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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 DP97 3 4
  • DEAD Box RNA Helicase 97 KDa 3 4
  • DEAD Box Protein 54 3 4
  • ATP-Dependent RNA Helicase DDX54 3
  • 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.

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
GH12I113183 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 560.8 -0.2 -175 3.7 PKNOX1 CLOCK FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B RITA1 DDX54 HECTD4 RBM19 RPL6 SLC8B1 CFAP73 DYNLL1P4 GC12M113186 ENSG00000257286
GH12I113220 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.6 -36.9 -36879 4.2 HDGF PKNOX1 CLOCK FOXA2 ARNT ZFP64 ARID4B NEUROD1 SIN3A DMAP1 TPCN1 IQCD RITA1 RASAL1 DDX54 ENSG00000201208 RBM19 ENSG00000277566
GH12I113356 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 10.7 -173.1 -173127 4 HDGF PKNOX1 ARNT MLX ARID4B SIN3A ZNF2 YY1 ZNF766 ZNF143 PLBD2 SLC8B1 RBM19 SDSL DDX54 RITA1 ENSG00000201208 RPL6 SDS LOC105369989
GH12I113226 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.6 -44.8 -44777 8.1 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 IRF4 SLC30A9 RITA1 RBM19 DDX54 ENSG00000201208 IQCD TPCN1 DTX1 ENSG00000277566
GH12I113152 Promoter/Enhancer 1.6 Ensembl ENCODE dbSUPER 11.7 +32.3 32288 0.7 SIN3A GLIS2 ARID2 E2F8 ZNF143 SP3 REST SNIP1 GMEB1 SMARCA4 RBM19 ENSG00000201208 DDX54 RITA1 CFAP73 ENSG00000199899 GC12M113158
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around DDX54 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the DDX54 gene promoter:

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)

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

No Post-translational modifications

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:

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 CatalyticActivity:
ATP + H(2)O = ADP + phosphate.
UniProtKB/Swiss-Prot Function:
Has RNA-dependent ATPase activity. Represses the transcriptional activity of nuclear receptors.

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 IDA,IEA 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:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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:0005737 cytoplasm IBA --
GO:0005794 Golgi apparatus IDA --
GO:0016020 membrane IDA,HDA 19946888
genes like me logo Genes that share ontologies with DDX54: view

Pathways & Interactions for DDX54 Gene

SuperPathways for DDX54 Gene

No Data Available

Gene Ontology (GO) - Biological Process for DDX54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006396 RNA processing IDA 12466272
GO:0010501 RNA secondary structure unwinding IBA --
GO:0016070 RNA metabolic process IDA 12466272
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 0

(1) Additional Compounds for DDX54 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 DDX54: view

Transcripts for DDX54 Gene

Unigene Clusters for DDX54 Gene

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

CRISPR Products

Inhibitory RNA Products

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, PaxDb, 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

Primer Products

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 33 34
  • 99.24 (n)
cow
(Bos Taurus)
Mammalia DDX54 33 34
  • 88.75 (n)
dog
(Canis familiaris)
Mammalia DDX54 33 34
  • 88.66 (n)
mouse
(Mus musculus)
Mammalia Ddx54 33 16 34
  • 83.16 (n)
rat
(Rattus norvegicus)
Mammalia Ddx54 33
  • 82.34 (n)
oppossum
(Monodelphis domestica)
Mammalia DDX54 34
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia DDX54 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves DDX54 33 34
  • 74.02 (n)
lizard
(Anolis carolinensis)
Reptilia DDX54 34
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ddx54 33
  • 63.31 (n)
Str.2961 33
zebrafish
(Danio rerio)
Actinopterygii ddx54 33 34
  • 65.06 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007511 33
  • 55.6 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG32344 33 34
  • 54.48 (n)
worm
(Caenorhabditis elegans)
Secernentea Y94H6A.5 33 34
  • 49.74 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F24684g 33
  • 48.17 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AEL086W 33
  • 47.46 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes DBP10 33 34 36
  • 46.42 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G77030 33
  • 50.13 (n)
rice
(Oryza sativa)
Liliopsida Os08g0416100 33
  • 51.41 (n)
Os.21287 33
bread mold
(Neurospora crassa)
Ascomycetes NCU07712 33
  • 55.56 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 50 (a)
OneToOne
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes dbp10 33
  • 47.97 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3817 33
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)

Paralogs for DDX54 Gene

No data available for Paralogs for DDX54 Gene

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 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
nsv519540 CNV gain+loss 19592680
esv996809 CNV deletion 20482838
esv3892265 CNV gain 25118596
esv3630792 CNV gain 21293372
dgv2884n54 CNV loss 21841781

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

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 22 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. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for DDX54 Gene

Sources for DDX54 Gene

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