54 Gene:

Hs.506861

Evidence on tissue expression from TISSUES for DDX54 Gene

  • Liver(4.3)
  • Kidney(4.2)
  • Lung(3.4)
  • Nervous system(3.1)
genes like me logo Genes that share expression patterns with DDX54: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX54 Gene

Orthologs for DDX54 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX54 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia DDX54 35 34
  • 99.24 (n)
OneToOne
cow
(Bos Taurus)
Mammalia DDX54 35 34
  • 88.75 (n)
OneToOne
dog
(Canis familiaris)
Mammalia DDX54 35 34
  • 88.66 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Ddx54 17 35 34
  • 83.16 (n)
rat
(Rattus norvegicus)
Mammalia Ddx54 34
  • 82.34 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia DDX54 35
  • 76 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia DDX54 35
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves DDX54 35 34
  • 74.02 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia DDX54 35
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx54 34
  • 63.31 (n)
Str.2961 34
zebrafish
(Danio rerio)
Actinopterygii ddx54 35 34 34
  • 65.06 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007511 34
  • 55.6 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32344 35 34
  • 54.48 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y94H6A.5 35 34
  • 49.74 (n)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F24684g 34
  • 48.17 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL086W 34
  • 47.46 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DBP10 37 35 34
  • 46.42 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G77030 34
  • 50.13 (n)
rice
(Oryza sativa)
Liliopsida Os08g0416100 34
  • 51.41 (n)
Os.21287 34
bread mold
(Neurospora crassa)
Ascomycetes NCU07712 34
  • 55.56 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 50 (a)
OneToOne
Cin.3817 34
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes dbp10 34
  • 47.97 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3817 34
Species where no ortholog for DDX54 was found in the sources mined by GeneCards:
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 DDX54 Gene

ENSEMBL:
Gene Tree for DDX54 (if available)
TreeFam:
Gene Tree for DDX54 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DDX54: view image

Paralogs for DDX54 Gene

(37) SIMAP similar genes for DDX54 Gene using alignment to 4 proteins:

  • DDX54_HUMAN
  • F8VRX4_HUMAN
  • H0YHH7_HUMAN
  • H0YHZ9_HUMAN
genes like me logo Genes that share paralogs with DDX54: view

Variants for DDX54 Gene

Sequence variations from dbSNP and Humsavar for DDX54 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000023461 -- 113,180,314(-) C/A/T intron_variant
rs1000047048 -- 113,164,346(-) C/T intron_variant
rs1000295980 -- 113,185,426(-) G/C coding_sequence_variant, missense_variant
rs1000337415 -- 113,169,032(-) C/T intron_variant
rs1000421181 -- 113,158,056(-) C/G 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for DDX54 Gene

Variant ID Type Subtype PubMed ID
dgv2884n54 CNV loss 21841781
esv3630792 CNV gain 21293372
esv3892265 CNV gain 25118596
esv996809 CNV deletion 20482838
nsv519540 CNV gain+loss 19592680

Variation tolerance for DDX54 Gene

Residual Variation Intolerance Score: 84.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.45; 82.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX54 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX54

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX54 Gene

Disorders for DDX54 Gene

Additional Disease Information for DDX54

No disorders were found for DDX54 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for DDX54 Gene

Publications for DDX54 Gene

  1. Regulation of nuclear receptor transcriptional activity by a novel DEAD box RNA helicase (DP97). (PMID: 12466272) Rajendran RR … Katzenellenbogen BS (The Journal of biological chemistry 2003) 2 3 4 23 58
  2. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  3. 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
  4. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A … Diaz JJ (Molecular biology of the cell 2002) 3 4 58
  5. Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function. (PMID: 29467282) Heidelberger JB … Beli P (EMBO reports 2018) 3 58

Products for DDX54 Gene

Sources for DDX54 Gene

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